Daily Papers

As LLM-based multi-agent systems (MAS) become more autonomous, their free-form interactions increasingly dominate system behavior. However, scaling the number of agents often amplifies context pressure, coordination errors, and system drift. It is well known that building robust MAS requires more than prompt tuning or increased model intelligence. It necessitates engineering discipline focused on architecture to manage complexity under uncertainty. We characterize agentic software by a core property: runtime generation and evolution under uncertainty. Drawing upon and extending software engineering experience, especially object-oriented programming, this paper introduces Loosely-Structured Software (LSS), a new class of software systems that shifts the engineering focus from constructing deterministic logic to managing the runtime entropy generated by View-constructed programming, semantic-driven self-organization, and endogenous evolution. To make this entropy governable, we introduce design principles under a three-layer engineering framework: View/Context Engineering to manage the execution environment and maintain task-relevant Views, Structure Engineering to organize dynamic binding over artifacts and agents, and Evolution Engineering to govern the lifecycle of self-rewriting artifacts. Building on this framework, we develop LSS design patterns as semantic control blocks that stabilize fluid, inference-mediated interactions while preserving agent adaptability. Together, these abstractions improve the designability, scalability, and evolvability of agentic infrastructure. We provide basic experimental validation of key mechanisms, demonstrating the effectiveness of LSS.

Large language models have demonstrated strong capabilities in individual software engineering tasks, yet most autonomous systems still treat issue resolution as a monolithic or pipeline-based process. In contrast, real-world software development is organized as a collaborative activity carried out by teams following shared methodologies, with clear role separation, communication, and review. In this work, we present a fully automated multi-agent system that explicitly models software engineering as an organizational process, replicating the structure of an engineering team. Built on top of agyn, an open-source platform for configuring agent teams, our system assigns specialized agents to roles such as coordination, research, implementation, and review, provides them with isolated sandboxes for experimentation, and enables structured communication. The system follows a defined development methodology for working on issues, including analysis, task specification, pull request creation, and iterative review, and operates without any human intervention. Importantly, the system was designed for real production use and was not tuned for SWE-bench. When evaluated post hoc on SWE-bench 500, it resolves 72.2% of tasks, outperforming single-agent baselines using comparable language models. Our results suggest that replicating team structure, methodology, and communication is a powerful paradigm for autonomous software engineering, and that future progress may depend as much on organizational design and agent infrastructure as on model improvements.

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet, a supervised deep-learning model to predict the fitness for protein mutants by leveraging both sequence and structure information, and exploiting attention mechanism. Our model integrates local evolutionary context from homologous sequences, the global evolutionary context encoding rich semantic from the universal protein sequence space and the structure information accounting for the microenvironment around each residue in a protein. We show that SESNet outperforms state-of-the-art models for predicting the sequence-function relationship on 26 deep mutational scanning datasets. More importantly, we propose a data augmentation strategy by leveraging the data from unsupervised models to pre-train our model. After that, our model can achieve strikingly high accuracy in prediction of the fitness of protein mutants, especially for the higher order variants (> 4 mutation sites), when finetuned by using only a small number of experimental mutation data (<50). The strategy proposed is of great practical value as the required experimental effort, i.e., producing a few tens of experimental mutation data on a given protein, is generally affordable by an ordinary biochemical group and can be applied on almost any protein.

Reinforcement learning is increasingly used for code-centric tasks. These tasks include code generation, summarization, understanding, repair, testing, and optimization. This trend is growing faster with large language models and autonomous agents. A key challenge is how to design reward signals that make sense for software. In many RL problems, the reward is a clear number. In software, this is often not possible. The goal is rarely a single numeric objective. Instead, rewards are usually proxies. Common proxies check if the code compiles, passes tests, or satisfies quality metrics. Many reward designs have been proposed for code-related tasks. However, the work is scattered across areas and papers. There is no single survey that brings these approaches together and shows the full landscape of reward design for RL in software. In this survey, we provide the first systematic and comprehensive review of reward engineering for RL in software tasks. We focus on existing methods and techniques. We structure the literature along three complementary dimensions, summarizing the reward-design choices within each. We conclude with challenges and recommendations in the reward design space for SE tasks.

We demonstrate CEDAR, an application for automating data science (DS) tasks with an agentic setup. Solving DS problems with LLMs is an underexplored area that has immense market value. The challenges are manifold: task complexities, data sizes, computational limitations, and context restrictions. We show that these can be alleviated via effective context engineering. We first impose structure into the initial prompt with DS-specific input fields, that serve as instructions for the agentic system. The solution is then materialized as an enumerated sequence of interleaved plan and code blocks generated by separate LLM agents, providing a readable structure to the context at any step of the workflow. Function calls for generating these intermediate texts, and for corresponding Python code, ensure that data stays local, and only aggregate statistics and associated instructions are injected into LLM prompts. Fault tolerance and context management are introduced via iterative code generation and smart history rendering. The viability of our agentic data scientist is demonstrated using canonical Kaggle challenges.

Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to compute molecular similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing the search results from five drug-like query molecules (penicillin G, nirmatrelvir, zidovudine, lysergic acid diethylamide, and fentanyl) and three dye-like query molecules (acid blue 25, avobenzone, and 2-diphenylaminocarbazole). We find that this novel method identifies molecules that are functionally similar to the query, indicated by the associated patent literature, and that many of these molecules are structurally distinct from the query, making them unlikely to be found with traditional chemical similarity search methods. This method may aid in the discovery of novel structural classes of molecules that achieve target functionality.

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

There has been a recent surge of interest in automating software engineering tasks using deep learning. This paper addresses the problem of code generation, where the goal is to generate target code given source code in a different language or a natural language description. Most state-of-the-art deep learning models for code generation use training strategies primarily designed for natural language. However, understanding and generating code requires a more rigorous comprehension of the code syntax and semantics. With this motivation, we develop an encoder-decoder Transformer model where both the encoder and decoder are explicitly trained to recognize the syntax and data flow in the source and target codes, respectively. We not only make the encoder structure-aware by leveraging the source code's syntax tree and data flow graph, but we also support the decoder in preserving the syntax and data flow of the target code by introducing two novel auxiliary tasks: AST (Abstract Syntax Tree) paths prediction and data flow prediction. To the best of our knowledge, this is the first work to introduce a structure-aware Transformer decoder that models both syntax and data flow to enhance the quality of generated code. The proposed StructCoder model achieves state-of-the-art performance on code translation and text-to-code generation tasks in the CodeXGLUE benchmark, and improves over baselines of similar size on the APPS code generation benchmark. Our code is publicly available at https://github.com/reddy-lab-code-research/StructCoder/.

A covariant formalism is used in order to examine the status of Maxwell equations and to unify the concept of balances, for all chemical engineering applications in relation with electrodynamics. The resulting formal structure serves as a discussion in studying the determinism of electromagnetic systems, and examining the theoretical foundations for a general classification of chemical engineering applications when non-conservative forces are concerned. A strategy for modeling such applications is then sketched and the balances for the main conserved and non-conserved extensive quantities are then summarized in their covariant and classical forms.

The digitization of complex technical systems, such as Piping and Instrumentation Diagrams (P&IDs), is crucial for efficient maintenance and operation of complex systems in hydraulic and process engineering. Previous approaches often rely on separate modules that analyze diagram elements individually, neglecting the diagram's overall structure. We address this limitation by proposing a novel approach that utilizes the Relationformer, a state-of-the-art deep learning architecture, to extract graphs from P&IDs. Our method leverages the ability of the Relationformer to simultaneously detect objects and their relationships in images, making it suitable for the task of graph extraction from engineering diagrams. We apply our proposed approach to both real-world and synthetically created P&ID datasets, and evaluate its effectiveness by comparing it with a modular digitization approach based on recent literature. We present PID2Graph, the first publicly accessible P&ID dataset featuring comprehensive labels for the graph structure, including symbols, nodes and their connections that is used for evaluation. To understand the effect of patching and stitching of both of the approaches, we compare values before and after merging the patches. For the real-world data, the Relationformer achieves convincing results, outperforming the modular digitization approach for edge detection by more than 25%. Our work provides a comprehensive framework for assessing the performance of P&ID digitization methods and opens up new avenues for research in this area using transformer architectures. The P&ID dataset used for evaluation will be published and publicly available upon acceptance of the paper.

Prompt design is a primary control interface for large language models (LLMs), yet standard evaluations largely reduce performance to answer correctness, obscuring why a prompt succeeds or fails and providing little actionable guidance. We propose PEEM (Prompt Engineering Evaluation Metrics), a unified framework for joint and interpretable evaluation of both prompts and responses. PEEM defines a structured rubric with 9 axes: 3 prompt criteria (clarity/structure, linguistic quality, fairness) and 6 response criteria (accuracy, coherence, relevance, objectivity, clarity, conciseness), and uses an LLM-based evaluator to output (i) scalar scores on a 1-5 Likert scale and (ii) criterion-specific natural-language rationales grounded in the rubric. Across 7 benchmarks and 5 task models, PEEM's accuracy axis strongly aligns with conventional accuracy while preserving model rankings (aggregate Spearman rho about 0.97, Pearson r about 0.94, p < 0.001). A multi-evaluator study with four models shows consistent relative judgments (pairwise rho = 0.68-0.85), supporting evaluator-agnostic deployment. Beyond alignment, PEEM captures complementary linguistic failure modes and remains informative under prompt perturbations: prompt-quality trends track downstream accuracy under iterative rewrites, semantic adversarial manipulations induce clear score degradation, and meaning-preserving paraphrases yield high stability (robustness rate about 76.7-80.6%). Finally, using only PEEM scores and rationales as feedback, a zero-shot prompt rewriting loop improves downstream accuracy by up to 11.7 points, outperforming supervised and RL-based prompt-optimization baselines. Overall, PEEM provides a reproducible, criterion-driven protocol that links prompt formulation to response behavior and enables systematic diagnosis and optimization of LLM interactions.

The proliferation of Large Language Models (LLMs) has catalyzed a shift towards autonomous agents capable of complex reasoning and tool use. However, current agent architectures are frequently constructed using imperative, ad hoc patterns. This results in brittle systems plagued by difficulties in state management, error handling, and concurrency. This paper introduces Monadic Context Engineering (MCE), a novel architectural paradigm leveraging the algebraic structures of Functors, Applicative Functors, and Monads to provide a formal foundation for agent design. MCE treats agent workflows as computational contexts where cross-cutting concerns, such as state propagation, short-circuiting error handling, and asynchronous execution, are managed intrinsically by the algebraic properties of the abstraction. We demonstrate how Monads enable robust sequential composition, how Applicatives provide a principled structure for parallel execution, and crucially, how Monad Transformers allow for the systematic composition of these capabilities. This layered approach enables developers to construct complex, resilient, and efficient AI agents from simple, independently verifiable components. We further extend this framework to describe Meta-Agents, which leverage MCE for generative orchestration, dynamically creating and managing sub-agent workflows through metaprogramming. Project Page: https://github.com/yifanzhang-pro/monadic-context-engineering.

Reverse engineering 3D computer-aided design (CAD) models from images is an important task for many downstream applications including interactive editing, manufacturing, architecture, robotics, etc. The difficulty of the task lies in vast representational disparities between the CAD output and the image input. CAD models are precise, programmatic constructs that involve sequential operations combining discrete command structure with continuous attributes, making it challenging to learn and optimize in an end-to-end fashion. Concurrently, input images introduce inherent challenges such as photometric variability and sensor noise, complicating the reverse engineering process. In this work, we introduce a novel approach that conditionally factorizes the task into two sub-problems. First, we leverage vision-language foundation models (VLMs), a finetuned Llama3.2, to predict the global discrete base structure with semantic information. Second, we propose TrAssembler that, conditioned on the discrete structure with semantics, predicts the continuous attribute values. To support the training of our TrAssembler, we further constructed an annotated CAD dataset of common objects from ShapeNet. Putting all together, our approach and data demonstrate significant first steps towards CAD-ifying images in the wild. Code and data can be found in https://github.com/qq456cvb/Img2CAD.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Foundation models have transformed automated code generation, yet autonomous software-engineering agents remain unreliable in realistic development settings. The dominant explanation locates this gap in model capability. We propose a different locus: software-engineering capability emerges from a model-harness-environment system, in which a runtime substrate -- the harness -- mediates how a foundation-model agent observes a project, acts on it, receives feedback, and establishes that a change is complete. We formalize this substrate as an AI Harness Engineering and identify eleven component responsibilities: task specification, context selection, tool access, project memory, task state, observability, failure attribution, verification, permissions, entropy auditing, and intervention recording. We operationalize the harness through a four-level ladder (H0-H3) that progressively exposes runtime support to the agent, and we propose a trace-based evaluation protocol that converts each agent run into an auditable episode package. Applied to a controlled validation task, the framework yields episode packages whose evidence structure varies systematically with harness level: lower levels produce only a final patch, higher levels produce reproduction logs, failure attributions, deterministic requirement checks, and structured verification reports. The framework reframes the central question of autonomous software engineering from whether a foundation model can produce a patch to whether the model-harness-environment system can produce a verifiably correct, attributed, and maintainable change. We outline a research program for the runtime systems that foundation-model software agents will require.

This lecture presents an overview of the basic concepts and fundamentals of Engineering Materials within the framework of accelerator applications. After a short introduction, main concepts relative to the structure of matter are reviewed, like crystalline structures, defects and dislocations, phase diagrams and transformations. The microscopic description is correlated with physical properties of materials, focusing in metallurgical aspects like deformation and strengthening. Main groups of materials are addressed and described, namely, metals and alloys, ceramics, polymers, composite materials, and advanced materials, where brush-strokes of tangible applications in particle accelerators and detectors are given. Deterioration aspects of materials are also presented, like corrosion in metals and degradation in plastics.

Multi-Agent Large Language Models (LLMs) are gaining significant attention for their ability to harness collective intelligence in complex problem-solving, decision-making, and planning tasks. This aligns with the concept of the wisdom of crowds, where diverse agents contribute collectively to generating effective solutions, making it particularly suitable for educational settings. Senior design projects, also known as capstone or final year projects, are pivotal in engineering education as they integrate theoretical knowledge with practical application, fostering critical thinking, teamwork, and real-world problem-solving skills. In this paper, we explore the use of Multi-Agent LLMs in supporting these senior design projects undertaken by engineering students, which often involve multidisciplinary considerations and conflicting objectives, such as optimizing technical performance while addressing ethical, social, and environmental concerns. We propose a framework where distinct LLM agents represent different expert perspectives, such as problem formulation agents, system complexity agents, societal and ethical agents, or project managers, thus facilitating a holistic problem-solving approach. This implementation leverages standard multi-agent system (MAS) concepts such as coordination, cooperation, and negotiation, incorporating prompt engineering to develop diverse personas for each agent. These agents engage in rich, collaborative dialogues to simulate human engineering teams, guided by principles from swarm AI to efficiently balance individual contributions towards a unified solution. We adapt these techniques to create a collaboration structure for LLM agents, encouraging interdisciplinary reasoning and negotiation similar to real-world senior design projects. To assess the efficacy of this framework, we collected six proposals of engineering and computer science of...

Harnesses are now central to coding-agent performance, mediating how models interact with tools and execution environments. Yet harness engineering remains a manual craft, because automating it faces a heterogeneous action space across editable components, voluminous trajectories that bury actionable signal, and edits whose effect is hard to attribute. We introduce Agentic Harness Engineering (AHE), a closed loop that addresses these challenges through three matched observability pillars: (1) component observability gives every editable harness component a file-level representation so the action space is explicit and revertible; (2) experience observability distills millions of raw trajectory tokens into a layered, drill-down evidence corpus that an evolving agent can actually consume; and (3) decision observability pairs every edit with a self-declared prediction, later verified against the next round's task-level outcomes. Together, these pillars turn every edit into a falsifiable contract, so harness evolution proceeds autonomously without collapsing into trial-and-error. Empirically, ten AHE iterations lift pass@1 on Terminal-Bench 2 from 69.7% to 77.0%, surpassing the human-designed harness Codex-CLI (71.9%) and the self-evolving baselines ACE and TF-GRPO. The frozen harness transfers without re-evolution: on SWE-bench-verified it tops aggregate success at 12% fewer tokens than the seed, and on Terminal-Bench 2 it yields +5.1 to +10.1pp cross-family gains across three alternate model families, indicating the evolved components encode general engineering experience rather than benchmark-specific tuning. Ablations localize the gain to tools, middleware, and long-term memory rather than the system prompt, suggesting factual harness structure transfers while prose-level strategy does not.

Large Language Model agents increasingly operate external systems through programmatic interfaces, yet practitioners lack empirical guidance on how to structure the context these agents consume. Using SQL generation as a proxy for programmatic agent operations, we present a systematic study of context engineering for structured data, comprising 9,649 experiments across 11 models, 4 formats (YAML, Markdown, JSON, Token-Oriented Object Notation [TOON]), and schemas ranging from 10 to 10,000 tables. Our findings challenge common assumptions. First, architecture choice is model-dependent: file-based context retrieval improves accuracy for frontier-tier models (Claude, GPT, Gemini; +2.7%, p=0.029) but shows mixed results for open source models (aggregate -7.7%, p<0.001), with deficits varying substantially by model. Second, format does not significantly affect aggregate accuracy (chi-squared=2.45, p=0.484), though individual models, particularly open source, exhibit format-specific sensitivities. Third, model capability is the dominant factor, with a 21 percentage point accuracy gap between frontier and open source tiers that dwarfs any format or architecture effect. Fourth, file-native agents scale to 10,000 tables through domain-partitioned schemas while maintaining high navigation accuracy. Fifth, file size does not predict runtime efficiency: compact or novel formats can incur a token overhead driven by grep output density and pattern unfamiliarity, with the magnitude depending on model capability. These findings provide practitioners with evidence-based guidance for deploying LLM agents on structured systems, demonstrating that architectural decisions should be tailored to model capability rather than assuming universal best practices.

To facilitate the transformation of legacy finite difference implementations into the Devito environment, this study develops an integrated AI agent framework. Retrieval-Augmented Generation (RAG) and open-source Large Language Models are combined through multi-stage iterative workflows in the system's hybrid LangGraph architecture. The agent constructs an extensive Devito knowledge graph through document parsing, structure-aware segmentation, extraction of entity relationships, and Leiden-based community detection. GraphRAG optimisation enhances query performance across semantic communities that include seismic wave simulation, computational fluid dynamics, and performance tuning libraries. A reverse engineering component derives three-level query strategies for RAG retrieval through static analysis of Fortran source code. To deliver precise contextual information for language model guidance, the multi-stage retrieval pipeline performs parallel searching, concept expansion, community-scale retrieval, and semantic similarity analysis. Code synthesis is governed by Pydantic-based constraints to guarantee structured outputs and reliability. A comprehensive validation framework integrates conventional static analysis with the G-Eval approach, covering execution correctness, structural soundness, mathematical consistency, and API compliance. The overall agent workflow is implemented on the LangGraph framework and adopts concurrent processing to support quality-based iterative refinement and state-aware dynamic routing. The principal contribution lies in the incorporation of feedback mechanisms motivated by reinforcement learning, enabling a transition from static code translation toward dynamic and adaptive analytical behavior.

Reproducibility and replicability are critical pillars of empirical research, particularly in machine learning, where they depend not only on the availability of models, but also on the datasets used to train and evaluate those models. In this paper, we introduce the Construction Industry Steel Ordering List (CISOL) dataset, which was developed with a focus on transparency to ensure reproducibility, replicability, and extensibility. CISOL provides a valuable new research resource and highlights the importance of having diverse datasets, even in niche application domains such as table extraction in civil engineering. CISOL is unique in that it contains real-world civil engineering documents from industry, making it a distinctive contribution to the field. The dataset contains more than 120,000 annotated instances in over 800 document images, positioning it as a medium-sized dataset that provides a robust foundation for Table Structure Recognition (TSR) and Table Detection (TD) tasks. Benchmarking results show that CISOL achieves 67.22 mAP@0.5:0.95:0.05 using the YOLOv8 model, outperforming the TSR-specific TATR model. This highlights the effectiveness of CISOL as a benchmark for advancing TSR, especially in specialized domains.

For multi-agent reinforcement learning systems (MARLS), the problem formulation generally involves investing massive reward engineering effort specific to a given problem. However, this effort often cannot be translated to other problems; worse, it gets wasted when system dynamics change drastically. This problem is further exacerbated in sparse reward scenarios, where a meaningful heuristic can assist in the policy convergence task. We propose GOVerned Reward Engineering Kernels (GOV-REK), which dynamically assign reward distributions to agents in MARLS during its learning stage. We also introduce governance kernels, which exploit the underlying structure in either state or joint action space for assigning meaningful agent reward distributions. During the agent learning stage, it iteratively explores different reward distribution configurations with a Hyperband-like algorithm to learn ideal agent reward models in a problem-agnostic manner. Our experiments demonstrate that our meaningful reward priors robustly jumpstart the learning process for effectively learning different MARL problems.

Agents based on large language models (LLMs) for machine learning engineering (MLE) can automatically implement ML models via code generation. However, existing approaches to build such agents often rely heavily on inherent LLM knowledge and employ coarse exploration strategies that modify the entire code structure at once. This limits their ability to select effective task-specific models and perform deep exploration within specific components, such as experimenting extensively with feature engineering options. To overcome these, we propose MLE-STAR, a novel approach to build MLE agents. MLE-STAR first leverages external knowledge by using a search engine to retrieve effective models from the web, forming an initial solution, then iteratively refines it by exploring various strategies targeting specific ML components. This exploration is guided by ablation studies analyzing the impact of individual code blocks. Furthermore, we introduce a novel ensembling method using an effective strategy suggested by MLE-STAR. Our experimental results show that MLE-STAR achieves medals in 64% of the Kaggle competitions on the MLE-bench Lite, significantly outperforming the best alternative.

Large Language Models (LLMs) excel in code generation yet struggle with modern AI software engineering tasks. Unlike traditional function-level or file-level coding tasks, AI software engineering requires not only basic coding proficiency but also advanced skills in managing and interacting with code repositories. However, existing methods often overlook the need for repository-level code understanding, which is crucial for accurately grasping the broader context and developing effective solutions. On this basis, we present RepoGraph, a plug-in module that manages a repository-level structure for modern AI software engineering solutions. RepoGraph offers the desired guidance and serves as a repository-wide navigation for AI software engineers. We evaluate RepoGraph on the SWE-bench by plugging it into four different methods of two lines of approaches, where RepoGraph substantially boosts the performance of all systems, leading to a new state-of-the-art among open-source frameworks. Our analyses also demonstrate the extensibility and flexibility of RepoGraph by testing on another repo-level coding benchmark, CrossCodeEval. Our code is available at https://github.com/ozyyshr/RepoGraph.

Abstractive summarization of scientific papers has always been a research focus, yet existing methods face two main challenges. First, most summarization models rely on Encoder-Decoder architectures that treat papers as sequences of words, thus fail to fully capture the structured information inherent in scientific papers. Second, existing research often use keyword mapping or feature engineering to identify the structural information, but these methods struggle with the structural flexibility of scientific papers and lack robustness across different disciplines. To address these challenges, we propose a two-stage abstractive summarization framework that leverages automatic recognition of structural functions within scientific papers. In the first stage, we standardize chapter titles from numerous scientific papers and construct a large-scale dataset for structural function recognition. A classifier is then trained to automatically identify the key structural components (e.g., Background, Methods, Results, Discussion), which provides a foundation for generating more balanced summaries. In the second stage, we employ Longformer to capture rich contextual relationships across sections and generating context-aware summaries. Experiments conducted on two domain-specific scientific paper summarization datasets demonstrate that our method outperforms advanced baselines, and generates more comprehensive summaries. The code and dataset can be accessed at https://github.com/tongbao96/code-for-SFR-AS.

The ModelWriter platform provides a generic framework for automated traceability analysis. In this paper, we demonstrate how this framework can be used to trace the consistency and completeness of technical documents that consist of a set of System Installation Design Principles used by Airbus to ensure the correctness of aircraft system installation. We show in particular, how the platform allows the integration of two types of reasoning: reasoning about the meaning of text using semantic parsing and description logic theorem proving; and reasoning about document structure using first-order relational logic and finite model finding for traceability analysis.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on heavy candidate sampling coupled with scoring, ranking, and fine-tuning steps. We challenge this paradigm with EquiBind, an SE(3)-equivariant geometric deep learning model performing direct-shot prediction of both i) the receptor binding location (blind docking) and ii) the ligand's bound pose and orientation. EquiBind achieves significant speed-ups and better quality compared to traditional and recent baselines. Further, we show extra improvements when coupling it with existing fine-tuning techniques at the cost of increased running time. Finally, we propose a novel and fast fine-tuning model that adjusts torsion angles of a ligand's rotatable bonds based on closed-form global minima of the von Mises angular distance to a given input atomic point cloud, avoiding previous expensive differential evolution strategies for energy minimization.

Generative AI (GenAI) has reshaped software system design by introducing foundation models as pre-trained subsystems that redefine architectures and operations. The emerging challenge is no longer model fine-tuning but context engineering-how systems capture, structure, and govern external knowledge, memory, tools, and human input to enable trustworthy reasoning. Existing practices such as prompt engineering, retrieval-augmented generation (RAG), and tool integration remain fragmented, producing transient artefacts that limit traceability and accountability. This paper proposes a file-system abstraction for context engineering, inspired by the Unix notion that 'everything is a file'. The abstraction offers a persistent, governed infrastructure for managing heterogeneous context artefacts through uniform mounting, metadata, and access control. Implemented within the open-source AIGNE framework, the architecture realises a verifiable context-engineering pipeline, comprising the Context Constructor, Loader, and Evaluator, that assembles, delivers, and validates context under token constraints. As GenAI becomes an active collaborator in decision support, humans play a central role as curators, verifiers, and co-reasoners. The proposed architecture establishes a reusable foundation for accountable and human-centred AI co-work, demonstrated through two exemplars: an agent with memory and an MCP-based GitHub assistant. The implementation within the AIGNE framework demonstrates how the architecture can be operationalised in developer and industrial settings, supporting verifiable, maintainable, and industry-ready GenAI systems.

Large Language Model (LLM) agents are increasingly deployed in complex, multi-step workflows involving planning, tool use, reflection, and interaction with external knowledge systems. These workflows generate rapidly expanding contexts that must be curated, transformed, and compressed to maintain fidelity, avoid attention dilution, and reduce inference cost. Prior work on summarization and query-aware compression largely ignores the multi-step, plan-aware nature of agentic reasoning. In this work, we introduce PAACE (Plan-Aware Automated Context Engineering), a unified framework for optimizing the evolving state of LLM agents through next-k-task relevance modeling, plan-structure analysis, instruction co-refinement, and function-preserving compression. PAACE comprises (1) PAACE-Syn, a large-scale generator of synthetic agent workflows annotated with stepwise compression supervision, and (2) PAACE-FT, a family of distilled, plan-aware compressors trained from successful teacher demonstrations. Experiments on long-horizon benchmarks (AppWorld, OfficeBench, and 8-Objective QA) demonstrate that PAACE consistently improves agent correctness while substantially reducing context load. On AppWorld, PAACE achieves higher accuracy than all baselines while lowering peak context and cumulative dependency. On OfficeBench and multi-hop QA, PAACE improves both accuracy and F1, achieving fewer steps, lower peak tokens, and reduced attention dependency. Distilled PAACE-FT retains 97 percent of the teacher's performance while reducing inference cost by over an order of magnitude, enabling practical deployment of plan-aware compression with compact models.

The remarkable mechanical properties of spider silk, including its tensile strength and extensibility, are primarily governed by the repetitive regions of the proteins that constitute the fiber, the major ampullate spidroins (MaSps). However, establishing correlations between mechanical characteristics and repeat sequences is challenging due to the intricate sequence-structure-function relationships of MaSps and the limited availability of annotated datasets. In this study, we present a novel computational framework for designing MaSp repeat sequences with customizable mechanical properties. To achieve this, we developed a lightweight GPT-based generative model by distilling the pre-trained ProtGPT2 protein language model. The distilled model was subjected to multilevel fine-tuning using curated subsets of the Spider Silkome dataset. Specifically, we adapt the model for MaSp repeat generation using 6,000 MaSp repeat sequences and further refine it with 572 repeats associated with experimentally determined fiber-level mechanical properties. Our model generates biologically plausible MaSp repeat regions tailored to specific mechanical properties while also predicting those properties for given sequences. Validation includes sequence-level analysis, assessing physicochemical attributes and expected distribution of key motifs as well as secondary structure compositions. A correlation study using BLAST on the Spider Silkome dataset and a test set of MaSp repeats with known mechanical properties further confirmed the predictive accuracy of the model. This framework advances the rational design of spider silk-inspired biomaterials, offering a versatile tool for engineering protein sequences with tailored mechanical attributes.

Language models are increasingly capable, yet still fail at a seemingly simple task of multi-digit multiplication. In this work, we study why, by reverse-engineering a model that successfully learns multiplication via implicit chain-of-thought, and report three findings: (1) Evidence of long-range structure: Logit attributions and linear probes indicate that the model encodes the necessary long-range dependencies for multi-digit multiplication. (2) Mechanism: the model encodes long-range dependencies using attention to construct a directed acyclic graph to ``cache'' and ``retrieve'' pairwise partial products. (3) Geometry: the model implements partial products in attention heads by forming Minkowski sums between pairs of digits, and digits are represented using a Fourier basis, both of which are intuitive and efficient representations that the standard fine-tuning model lacks. With these insights, we revisit the learning dynamics of standard fine-tuning and find that the model converges to a local optimum that lacks the required long-range dependencies. We further validate this understanding by introducing an auxiliary loss that predicts the ``running sum'' via a linear regression probe, which provides an inductive bias that enables the model to successfully learn multi-digit multiplication. In summary, by reverse-engineering the mechanisms of an implicit chain-of-thought model we uncover a pitfall for learning long-range dependencies in Transformers and provide an example of how the correct inductive bias can address this issue.

Establishing precise traceability between embedded systems datasheets and their corresponding code implementations remains a fundamental challenge in systems engineering, particularly for low-level software where manual mapping between specification documents and large code repositories is infeasible. Existing Traceability Link Recovery approaches primarily rely on lexical similarity and information retrieval techniques, which struggle to capture the semantic, structural, and symbol level relationships prevalent in embedded systems software. We present a hierarchical datasheet-to-code mapping methodology that employs large language models for semantic analysis while explicitly structuring the traceability process across multiple abstraction levels. Rather than performing direct specification-to-code matching, the proposed approach progressively narrows the search space through repository-level structure inference, file-level relevance estimation, and fine-grained symbollevel alignment. The method extends beyond function-centric mapping by explicitly covering macros, structs, constants, configuration parameters, and register definitions commonly found in systems-level C/C++ codebases. We evaluate the approach on multiple open-source embedded systems repositories using manually curated datasheet-to-code ground truth. Experimental results show substantial improvements over traditional information-retrieval-based baselines, achieving up to 73.3% file mapping accuracy. We significantly reduce computational overhead, lowering total LLM token consumption by 84% and end-to-end runtime by approximately 80%. This methodology supports automated analysis of large embedded software systems and enables downstream applications such as training data generation for systems-aware machine learning models, standards compliance verification, and large-scale specification coverage analysis.

Large language model (LLM) agents are increasingly built less by changing model weights than by reorganizing the runtime around them. Capabilities that earlier systems expected the model to recover internally are now externalized into memory stores, reusable skills, interaction protocols, and the surrounding harness that makes these modules reliable in practice. This paper reviews that shift through the lens of externalization. Drawing on the idea of cognitive artifacts, we argue that agent infrastructure matters not merely because it adds auxiliary components, but because it transforms hard cognitive burdens into forms that the model can solve more reliably. Under this view, memory externalizes state across time, skills externalize procedural expertise, protocols externalize interaction structure, and harness engineering serves as the unification layer that coordinates them into governed execution. We trace a historical progression from weights to context to harness, analyze memory, skills, and protocols as three distinct but coupled forms of externalization, and examine how they interact inside a larger agent system. We further discuss the trade-off between parametric and externalized capability, identify emerging directions such as self-evolving harnesses and shared agent infrastructure, and discuss open challenges in evaluation, governance, and the long-term co-evolution of models and external infrastructure. The result is a systems-level framework for explaining why practical agent progress increasingly depends not only on stronger models, but on better external cognitive infrastructure.

Fluid-structure interaction is common in engineering and natural systems, where floating-body motion is governed by added mass, drag, and background flows. Modeling these dissipative dynamics is difficult: black-box neural models regress state derivatives with limited interpretability and unstable long-horizon predictions. We propose Floating-Body Hydrodynamic Neural Networks (FHNN), a physics-structured framework that predicts interpretable hydrodynamic parameters such as directional added masses, drag coefficients, and a streamfunction-based flow, and couples them with analytic equations of motion. This design constrains the hypothesis space, enhances interpretability, and stabilizes integration. On synthetic vortex datasets, FHNN achieves up to an order-of-magnitude lower error than Neural ODEs, recovers physically consistent flow fields. Compared with Hamiltonian and Lagrangian neural networks, FHNN more effectively handles dissipative dynamics while preserving interpretability, which bridges the gap between black-box learning and transparent system identification.

The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models' (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM's capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and others parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.

Compound identification and structure annotation from mass spectra is a well-established task widely applied in drug detection, criminal forensics, small molecule biomarker discovery and chemical engineering. We propose SpecTUS: Spectral Translator for Unknown Structures, a deep neural model that addresses the task of structural annotation of small molecules from low-resolution gas chromatography electron ionization mass spectra (GC-EI-MS). Our model analyzes the spectra in de novo manner -- a direct translation from the spectra into 2D-structural representation. Our approach is particularly useful for analyzing compounds unavailable in spectral libraries. In a rigorous evaluation of our model on the novel structure annotation task across different libraries, we outperformed standard database search techniques by a wide margin. On a held-out testing set, including 28267 spectra from the NIST database, we show that our model's single suggestion perfectly reconstructs 43\% of the subset's compounds. This single suggestion is strictly better than the candidate of the database hybrid search (common method among practitioners) in 76\% of cases. In a~still affordable scenario of~10 suggestions, perfect reconstruction is achieved in 65\%, and 84\% are better than the hybrid search.

Continual learning, the ability of AI systems to improve through sequential experience, has attracted substantial interest, but no high-quality benchmark exists to evaluate it. We introduce Continual Learning Bench (CL-Bench), the first difficult, expert-validated benchmark designed to measure whether LLM-based systems genuinely improve with experience. CL-Bench spans six diverse domains (software engineering, signal processing, disease outbreak forecasting, database querying, strategic game-playing, and demand forecasting), each validated by domain experts and designed so that tasks share a learnable latent structure (codebase layout, disease outbreak dynamics, opponent strategies) that a stateful system can discover online but a stateless one cannot. We evaluate frontier models across several agent architectures, from naive in-context learning (ICL) to dedicated memory systems, introducing a gain metric to isolate learning from prior capabilities. We find that these systems leave headroom for improved continual learning: agents frequently overfit to immediate observations or fail to reuse knowledge across instances, and dedicated memory systems do not fix this -- in fact, naive ICL outperforms systems dedicated to memory management. CL-Bench is the first benchmark to evaluate continual learning across diverse real-world domains with expert-validated tasks and isolate online learning from underlying model capability, showing a need for better continual learning systems.

Large language models are increasingly used within larger systems ("LLM agents"). These make a sequence of LLM calls, each call providing the LLM with a combination of instructions, observations, and interaction history. The design of the encoded information and its structure play a central role in the quality of the resulting system, leading to efforts spent on context engineering. It is therefore critical to communicate the composition of the LLM context in a system, and how it evolves over time. Yet, no standard exists for doing so: context construction is typically conveyed through informal prose, ad hoc diagrams, or direct inspection of code, none of which precisely capture how a prompt evolves across interaction steps or how two context representation strategies differ. To remedy this, we introduce the Agentic Context Description Language (ACDL), a language for specifying the structure and dynamics of LLM input contexts in a precise, readable, and standard manner, along with visualizations. ACDL provides constructs for specifying context aspects such as role message sequences, dynamic content, time-indexed references, and conditional or iterative structure, capturing the full architecture of a prompt independently of any particular implementation. ACDL diagrams can be hand drawn on a whiteboard, or written in formal language which can then be rendered. We describe the language, demonstrate it by documenting several existing systems and their variants, and encourage the community to adopt it for describing LLM systems context, both in day-to-day communication and in papers. Tooling, examples and documentation are available at www.acdlang.org.

In this work, we present a computing platform named digital twin brain (DTB) that can simulate spiking neuronal networks of the whole human brain scale and more importantly, a personalized biological brain structure. In comparison to most brain simulations with a homogeneous global structure, we highlight that the sparseness, couplingness and heterogeneity in the sMRI, DTI and PET data of the brain has an essential impact on the efficiency of brain simulation, which is proved from the scaling experiments that the DTB of human brain simulation is communication-intensive and memory-access intensive computing systems rather than computation-intensive. We utilize a number of optimization techniques to balance and integrate the computation loads and communication traffics from the heterogeneous biological structure to the general GPU-based HPC and achieve leading simulation performance for the whole human brain-scaled spiking neuronal networks. On the other hand, the biological structure, equipped with a mesoscopic data assimilation, enables the DTB to investigate brain cognitive function by a reverse-engineering method, which is demonstrated by a digital experiment of visual evaluation on the DTB. Furthermore, we believe that the developing DTB will be a promising powerful platform for a large of research orients including brain-inspiredintelligence, rain disease medicine and brain-machine interface.

Industrial Computer-Aided Design (CAD) code generation requires models to produce executable parametric programs from visual or textual inputs. Beyond recognizing the outer shape of a part, this task involves understanding its 3D structure, inferring engineering parameters, and choosing CAD operations that reflect how the part would be designed and manufactured. Despite the promise of Multimodal large language models (MLLMs) for this task, they are rarely evaluated on whether these capabilities jointly hold in realistic industrial CAD settings. We present BenchCAD, a unified benchmark for industrial CAD reasoning. BenchCAD contains 17,900 execution-verified CadQuery programs across 106 industrial part families, including bevel gears, compression springs, twist drills, and other reusable engineering designs. It evaluates models through visual question answering, code question answering, image-to-code generation, and instruction-guided code editing, enabling fine-grained analysis across perception, parametric abstraction, and executable program synthesis. Across 10+ frontier models, BenchCAD shows that current systems often recover coarse outer geometry but fail to produce faithful parametric CAD programs. Common failures include missing fine 3D structure, misinterpreting industrial design parameters, and replacing essential operations such as sweeps, lofts, and twist-extrudes with simpler sketch-and-extrude patterns. Fine-tuning and reinforcement learning improve in-distribution performance, but generalization to unseen part families remains limited. These results position BenchCAD as a benchmark for measuring and improving the industrial readiness of multimodal CAD automation.

Protein inverse folding, the design of an amino acid sequence based on a target 3D structure, is a fundamental problem of computational protein engineering. Existing methods either generate sequences without leveraging external knowledge or relying on protein language models (PLMs). The former omits the evolutionary information stored in protein databases, while the latter is parameter-inefficient and inflexible to adapt to ever-growing protein data. To overcome the above drawbacks, in this paper we propose a novel method, called retrieval-augmented denoising diffusion (RadDiff), for protein inverse folding. Given the target protein backbone, RadDiff uses a hierarchical search strategy to efficiently retrieve structurally similar proteins from large protein databases. The retrieved structures are then aligned residue-by-residue to the target to construct a position-specific amino acid profile, which serves as an evolutionary-informed prior that conditions the denoising process. A lightweight integration module is further designed to incorporate this prior effectively. Experimental results on the CATH, PDB, and TS50 datasets show that RadDiff consistently outperforms existing methods, improving sequence recovery rate by up to 19%. Experimental results also demonstrate that RadDiff generates highly foldable sequences and scales effectively with database size.

Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLASMA, the first deep learning framework for efficient and interpretable residue-level protein substructure alignment. We reformulate the problem as a regularized optimal transport task and leverage differentiable Sinkhorn iterations. For a pair of input protein structures, PLASMA outputs a clear alignment matrix with an interpretable overall similarity score. Through extensive quantitative evaluations and three biological case studies, we demonstrate that PLASMA achieves accurate, lightweight, and interpretable residue-level alignment. Additionally, we introduce PLASMA-PF, a training-free variant that provides a practical alternative when training data are unavailable. Our method addresses a critical gap in protein structure analysis tools and offers new opportunities for functional annotation, evolutionary studies, and structure-based drug design. Reproducibility is ensured via our official implementation at https://github.com/ZW471/PLASMA-Protein-Local-Alignment.git.

Multi-agent LLM ensembles can converge on coordinated, socially harmful equilibria. This paper advances an experimental framework for evaluating Institutional AI, our system-level approach to AI alignment that reframes alignment from preference engineering in agent-space to mechanism design in institution-space. Central to this approach is the governance graph, a public, immutable manifest that declares legal states, transitions, sanctions, and restorative paths; an Oracle/Controller runtime interprets this manifest, attaching enforceable consequences to evidence of coordination while recording a cryptographically keyed, append-only governance log for audit and provenance. We apply the Institutional AI framework to govern the Cournot collusion case documented by prior work and compare three regimes: Ungoverned (baseline incentives from the structure of the Cournot market), Constitutional (a prompt-only policy-as-prompt prohibition implemented as a fixed written anti-collusion constitution, and Institutional (governance-graph-based). Across six model configurations including cross-provider pairs (N=90 runs/condition), the Institutional regime produces large reductions in collusion: mean tier falls from 3.1 to 1.8 (Cohen's d=1.28), and severe-collusion incidence drops from 50% to 5.6%. The prompt-only Constitutional baseline yields no reliable improvement, illustrating that declarative prohibitions do not bind under optimisation pressure. These results suggest that multi-agent alignment may benefit from being framed as an institutional design problem, where governance graphs can provide a tractable abstraction for alignment-relevant collective behavior.

Large language models (LLMs) have shown remarkable ability to generate code, yet their outputs often violate syntactic or semantic constraints when guided only through natural language prompts. We introduce TreeCoder, the most general and flexible framework to date for exploring decoding strategies, constraints, and hyperparameters in LLMs, and use it in code generation to enforce correctness and structure during decoding rather than relying on prompt engineering. TreeCoder represents decoding as a tree search over candidate programs, where both decoding strategies and constraint functions - such as style, syntax, execution - are treated as first-class, optimisable components. This design enables systematic exploration and automatic tuning of decoding configurations using standard optimisation techniques. Experiments on the MBPP (Python) and SQL-Spider benchmarks show that TreeCoder consistently improves accuracy across open-source models such as CodeLlama, Mistral and DeepSeek, often outperforming their unconstrained baselines by considerable margins.

Agentic Software Engineering (SE 3.0) represents a new era where intelligent agents are tasked not with simple code generation, but with achieving complex, goal-oriented SE objectives. To harness these new capabilities while ensuring trustworthiness, we must recognize a fundamental duality within the SE field in the Agentic SE era, comprising two symbiotic modalities: SE for Humans and SE for Agents. This duality demands a radical reimagining of the foundational pillars of SE (actors, processes, tools, and artifacts) which manifest differently across each modality. We propose two purpose-built workbenches to support this vision. The Agent Command Environment (ACE) serves as a command center where humans orchestrate and mentor agent teams, handling outputs such as Merge-Readiness Packs (MRPs) and Consultation Request Packs (CRPs). The Agent Execution Environment (AEE) is a digital workspace where agents perform tasks while invoking human expertise when facing ambiguity or complex trade-offs. This bi-directional partnership, which supports agent-initiated human callbacks and handovers, gives rise to new, structured engineering activities (i.e., processes) that redefine human-AI collaboration, elevating the practice from agentic coding to true agentic software engineering. This paper presents the Structured Agentic Software Engineering (SASE) vision, outlining several of the foundational pillars for the future of SE. The paper culminates in a research roadmap that identifies a few key challenges and opportunities while briefly discussing the resulting impact of this future on SE education. Our goal is not to offer a definitive solution, but to provide a conceptual scaffold with structured vocabulary to catalyze a community-wide dialogue, pushing the SE community to think beyond its classic, human-centric tenets toward a disciplined, scalable, and trustworthy agentic future.

Agentic AI marks a major shift in how autonomous systems reason, plan, and execute multi-step tasks. Unlike traditional single model prompting, agentic workflows integrate multiple specialized agents with different Large Language Models(LLMs), tool-augmented capabilities, orchestration logic, and external system interactions to form dynamic pipelines capable of autonomous decision-making and action. As adoption accelerates across industry and research, organizations face a central challenge: how to design, engineer, and operate production-grade agentic AI workflows that are reliable, observable, maintainable, and aligned with safety and governance requirements. This paper provides a practical, end-to-end guide for designing, developing, and deploying production-quality agentic AI systems. We introduce a structured engineering lifecycle encompassing workflow decomposition, multi-agent design patterns, Model Context Protocol(MCP), and tool integration, deterministic orchestration, Responsible-AI considerations, and environment-aware deployment strategies. We then present nine core best practices for engineering production-grade agentic AI workflows, including tool-first design over MCP, pure-function invocation, single-tool and single-responsibility agents, externalized prompt management, Responsible-AI-aligned model-consortium design, clean separation between workflow logic and MCP servers, containerized deployment for scalable operations, and adherence to the Keep it Simple, Stupid (KISS) principle to maintain simplicity and robustness. To demonstrate these principles in practice, we present a comprehensive case study: a multimodal news-analysis and media-generation workflow. By combining architectural guidance, operational patterns, and practical implementation insights, this paper offers a foundational reference to build robust, extensible, and production-ready agentic AI workflows.

The rapid evolution of modern malware presents significant challenges to the development of effective defense mechanisms. Traditional cyber deception techniques often rely on static or manually configured parameters, limiting their adaptability to dynamic and sophisticated threats. This study leverages Generative AI (GenAI) models to automate the creation of adaptive cyber deception ploys, focusing on structured prompt engineering (PE) to enhance relevance, actionability, and deployability. We introduce a systematic framework (SPADE) to address inherent challenges large language models (LLMs) pose to adaptive deceptions, including generalized outputs, ambiguity, under-utilization of contextual information, and scalability constraints. Evaluations across diverse malware scenarios using metrics such as Recall, Exact Match (EM), BLEU Score, and expert quality assessments identified ChatGPT-4o as the top performer. Additionally, it achieved high engagement (93%) and accuracy (96%) with minimal refinements. Gemini and ChatGPT-4o Mini demonstrated competitive performance, with Llama3.2 showing promise despite requiring further optimization. These findings highlight the transformative potential of GenAI in automating scalable, adaptive deception strategies and underscore the critical role of structured PE in advancing real-world cybersecurity applications.

This study introduces Conversation Routines (CR), a structured prompt engineering framework for developing task-oriented dialog systems using Large Language Models (LLMs). While LLMs demonstrate remarkable natural language understanding capabilities, engineering them to reliably execute complex business workflows remains challenging. The proposed CR framework enables the development of Conversation Agentic Systems (CAS) through natural language specifications, embedding task-oriented logic within LLM prompts. This approach provides a systematic methodology for designing and implementing complex conversational workflows while maintaining behavioral consistency. We demonstrate the framework's effectiveness through two proof-of-concept implementations: a Train Ticket Booking System and an Interactive Troubleshooting Copilot. These case studies validate CR's capability to encode sophisticated behavioral patterns and decision logic while preserving natural conversational flexibility. Results show that CR enables domain experts to design conversational workflows in natural language while leveraging custom functions (tools) developed by software engineers, creating an efficient division of responsibilities where developers focus on core API implementation and domain experts handle conversation design. While the framework shows promise in accessibility and adaptability, we identify key challenges including computational overhead, non-deterministic behavior, and domain-specific logic optimization. Future research directions include CR evaluation methods based on prompt engineering frameworks driven by goal-oriented grading criteria, improving scalability for complex multi-agent interactions, and enhancing system robustness to address the identified limitations across diverse business applications.

Despite the growing interest in replicating the scaled success of large language models (LLMs) in industrial search and recommender systems, most existing industrial efforts remain limited to transplanting Transformer architectures, which bring only incremental improvements over strong Deep Learning Recommendation Models (DLRMs). From a first principle perspective, the breakthroughs of LLMs stem not only from their architectures but also from two complementary mechanisms: context engineering, which enriches raw input queries with contextual cues to better elicit model capabilities, and multi-step reasoning, which iteratively refines model outputs through intermediate reasoning paths. However, these two mechanisms and their potential to unlock substantial improvements remain largely underexplored in industrial ranking systems. In this paper, we propose OnePiece, a unified framework that seamlessly integrates LLM-style context engineering and reasoning into both retrieval and ranking models of industrial cascaded pipelines. OnePiece is built on a pure Transformer backbone and further introduces three key innovations: (1) structured context engineering, which augments interaction history with preference and scenario signals and unifies them into a structured tokenized input sequence for both retrieval and ranking; (2) block-wise latent reasoning, which equips the model with multi-step refinement of representations and scales reasoning bandwidth via block size; (3) progressive multi-task training, which leverages user feedback chains to effectively supervise reasoning steps during training. OnePiece has been deployed in the main personalized search scenario of Shopee and achieves consistent online gains across different key business metrics, including over +2% GMV/UU and a +2.90% increase in advertising revenue.

Recent progress in large language models (LLMs) has advanced automatic code generation, yet most approaches rely on direct, single-step translation from problem descriptions to code, disregarding structured software engineering practices. We introduce a lifecycle-aware framework that systematically incorporates intermediate artifacts such as requirements analysis, state machine modeling, and pseudocode into both the training and inference stages. This design aligns code generation with standard software development phases and enables more structured reasoning. Experiments show that lifecycle-level fine-tuning improves code correctness by up to 75% over the same model before fine-tuning, with performance gains compounding across intermediate stages. Multi-step inference consistently surpasses single-step generation, demonstrating the effectiveness of intermediate scaffolding. Notably, open-source LLMs, once fine-tuned under our framework, match or slightly outperform models pretrained on code. When applied to DeepSeek-Coder-1.3B, our framework yields relative CodeBLEU improvements of 34.3%, 20.0%, 11.2%, and 22.3% over ChatGPT-3.5, ChatGPT-4o-mini, DeepSeek-R1, and LLaMA-8B, respectively. Our pipeline also proves robust with up to 80\% less training data, confirming its resilience. Ablation studies further reveal that each intermediate artifact contributes distinctly to final code quality, with state machine modeling yielding the most substantial impact. Our source code and detailed experimental data are available at https://anonymous.4open.science/r/Lifecycle-Aware-3CCB.

Automated analysis for engineering structures offers considerable potential for boosting efficiency by minimizing repetitive tasks. Although AI-driven methods are increasingly common, no systematic framework yet leverages Large Language Models (LLMs) for automatic structural analysis. To address this gap, we propose a novel framework that integrates LLMs with structural analysis software. LLMs serve as the core engine: they parse structural descriptions from text and translate them into executable Python scripts. Moreover, the framework integrates the generative capabilities of LLMs with code-based finite element (FE) tools like OpenSeesPy. It employs domain-specific prompt design and in-context learning strategies to enhance the LLM's problem-solving capabilities and generative stability, enabling fully automated structural analysis from descriptive text to model outputs. In our experiments, we introduce a well-curated small-scale benchmark dataset of 20 structural analysis word problems (SAWPs) with ground-truth solutions and evaluate the performance of different LLMs within our framework in solving these SAWPs. The role of system instructions, crafted by structural engineers, is also investigated to understand their impact on LLM-driven structural analysis. Additionally, the generative stability of our framework is examined. Through multiple validation experiments on the benchmark, our results demonstrate that the proposed framework can substantially increase the level of automation in solving SAWPs compared to traditional methods. Quantitatively, the framework, built on GPT-4o, achieved 100% accuracy, surpassing GPT-4 (85%), Gemini 1.5 Pro (80%), and Llama-3.3 (30%) on the test examples. Furthermore, integrating domain-specific instructions enhanced performance by 30% on problems with asymmetrical structural configurations.

Modern Electronic Design Automation (EDA) workflows, especially the RTL-to-GDSII flow, require heavily manual scripting and demonstrate a multitude of tool-specific interactions which limits scalability and efficiency. While LLMs introduces strides for automation, existing LLM solutions require expensive fine-tuning and do not contain standardized frameworks for integration and evaluation. We introduce AutoEDA, a framework for EDA automation that leverages paralleled learning through the Model Context Protocol (MCP) specific for standardized and scalable natural language experience across the entire RTL-to-GDSII flow. AutoEDA limits fine-tuning through structured prompt engineering, implements intelligent parameter extraction and task decomposition, and provides an extended CodeBLEU metric to evaluate the quality of TCL scripts. Results from experiments over five previously curated benchmarks show improvements in automation accuracy and efficiency, as well as script quality when compared to existing methods. AutoEDA is released open-sourced to support reproducibility and the EDA community. Available at: https://github.com/AndyLu666/MCP-EDA-Server

Despite the growing use of large language models (LLMs) in clinical dialogue systems, existing evaluations focus on task completion or fluency, offering little insight into the behavioral and risk management requirements essential for safety-critical systems. This paper presents MATRIX (Multi-Agent simulaTion fRamework for safe Interactions and conteXtual clinical conversational evaluation), a structured, extensible framework for safety-oriented evaluation of clinical dialogue agents. MATRIX integrates three components: (1) a safety-aligned taxonomy of clinical scenarios, expected system behaviors and failure modes derived through structured safety engineering methods; (2) BehvJudge, an LLM-based evaluator for detecting safety-relevant dialogue failures, validated against expert clinician annotations; and (3) PatBot, a simulated patient agent capable of producing diverse, scenario-conditioned responses, evaluated for realism and behavioral fidelity with human factors expertise, and a patient-preference study. Across three experiments, we show that MATRIX enables systematic, scalable safety evaluation. BehvJudge with Gemini 2.5-Pro achieves expert-level hazard detection (F1 0.96, sensitivity 0.999), outperforming clinicians in a blinded assessment of 240 dialogues. We also conducted one of the first realism analyses of LLM-based patient simulation, showing that PatBot reliably simulates realistic patient behavior in quantitative and qualitative evaluations. Using MATRIX, we demonstrate its effectiveness in benchmarking five LLM agents across 2,100 simulated dialogues spanning 14 hazard scenarios and 10 clinical domains. MATRIX is the first framework to unify structured safety engineering with scalable, validated conversational AI evaluation, enabling regulator-aligned safety auditing. We release all evaluation tools, prompts, structured scenarios, and datasets.

Modernizing legacy COBOL systems remains difficult due to scarce expertise, large and long-lived codebases, and strict correctness requirements. Recent large language model (LLM)-based modernization systems increasingly rely on agentic workflows in which the model controls multi-step tool execution. However, it remains unclear whether delegating execution control to the LLM improves correctness, robustness, or efficiency in structured software engineering workflows. We present a controlled empirical study of deterministic and LLM-controlled orchestration for COBOL-to-Python modernization. Using a unified experimental framework, we hold the language models, prompts, tools, configurations, and source programs constant while varying only the execution control strategy. This isolates orchestration as the sole experimental variable. We evaluate both approaches using functional correctness, robustness across repeated stochastic runs, and computational efficiency. Across multiple models, deterministic orchestration achieves comparable computational accuracy to LLM-controlled orchestration while improving worst-case robustness and reducing performance variability across runs. Deterministic execution also reduces token consumption by up to 3.5x, leading to substantially lower operational cost. These results suggest that, in structured modernization workflows with explicit validation stages, fixed execution policies provide more stable and cost-efficient behavior than fully agentic orchestration without reducing translation quality.

Structural modeling is a fundamental component of computational engineering science, in which even minor physical inconsistencies or specification violations may invalidate downstream simulations. The potential of large language models (LLMs) for automatic generation of modeling code has been demonstrated. However, non-executable or physically inconsistent outputs remain prevalent under stringent engineering constraints. A framework for physics-consistent automatic building modeling is therefore proposed, integrating domain knowledge construction, constraint-oriented model alignment, and verification-driven evaluation. CivilInstruct is introduced as a domain-specific dataset that formalizes structural engineering knowledge and constraint reasoning to enable simulation-ready model generation. A two-stage fine-tuning strategy is further employed to enforce constraint satisfaction and application programming interface compliance, substantially reducing hallucinated and non-conforming outputs. MBEval is presented as a verification-driven benchmark that evaluates executability and structural dynamics consistency through closed-loop validation. Experimental results show consistent improvements over baselines across rigorous verification metrics. Our code is available at https://github.com/Jovanqing/AutoBM.

Structural topology optimization (TO) is central to engineering design but remains computationally intensive due to complex physics and hard constraints. Existing deep-learning methods are limited to fixed square grids, a few hand-coded boundary conditions, and post-hoc optimization, preventing general deployment. We introduce Optimize Any Topology (OAT), a foundation-model framework that directly predicts minimum-compliance layouts for arbitrary aspect ratios, resolutions, volume fractions, loads, and fixtures. OAT combines a resolution- and shape-agnostic autoencoder with an implicit neural-field decoder and a conditional latent-diffusion model trained on OpenTO, a new corpus of 2.2 million optimized structures covering 2 million unique boundary-condition configurations. On four public benchmarks and two challenging unseen tests, OAT lowers mean compliance up to 90% relative to the best prior models and delivers sub-1 second inference on a single GPU across resolutions from 64 x 64 to 256 x 256 and aspect ratios as high as 10:1. These results establish OAT as a general, fast, and resolution-free framework for physics-aware topology optimization and provide a large-scale dataset to spur further research in generative modeling for inverse design. Code & data can be found at https://github.com/ahnobari/OptimizeAnyTopology.

Machine learning (ML) is increasingly used in structural engineering and design, yet its broader adoption is hampered by the lack of openly accessible datasets of structural systems. We introduce BridgeNet, a publicly available graph-based dataset of 20,000 form-found bridge structures aimed at enabling Graph ML and multi-modal learning in the context of conceptual structural design. Each datapoint consists of (i) a pin-jointed equilibrium wireframe model generated with the Combinatorial Equilibrium Modeling (CEM) form-finding method, (ii) a volumetric 3D mesh obtained through force-informed materialization, and (iii) rendered images from two canonical camera angles. The resulting dataset is modality-rich and application-agnostic, supporting tasks such as CEM-specific edge classification and parameter inference, surrogate modeling of form-finding, cross-modal reconstruction between graphs, meshes and images, and generative structural design. BridgeNet addresses a key bottleneck in data-driven applications for structural engineering and design by providing a dataset that facilitates the development of new ML-based approaches for equilibrium bridge structures.

Structural optimization is a popular method for designing objects such as bridge trusses, airplane wings, and optical devices. Unfortunately, the quality of solutions depends heavily on how the problem is parameterized. In this paper, we propose using the implicit bias over functions induced by neural networks to improve the parameterization of structural optimization. Rather than directly optimizing densities on a grid, we instead optimize the parameters of a neural network which outputs those densities. This reparameterization leads to different and often better solutions. On a selection of 116 structural optimization tasks, our approach produces the best design 50% more often than the best baseline method.

We introduce a novel dataset designed to benchmark the physical and spatial reasoning capabilities of Large Language Models (LLM) based on topology optimization, a method for computing optimal material distributions within a design space under prescribed loads and supports. In this dataset, LLMs are provided with conditions such as 2D boundary, applied forces and supports, and must reason about the resulting optimal material distribution. The dataset includes a variety of tasks, ranging from filling in masked regions within partial structures to predicting complete material distributions. Solving these tasks requires understanding the flow of forces and the required material distribution under given constraints, without access to simulation tools or explicit physical models, challenging models to reason about structural stability and spatial organization. Our dataset targets the evaluation of spatial and physical reasoning abilities in 2D settings, offering a complementary perspective to traditional language and logic benchmarks.

Efficient and accurate extraction of key information from 2D engineering drawings is essential for advancing digital manufacturing workflows. Such information includes geometric dimensioning and tolerancing (GD&T), measures, material specifications, and textual annotations. Manual extraction is slow and labor-intensive, while generic OCR models often fail due to complex layouts, engineering symbols, and rotated text, leading to incomplete and unreliable outputs. These limitations result in incomplete and unreliable outputs. To address these challenges, we propose a hybrid vision-language framework that integrates a rotation-aware object detection model (YOLOv11-obb) with a transformer-based vision-language parser. Our structured pipeline applies YOLOv11-OBB to localize annotations and extract oriented bounding box (OBB) patches, which are then parsed into structured outputs using a fine-tuned, lightweight vision-language model (VLM). We curate a dataset of 1,367 2D mechanical drawings annotated across nine key categories. YOLOv11-OBB is trained on this dataset to detect OBBs and extract annotation patches. These are parsed using two open-source VLMs: Donut and Florence-2. Both models are lightweight and well-suited for specialized industrial tasks under limited computational overhead. Following fine-tuning of both models on the curated dataset of image patches paired with structured annotation labels, a comparative experiment is conducted to evaluate parsing performance across four key metrics. Donut outperforms Florence-2, achieving 88.5% precision, 99.2% recall, and a 93.5% F1-score, with a hallucination rate of 11.5%. Finally, a case study demonstrates how the extracted structured information supports downstream manufacturing tasks such as process and tool selection, showcasing the practical utility of the proposed framework in modernizing 2D drawing interpretation.

This paper introduces YOLOv8-TO, a novel approach for reverse engineering of topology-optimized structures into interpretable geometric parameters using the YOLOv8 instance segmentation model. Density-based topology optimization methods require post-processing to convert the optimal density distribution into a parametric representation for design exploration and integration with CAD tools. Traditional methods such as skeletonization struggle with complex geometries and require manual intervention. YOLOv8-TO addresses these challenges by training a custom YOLOv8 model to automatically detect and reconstruct structural components from binary density distributions. The model is trained on a diverse dataset of both optimized and random structures generated using the Moving Morphable Components method. A custom reconstruction loss function based on the dice coefficient of the predicted geometry is used to train the new regression head of the model via self-supervised learning. The method is evaluated on test sets generated from different topology optimization methods, including out-of-distribution samples, and compared against a skeletonization approach. Results show that YOLOv8-TO significantly outperforms skeletonization in reconstructing visually and structurally similar designs. The method showcases an average improvement of 13.84% in the Dice coefficient, with peak enhancements reaching 20.78%. The method demonstrates good generalization to complex geometries and fast inference times, making it suitable for integration into design workflows using regular workstations. Limitations include the sensitivity to non-max suppression thresholds. YOLOv8-TO represents a significant advancement in topology optimization post-processing, enabling efficient and accurate reverse engineering of optimized structures for design exploration and manufacturing.

Machine learning (ML) and deep learning (DL) techniques have gained significant attention as reduced order models (ROMs) to computationally expensive structural analysis methods, such as finite element analysis (FEA). Graph neural network (GNN) is a particular type of neural network which processes data that can be represented as graphs. This allows for efficient representation of complex geometries that can change during conceptual design of a structure or a product. In this study, we propose a novel graph embedding technique for efficient representation of 3D stiffened panels by considering separate plate domains as vertices. This approach is considered using Graph Sampling and Aggregation (GraphSAGE) to predict stress distributions in stiffened panels with varying geometries. A comparison between a finite-element-vertex graph representation is conducted to demonstrate the effectiveness of the proposed approach. A comprehensive parametric study is performed to examine the effect of structural geometry on the prediction performance. Our results demonstrate the immense potential of graph neural networks with the proposed graph embedding method as robust reduced-order models for 3D structures.

As LLMs advance their reasoning capabilities about the physical world, the absence of rigorous benchmarks for evaluating their ability to generate scientifically valid physical models has become a critical gap. Computational mechanics, which develops and applies mathematical models and numerical methods to predict the behavior of physical systems under forces, deformation, and constraints, provides an ideal foundation for structured scientific reasoning evaluation. Problems follow clear mathematical structure, enforce strict physical and numerical constraints, and support objective verification. The discipline requires constructing explicit models of physical systems and reasoning about geometry, spatial relationships, and material behavior, connecting directly to emerging AI goals in physical reasoning and world modeling. We introduce FEM-Bench, a computational mechanics benchmark designed to evaluate the ability of LLMs to generate correct finite element method (FEM) and related code. FEM-Bench 2025 contains a suite of introductory but nontrivial tasks aligned with material from a first graduate course on computational mechanics. These tasks capture essential numerical and physical modeling challenges while representing only a small fraction of the complexity present in the discipline. Despite their simplicity, state-of-the-art LLMs do not reliably solve all of them. In a five attempt run, the best performing model at function writing, Gemini 3 Pro, completed 30/33 tasks at least once and 26/33 tasks all five times. The best performing model at unit test writing, GPT-5, had an Average Joint Success Rate of 73.8%. Other popular models showed broad performance variation. FEM-Bench establishes a structured foundation for evaluating AI-generated scientific code, and future iterations will incorporate increasingly sophisticated tasks to track progress as models evolve.

Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.

Natural structural materials, such as bone and wood, can autonomously adapt their mechanical properties in response to loading to prevent failure. They smartly control the addition of material in locations of high stress by utilizing locally available resources guided by biological signals. On the contrary, synthetic structural materials have unchanging mechanical properties limiting their mechanical performance and service life. Here, a material system that autonomously adapts its mechanical properties in response to mechanical loading is reported inspired by the mineralization process of bone. It is observed that charges from piezoelectric scaffolds can induce mineralization from media with mineral ions. The material system adapts to mechanical loading by inducing mineral deposition in proportion to the magnitude of the loading and the resulting piezoelectric charges. Moreover, the mechanism allows a simple one-step route for making graded materials by controlling stress distribution along the scaffold. The findings can pave the way for a new class of self-adaptive materials that reinforce the region of high stress or induce deposition of minerals on the damaged areas from the increase in stress to prevent/mitigate failure. They can also contribute to addressing the current challenges of synthetic materials for load-bearing applications from self-adaptive capabilities.

Generative models have had a profound impact on vision and language, paving the way for a new era of multimodal generative applications. While these successes have inspired researchers to explore using generative models in science and engineering to accelerate the design process and reduce the reliance on iterative optimization, challenges remain. Specifically, engineering optimization methods based on physics still outperform generative models when dealing with constrained environments where data is scarce and precision is paramount. To address these challenges, we introduce Diffusion Optimization Models (DOM) and Trajectory Alignment (TA), a learning framework that demonstrates the efficacy of aligning the sampling trajectory of diffusion models with the optimization trajectory derived from traditional physics-based methods. This alignment ensures that the sampling process remains grounded in the underlying physical principles. Our method allows for generating feasible and high-performance designs in as few as two steps without the need for expensive preprocessing, external surrogate models, or additional labeled data. We apply our framework to structural topology optimization, a fundamental problem in mechanical design, evaluating its performance on in- and out-of-distribution configurations. Our results demonstrate that TA outperforms state-of-the-art deep generative models on in-distribution configurations and halves the inference computational cost. When coupled with a few steps of optimization, it also improves manufacturability for out-of-distribution conditions. By significantly improving performance and inference efficiency, DOM enables us to generate high-quality designs in just a few steps and guide them toward regions of high performance and manufacturability, paving the way for the widespread application of generative models in large-scale data-driven design.

In this paper, we provide two case studies to demonstrate how artificial intelligence can empower civil engineering. In the first case, a machine learning-assisted framework, BRAILS, is proposed for city-scale building information modeling. Building information modeling (BIM) is an efficient way of describing buildings, which is essential to architecture, engineering, and construction. Our proposed framework employs deep learning technique to extract visual information of buildings from satellite/street view images. Further, a novel machine learning (ML)-based statistical tool, SURF, is proposed to discover the spatial patterns in building metadata. The second case focuses on the task of soft-story building classification. Soft-story buildings are a type of buildings prone to collapse during a moderate or severe earthquake. Hence, identifying and retrofitting such buildings is vital in the current earthquake preparedness efforts. For this task, we propose an automated deep learning-based procedure for identifying soft-story buildings from street view images at a regional scale. We also create a large-scale building image database and a semi-automated image labeling approach that effectively annotates new database entries. Through extensive computational experiments, we demonstrate the effectiveness of the proposed method.

Large language model (LLM) applications such as agents and domain-specific reasoning increasingly rely on context adaptation -- modifying inputs with instructions, strategies, or evidence, rather than weight updates. Prior approaches improve usability but often suffer from brevity bias, which drops domain insights for concise summaries, and from context collapse, where iterative rewriting erodes details over time. Building on the adaptive memory introduced by Dynamic Cheatsheet, we introduce ACE (Agentic Context Engineering), a framework that treats contexts as evolving playbooks that accumulate, refine, and organize strategies through a modular process of generation, reflection, and curation. ACE prevents collapse with structured, incremental updates that preserve detailed knowledge and scale with long-context models. Across agent and domain-specific benchmarks, ACE optimizes contexts both offline (e.g., system prompts) and online (e.g., agent memory), consistently outperforming strong baselines: +10.6% on agents and +8.6% on finance, while significantly reducing adaptation latency and rollout cost. Notably, ACE could adapt effectively without labeled supervision and instead by leveraging natural execution feedback. On the AppWorld leaderboard, ACE matches the top-ranked production-level agent on the overall average and surpasses it on the harder test-challenge split, despite using a smaller open-source model. These results show that comprehensive, evolving contexts enable scalable, efficient, and self-improving LLM systems with low overhead.

Multimodal Foundation Models (MMFMs) have shown remarkable performance on various computer vision and natural language processing tasks. However, their performance on particular tasks such as document understanding is still limited. They also require more compute, time, and engineering resources to finetune and deploy compared to traditional, unimodal models. In this report, we present Multimodal Structured Generation, a general framework which constrains the output logits of frozen MMFMs to force them to reason before responding with structured outputs that downstream APIs can parse and use. We provide a detailed account of our approach, including the technical details, theoretical discussions, and final evaluation results in the 2nd Multimodal Foundation Models Challenge hosted by the Computer Vision and Pattern Recognition (CVPR) conference. Our approach achieved the second highest score in the hidden test set for Phase 2 and third highest overall. This shows the method's ability to generalize to unseen tasks. And that simple engineering can beat expensive & complicated modelling steps as we first discussed in our paper, Retrieval Augmented Structured Generation: Business Document Information Extraction as Tool Use. All of our scripts, deployment steps, and evaluation results can be accessed in https://github.com/leloykun/MMFM-Challenge

We argue that generative text-to-image models often struggle with prompt adherence due to the noisy and unstructured nature of large-scale datasets like LAION-5B. This forces users to rely heavily on prompt engineering to elicit desirable outputs. In this work, we propose that enforcing a consistent caption structure during training can significantly improve model controllability and alignment. We introduce Re-LAION-Caption 19M, a high-quality subset of Re-LAION-5B, comprising 19 million 1024x1024 images with captions generated by a Mistral 7B Instruct-based LLaVA-Next model. Each caption follows a four-part template: subject, setting, aesthetics, and camera details. We fine-tune PixArt-Sigma and Stable Diffusion 2 using both structured and randomly shuffled captions, and show that structured versions consistently yield higher text-image alignment scores using visual question answering (VQA) models. The dataset is publicly available at https://huggingface.co/datasets/supermodelresearch/Re-LAION-Caption19M.

Computer-aided design (CAD) is the backbone of modern industrial design, yet learned CAD generators still fall short of real engineering pipelines: they neither iterate like engineers nor evaluate what engineering requires. Prior work has treated CAD generation as two disjoint steps, part synthesis and assembly, where the former is graded by proximity to a gold reference and the latter, when handled at all, is reduced to a separate constraint solving step. In this work, we introduce a more industry-native task formulation that requires a model to produce a fully assembled multi-part STEP file from a free-form engineering brief, which is then validated via finite element analysis (FEA). FEA validation reveals that Codex (GPT-5.5) and Claude Code (Opus-4.7) agents do not produce a single strict-passing artifact in the main first-attempt sweep, with the best configuration meeting only about 20% of typed requirements on average. Moreover, we introduce two additional supervision signals, a novel text-only blueprint schema and a 21-view image renderer that aids the agent's visual inspection, that better align the generation loop with how engineers iterate in practice. On S2O and Fusion360, the same feedback tools improve geometric reconstruction, with GPT-5.5/xhigh rising from 0.444 to 0.592 Box-IoU on S2O and from 0.397 to 0.505 on Fusion360. Together these signals move CAD programs toward artifacts that are not only visually plausible but also checked against physical and structural requirements.

Native 3D generative models have achieved remarkable fidelity and speed, yet they suffer from a critical limitation: inability to prescribe precise structural articulations, where precise structural control within the native 3D space remains underexplored. This paper proposes SK-Adapter, a simple and yet highly efficient and effective framework that unlocks precise skeletal manipulation for native 3D generation. Moving beyond text or image prompts, which can be ambiguous for precise structure, we treat the 3D skeleton as a first-class control signal. SK-Adapter is a lightweight structural adapter network that encodes joint coordinates and topology into learnable tokens, which are injected into the frozen 3D generation backbone via cross-attention. This smart design allows the model to not only effectively "attend" to specific 3D structural constraints but also preserve its original generative priors. To bridge the data gap, we contribute Objaverse-TMS dataset, a large-scale dataset of 24k text-mesh-skeleton pairs. Extensive experiments confirm that our method achieves robust structural control while preserving the geometry and texture quality of the foundation model, significantly outperforming existing baselines. Furthermore, we extend this capability to local 3D editing, enabling the region specific editing of existing assets with skeletal guidance, which is unattainable by previous methods. Project Page: https://sk-adapter.github.io/

Prompt engineering has emerged as an indispensable technique for extending the capabilities of large language models (LLMs) and vision-language models (VLMs). This approach leverages task-specific instructions, known as prompts, to enhance model efficacy without modifying the core model parameters. Rather than updating the model parameters, prompts allow seamless integration of pre-trained models into downstream tasks by eliciting desired model behaviors solely based on the given prompt. Prompts can be natural language instructions that provide context to guide the model or learned vector representations that activate relevant knowledge. This burgeoning field has enabled success across various applications, from question-answering to commonsense reasoning. However, there remains a lack of systematic organization and understanding of the diverse prompt engineering methods and techniques. This survey paper addresses the gap by providing a structured overview of recent advancements in prompt engineering, categorized by application area. For each prompting approach, we provide a summary detailing the prompting methodology, its applications, the models involved, and the datasets utilized. We also delve into the strengths and limitations of each approach and include a taxonomy diagram and table summarizing datasets, models, and critical points of each prompting technique. This systematic analysis enables a better understanding of this rapidly developing field and facilitates future research by illuminating open challenges and opportunities for prompt engineering.

Engineering efficient implementations of compact and succinct structures is a time-consuming and challenging task, since there is no standard library of easy-to- use, highly optimized, and composable components. One consequence is that measuring the practical impact of new theoretical proposals is a difficult task, since older base- line implementations may not rely on the same basic components, and reimplementing from scratch can be very time-consuming. In this paper we present a framework for experimentation with succinct data structures, providing a large set of configurable components, together with tests, benchmarks, and tools to analyze resource requirements. We demonstrate the functionality of the framework by recomposing succinct solutions for document retrieval.

Long conversations with an AI agent create a simple problem for one user: the history is useful, but carrying it verbatim is expensive. We study personalized agent memory: one user's conversation history with an agent, distilled into a compact retrieval layer for later search. Each exchange is compressed into a compound object with four fields (exchange_core, specific_context, thematic room_assignments, and regex-extracted files_touched). The searchable distilled text averages 38 tokens per exchange. Applied to 4,182 conversations (14,340 exchanges) from 6 software engineering projects, the method reduces average exchange length from 371 to 38 tokens, yielding 11x compression. We evaluate whether personalized recall survives that compression using 201 recall-oriented queries, 107 configurations spanning 5 pure and 5 cross-layer search modes, and 5 LLM graders (214,519 consensus-graded query-result pairs). The best pure distilled configuration reaches 96% of the best verbatim MRR (0.717 vs 0.745). Results are mechanism-dependent. All 20 vector search configurations remain non-significant after Bonferroni correction, while all 20 BM25 configurations degrade significantly (effect sizes |d|=0.031-0.756). The best cross-layer setup slightly exceeds the best pure verbatim baseline (MRR 0.759). Structured distillation compresses single-user agent memory without uniformly sacrificing retrieval quality. At 1/11 the context cost, thousands of exchanges fit within a single prompt while the verbatim source remains available for drill-down. We release the implementation and analysis pipeline as open-source software.

LLMs have demonstrated commendable performance across diverse domains. Nevertheless, formulating high-quality prompts to instruct LLMs proficiently poses a challenge for non-AI experts. Existing research in prompt engineering suggests somewhat scattered optimization principles and designs empirically dependent prompt optimizers. Unfortunately, these endeavors lack a structured design template, incurring high learning costs and resulting in low reusability. In addition, it is not conducive to the iterative updating of prompts. Inspired by structured reusable programming languages, we propose LangGPT, a dual-layer prompt design framework as the programming language for LLMs. LangGPT has an easy-to-learn normative structure and provides an extended structure for migration and reuse. Experiments illustrate that LangGPT significantly enhances the performance of LLMs. Moreover, the case study shows that LangGPT leads LLMs to generate higher-quality responses. Furthermore, we analyzed the ease of use and reusability of LangGPT through a user survey in our online community.

This paper delves into the pivotal role of prompt engineering in unleashing the capabilities of Large Language Models (LLMs). Prompt engineering is the process of structuring input text for LLMs and is a technique integral to optimizing the efficacy of LLMs. This survey elucidates foundational principles of prompt engineering, such as role-prompting, one-shot, and few-shot prompting, as well as more advanced methodologies such as the chain-of-thought and tree-of-thoughts prompting. The paper sheds light on how external assistance in the form of plugins can assist in this task, and reduce machine hallucination by retrieving external knowledge. We subsequently delineate prospective directions in prompt engineering research, emphasizing the need for a deeper understanding of structures and the role of agents in Artificial Intelligence-Generated Content (AIGC) tools. We discuss how to assess the efficacy of prompt methods from different perspectives and using different methods. Finally, we gather information about the application of prompt engineering in such fields as education and programming, showing its transformative potential. This comprehensive survey aims to serve as a friendly guide for anyone venturing through the big world of LLMs and prompt engineering.

Reliably transferring specialized human knowledge from text into large language models remains a fundamental challenge in artificial intelligence. Fine-tuning on domain corpora has enabled substantial capability gains, but the process operates without feedback: when a model fails on a domain task, there is no method to diagnose what is deficient in the training data, and the only recourse is to add more data indiscriminately. Here we show that when a structured knowledge representation extracted from the source corpus serves as the shared foundation for both training data and evaluation, the complete data-engineering lifecycle maps onto the software development lifecycle in a precise and operative way: training data becomes source code specifying what the model should learn, model training becomes compilation, benchmarking becomes unit testing, and failure-driven data repair becomes debugging. Under this correspondence, model failures decompose into concept-level gaps and reasoning-chain breaks that can be traced back to specific deficiencies in the data and repaired through targeted patches, with each repair cycle producing consistent improvements across model scales and architectures without degrading general capabilities. We formalize this principle as Programming with Data and instantiate it across sixteen disciplines spanning the natural sciences, engineering, biomedicine, and the social sciences, releasing a structured knowledge base, benchmark suite, and training corpus as open resources. By demonstrating that the relationship between training data and model behaviour is structurally traceable and systematically repairable, this work establishes a principled foundation for the reliable engineering of human expertise into language models.

Multimodal Large Language Models (MLLMs) are set to transform how machines process and generate human-like responses by integrating diverse modalities such as text, images, and code. Yet, effectively harnessing their capabilities hinges on optimal prompt engineering. We present a comprehensive experimental evaluation of seven prompt engineering methods applied to 13 open-source MLLMs over 24 tasks spanning Reasoning and Compositionality, Multimodal Understanding and Alignment, Complex Code Generation and Execution, and Knowledge Retrieval and Integration. Our approach stratifies models by parameter count into Small (<4B), Medium (4B-10B), and Large (>10B) categories and compares prompting techniques including Zero-Shot, One-Shot, Few-Shot, Chain-of-Thought, Analogical, Generated Knowledge, and Tree-of-Thought. While Large MLLMs excel in structured tasks such as code generation, achieving accuracies up to 96.88% under Few-Shot prompting, all models struggle with complex reasoning and abstract understanding, often yielding accuracies below 60% and high hallucination rates. Structured reasoning prompts frequently increased hallucination up to 75% in small models and led to longer response times (over 20 seconds in Large MLLMs), while simpler prompting methods provided more concise and efficient outputs. No single prompting method uniformly optimises all task types. Instead, adaptive strategies combining example-based guidance with selective structured reasoning are essential to enhance robustness, efficiency, and factual accuracy. Our findings offer practical recommendations for prompt engineering and support more reliable deployment of MLLMs across applications including AI-assisted coding, knowledge retrieval, and multimodal content understanding.

Knowledge Graphs (KG) provide us with a structured, flexible, transparent, cross-system, and collaborative way of organizing our knowledge and data across various domains in society and industrial as well as scientific disciplines. KGs surpass any other form of representation in terms of effectiveness. However, Knowledge Graph Engineering (KGE) requires in-depth experiences of graph structures, web technologies, existing models and vocabularies, rule sets, logic, as well as best practices. It also demands a significant amount of work. Considering the advancements in large language models (LLMs) and their interfaces and applications in recent years, we have conducted comprehensive experiments with ChatGPT to explore its potential in supporting KGE. In this paper, we present a selection of these experiments and their results to demonstrate how ChatGPT can assist us in the development and management of KGs.

Large Language Models (LLMs), like ChatGPT, have demonstrated vast potential but also introduce challenges related to content constraints and potential misuse. Our study investigates three key research questions: (1) the number of different prompt types that can jailbreak LLMs, (2) the effectiveness of jailbreak prompts in circumventing LLM constraints, and (3) the resilience of ChatGPT against these jailbreak prompts. Initially, we develop a classification model to analyze the distribution of existing prompts, identifying ten distinct patterns and three categories of jailbreak prompts. Subsequently, we assess the jailbreak capability of prompts with ChatGPT versions 3.5 and 4.0, utilizing a dataset of 3,120 jailbreak questions across eight prohibited scenarios. Finally, we evaluate the resistance of ChatGPT against jailbreak prompts, finding that the prompts can consistently evade the restrictions in 40 use-case scenarios. The study underscores the importance of prompt structures in jailbreaking LLMs and discusses the challenges of robust jailbreak prompt generation and prevention.

Reconstructing 3D objects into editable programs is pivotal for applications like reverse engineering and shape editing. However, existing methods often rely on limited domain-specific languages (DSLs) and small-scale datasets, restricting their ability to model complex geometries and structures. To address these challenges, we introduce MeshCoder, a novel framework that reconstructs complex 3D objects from point clouds into editable Blender Python scripts. We develop a comprehensive set of expressive Blender Python APIs capable of synthesizing intricate geometries. Leveraging these APIs, we construct a large-scale paired object-code dataset, where the code for each object is decomposed into distinct semantic parts. Subsequently, we train a multimodal large language model (LLM) that translates 3D point cloud into executable Blender Python scripts. Our approach not only achieves superior performance in shape-to-code reconstruction tasks but also facilitates intuitive geometric and topological editing through convenient code modifications. Furthermore, our code-based representation enhances the reasoning capabilities of LLMs in 3D shape understanding tasks. Together, these contributions establish MeshCoder as a powerful and flexible solution for programmatic 3D shape reconstruction and understanding.

Engineering construction automation aims to transform natural language specifications into physically viable structures, requiring complex integrated reasoning under strict physical constraints. While modern LLMs possess broad knowledge and strong reasoning capabilities that make them promising candidates for this domain, their construction competencies remain largely unevaluated. To address this gap, we introduce BuildArena, the first physics-aligned interactive benchmark designed for language-driven engineering construction. It contributes to the community in four aspects: (1) a highly customizable benchmarking framework for in-depth comparison and analysis of LLMs; (2) an extendable task design strategy spanning static and dynamic mechanics across multiple difficulty tiers; (3) a 3D Spatial Geometric Computation Library for supporting construction based on language instructions; (4) a baseline LLM agentic workflow that effectively evaluates diverse model capabilities. On eight frontier LLMs, BuildArena comprehensively evaluates their capabilities for language-driven and physics-grounded construction automation. The project page is at https://build-arena.github.io/.

We propose an intuitive LLM prompting framework (AgentKit) for multifunctional agents. AgentKit offers a unified framework for explicitly constructing a complex "thought process" from simple natural language prompts. The basic building block in AgentKit is a node, containing a natural language prompt for a specific subtask. The user then puts together chains of nodes, like stacking LEGO pieces. The chains of nodes can be designed to explicitly enforce a naturally structured "thought process". For example, for the task of writing a paper, one may start with the thought process of 1) identify a core message, 2) identify prior research gaps, etc. The nodes in AgentKit can be designed and combined in different ways to implement multiple advanced capabilities including on-the-fly hierarchical planning, reflection, and learning from interactions. In addition, due to the modular nature and the intuitive design to simulate explicit human thought process, a basic agent could be implemented as simple as a list of prompts for the subtasks and therefore could be designed and tuned by someone without any programming experience. Quantitatively, we show that agents designed through AgentKit achieve SOTA performance on WebShop and Crafter. These advances underscore AgentKit's potential in making LLM agents effective and accessible for a wider range of applications. https://github.com/holmeswww/AgentKit

Large language models (LLMs) have shown remarkable performance on many different Natural Language Processing (NLP) tasks. Prompt engineering plays a key role in adding more to the already existing abilities of LLMs to achieve significant performance gains on various NLP tasks. Prompt engineering requires composing natural language instructions called prompts to elicit knowledge from LLMs in a structured way. Unlike previous state-of-the-art (SoTA) models, prompt engineering does not require extensive parameter re-training or fine-tuning based on the given NLP task and thus solely operates on the embedded knowledge of LLMs. Additionally, LLM enthusiasts can intelligently extract LLMs' knowledge through a basic natural language conversational exchange or prompt engineering, allowing more and more people even without deep mathematical machine learning background to experiment with LLMs. With prompt engineering gaining popularity in the last two years, researchers have come up with numerous engineering techniques around designing prompts to improve accuracy of information extraction from the LLMs. In this paper, we summarize different prompting techniques and club them together based on different NLP tasks that they have been used for. We further granularly highlight the performance of these prompting strategies on various datasets belonging to that NLP task, talk about the corresponding LLMs used, present a taxonomy diagram and discuss the possible SoTA for specific datasets. In total, we read and present a survey of 44 research papers which talk about 39 different prompting methods on 29 different NLP tasks of which most of them have been published in the last two years.

Engineering Design is undergoing a transformative shift with the advent of AI, marking a new era in how we approach product, system, and service planning. Large language models have demonstrated impressive capabilities in enabling this shift. Yet, with text as their only input modality, they cannot leverage the large body of visual artifacts that engineers have used for centuries and are accustomed to. This gap is addressed with the release of multimodal vision language models, such as GPT-4V, enabling AI to impact many more types of tasks. In light of these advancements, this paper presents a comprehensive evaluation of GPT-4V, a vision language model, across a wide spectrum of engineering design tasks, categorized into four main areas: Conceptual Design, System-Level and Detailed Design, Manufacturing and Inspection, and Engineering Education Tasks. Our study assesses GPT-4V's capabilities in design tasks such as sketch similarity analysis, concept selection using Pugh Charts, material selection, engineering drawing analysis, CAD generation, topology optimization, design for additive and subtractive manufacturing, spatial reasoning challenges, and textbook problems. Through this structured evaluation, we not only explore GPT-4V's proficiency in handling complex design and manufacturing challenges but also identify its limitations in complex engineering design applications. Our research establishes a foundation for future assessments of vision language models, emphasizing their immense potential for innovating and enhancing the engineering design and manufacturing landscape. It also contributes a set of benchmark testing datasets, with more than 1000 queries, for ongoing advancements and applications in this field.

Large Language Model (LLM) agents have shown great potential for solving real-world problems and promise to be a solution for tasks automation in industry. However, more benchmarks are needed to systematically evaluate automation agents from an industrial perspective, for example, in Civil Engineering. Therefore, we propose DrafterBench for the comprehensive evaluation of LLM agents in the context of technical drawing revision, a representation task in civil engineering. DrafterBench contains twelve types of tasks summarized from real-world drawing files, with 46 customized functions/tools and 1920 tasks in total. DrafterBench is an open-source benchmark to rigorously test AI agents' proficiency in interpreting intricate and long-context instructions, leveraging prior knowledge, and adapting to dynamic instruction quality via implicit policy awareness. The toolkit comprehensively assesses distinct capabilities in structured data comprehension, function execution, instruction following, and critical reasoning. DrafterBench offers detailed analysis of task accuracy and error statistics, aiming to provide deeper insight into agent capabilities and identify improvement targets for integrating LLMs in engineering applications. Our benchmark is available at https://github.com/Eason-Li-AIS/DrafterBench, with the test set hosted at https://huggingface.co/datasets/Eason666/DrafterBench.

AI for software engineering has made remarkable progress recently, becoming a notable success within generative AI. Despite this, there are still many challenges that need to be addressed before automated software engineering reaches its full potential. It should be possible to reach high levels of automation where humans can focus on the critical decisions of what to build and how to balance difficult tradeoffs while most routine development effort is automated away. Reaching this level of automation will require substantial research and engineering efforts across academia and industry. In this paper, we aim to discuss progress towards this in a threefold manner. First, we provide a structured taxonomy of concrete tasks in AI for software engineering, emphasizing the many other tasks in software engineering beyond code generation and completion. Second, we outline several key bottlenecks that limit current approaches. Finally, we provide an opinionated list of promising research directions toward making progress on these bottlenecks, hoping to inspire future research in this rapidly maturing field.

Resided at the intersection of multi-fidelity optimization (MFO) and Bayesian optimization (BO), MF BO has found a niche in solving expensive engineering design optimization problems, thanks to its advantages in incorporating physical and mathematical understandings of the problems, saving resources, addressing exploitation-exploration trade-off, considering uncertainty, and processing parallel computing. The increasing number of works dedicated to MF BO suggests the need for a comprehensive review of this advanced optimization technique. In this paper, we survey recent developments of two essential ingredients of MF BO: Gaussian process (GP) based MF surrogates and acquisition functions. We first categorize the existing MF modeling methods and MFO strategies to locate MF BO in a large family of surrogate-based optimization and MFO algorithms. We then exploit the common properties shared between the methods from each ingredient of MF BO to describe important GP-based MF surrogate models and review various acquisition functions. By doing so, we expect to provide a structured understanding of MF BO. Finally, we attempt to reveal important aspects that require further research for applications of MF BO in solving intricate yet important design optimization problems, including constrained optimization, high-dimensional optimization, optimization under uncertainty, and multi-objective optimization.

As language models (LMs) are increasingly adopted across domains, high-quality benchmarking frameworks that accurately estimate performance are essential for guiding deployment decisions. While frameworks such as Holistic Evaluation of Language Models (HELM) enable broad evaluation across tasks, they often rely on fixed prompts that fail to generalize across LMs, yielding unrepresentative performance estimates. Unless we approximate each LM's ceiling (maximum achievable via changes to the prompt), we risk underestimating performance. Declarative prompting frameworks, such as DSPy, offer a scalable alternative to manual prompt engineering by crafting structured prompts that can be optimized per task. However, such frameworks have not been systematically evaluated across established benchmarks. We present a reproducible DSPy+HELM framework that introduces structured prompting methods which elicit reasoning, enabling more accurate LM benchmarking. Using four prompting methods, we evaluate four frontier LMs across seven benchmarks (general/medical domain) against existing HELM baseline scores. We find that without structured prompting: (i) HELM underestimates LM performance (by 4% average), (ii) performance estimates vary more across benchmarks (+2% standard deviation), (iii) performance gaps are misrepresented (leaderboard rankings flip on 3/7 benchmarks), and (iv) introducing chain-of-thought reduces LM sensitivity to prompt design (smaller Δ across prompts). To our knowledge, this is the first benchmarking study to systematically integrate structured prompting into an established evaluation framework, demonstrating how scalable performance-ceiling approximation yields more robust, decision-useful benchmarks. We open-source (i) DSPy+HELM Integration (https://github.com/stanford-crfm/helm/pull/3893) and (ii) Prompt Optimization Pipeline (https://github.com/StanfordMIMI/dspy-helm).

Robotic instruction following tasks require seamless integration of visual perception, task planning, target localization, and motion execution. However, existing task planning methods for instruction following are either data-driven or underperform in zero-shot scenarios due to difficulties in grounding lengthy instructions into actionable plans under operational constraints. To address this, we propose FlowPlan, a structured multi-stage LLM workflow that elevates zero-shot pipeline and bridges the performance gap between zero-shot and data-driven in-context learning methods. By decomposing the planning process into modular stages--task information retrieval, language-level reasoning, symbolic-level planning, and logical evaluation--FlowPlan generates logically coherent action sequences while adhering to operational constraints and further extracts contextual guidance for precise instance-level target localization. Benchmarked on the ALFRED and validated in real-world applications, our method achieves competitive performance relative to data-driven in-context learning methods and demonstrates adaptability across diverse environments. This work advances zero-shot task planning in robotic systems without reliance on labeled data. Project website: https://instruction-following-project.github.io/.

The growing importance of textual and relational systems has driven interest in enhancing large language models (LLMs) for graph-structured data, particularly Text-Attributed Graphs (TAGs), where samples are represented by textual descriptions interconnected by edges. While research has largely focused on developing specialized graph LLMs through task-specific instruction tuning, a comprehensive benchmark for evaluating LLMs solely through prompt design remains surprisingly absent. Without such a carefully crafted evaluation benchmark, most if not all, tailored graph LLMs are compared against general LLMs using simplistic queries (e.g., zero-shot reasoning with LLaMA), which can potentially camouflage many advantages as well as unexpected predicaments of them. To achieve more general evaluations and unveil the true potential of LLMs for graph tasks, we introduce Graph In-context Learning (GraphICL) Benchmark, a comprehensive benchmark comprising novel prompt templates designed to capture graph structure and handle limited label knowledge. Our systematic evaluation shows that general-purpose LLMs equipped with our GraphICL outperform state-of-the-art specialized graph LLMs and graph neural network models in resource-constrained settings and out-of-domain tasks. These findings highlight the significant potential of prompt engineering to enhance LLM performance on graph learning tasks without training and offer a strong baseline for advancing research in graph LLMs.

Computer-Aided Design (CAD) model reconstruction from point clouds is an important problem at the intersection of computer vision, graphics, and machine learning; it saves the designer significant time when iterating on in-the-wild objects. Recent advancements in this direction achieve relatively reliable semantic segmentation but still struggle to produce an adequate topology of the CAD model. In this work, we analyze the current state of the art for that ill-posed task and identify shortcomings of existing methods. We propose a hybrid analytic-neural reconstruction scheme that bridges the gap between segmented point clouds and structured CAD models and can be readily combined with different segmentation backbones. Moreover, to power the surface fitting stage, we propose a novel implicit neural representation of freeform surfaces, driving up the performance of our overall CAD reconstruction scheme. We extensively evaluate our method on the popular ABC benchmark of CAD models and set a new state-of-the-art for that dataset. Project page: https://www.obukhov.ai/point2cad}{https://www.obukhov.ai/point2cad.

Facing with grave climate change and enormous energy demand, catalyzer gets more and more important due to its significant effect on reducing fossil fuels consumption. Hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) by water splitting are feasible ways to produce clean sustainable energy. Here we systematically explored atomic structures and related STM images of Se defects in PtSe2. The equilibrium fractions of vacancies under variable conditions were detailly predicted. Besides, we found the vacancies are highly kinetic stable, without recovering or aggregation. The Se vacancies in PtSe2 can dramatically enhance the HER performance, comparing with, even better than Pt(111). Beyond, we firstly revealed that PtSe2 monolayer with Se vacancies is also a good OER catalyst. The excellent bipolar catalysis of Se vacancies were further confirmed by experimental measurements. We produced defective PtSe2 by direct selenization of Pt foil at 773 K using a CVD process. Then we observed the HER and OER performance of defective PtSe2 is much highly efficient than Pt foils by a series of measurements. Our work with compelling theoretical and experimental studies indicates PtSe2 with Se defects is an ideal bipolar candidate for HER and OER.

Structured access is an emerging paradigm for the safe deployment of artificial intelligence (AI). Instead of openly disseminating AI systems, developers facilitate controlled, arm's length interactions with their AI systems. The aim is to prevent dangerous AI capabilities from being widely accessible, whilst preserving access to AI capabilities that can be used safely. The developer must both restrict how the AI system can be used, and prevent the user from circumventing these restrictions through modification or reverse engineering of the AI system. Structured access is most effective when implemented through cloud-based AI services, rather than disseminating AI software that runs locally on users' hardware. Cloud-based interfaces provide the AI developer greater scope for controlling how the AI system is used, and for protecting against unauthorized modifications to the system's design. This chapter expands the discussion of "publication norms" in the AI community, which to date has focused on the question of how the informational content of AI research projects should be disseminated (e.g., code and models). Although this is an important question, there are limits to what can be achieved through the control of information flows. Structured access views AI software not only as information that can be shared but also as a tool with which users can have arm's length interactions. There are early examples of structured access being practiced by AI developers, but there is much room for further development, both in the functionality of cloud-based interfaces and in the wider institutional framework.

Crash simulation is a cornerstone of modern vehicle development because it reduces the need for costly physical prototypes, accelerates safety-driven design iteration, and increasingly supports virtual testing workflows. At the same time, modeling structural crash mechanics remains exceptionally challenging: the response is governed by nonlinear contact, large deformation, material plasticity, failure, and complex multi-body interactions evolving over space and time on high-resolution finite-element meshes. In this work, we introduce CarCrashNet, a public high-fidelity open-source benchmark for data-driven structural crash simulation. CarCrashNet combines component-scale and full-vehicle simulations in a multi-modal format, including more than 14{,}000 bumper-beam pole-impact simulations with varying geometry, materials, and boundary conditions, together with 825 full-vehicle crash simulations built from three industry-standard vehicle models of increasing structural complexity: Dodge Neon, Toyota Yaris, and Chevrolet Silverado. To establish the reliability of the benchmark, we validate our open-source finite-element workflow based on OpenRadioss against both experimental crash data and the commercial solver Ansys LS-DYNA. We also introduce CrashSolver, a machine-learning model designed for full-vehicle crash prediction from high-resolution finite-element crash data. We further perform extensive benchmarking across the released datasets and evaluate CrashSolver against state-of-the-art geometric deep learning and transformer-based neural solvers. Our results position CarCrashNet as a foundation for reproducible research in structural simulation, crashworthiness modeling, and AI-driven virtual crash testing. The dataset is available at https://github.com/Mohamedelrefaie/CarCrashNet.

Agent skills, structured procedural knowledge packages injected at inference time, are increasingly used to augment LLM agents on software engineering tasks. However, their real utility in end-to-end development settings remains unclear. We present SWE-Skills-Bench, the first requirement-driven benchmark that isolates the marginal utility of agent skills in real-world software engineering (SWE). It pairs 49 public SWE skills with authentic GitHub repositories pinned at fixed commits and requirement documents with explicit acceptance criteria, yielding approximately 565 task instances across six SWE subdomains. We introduce a deterministic verification framework that maps each task's acceptance criteria to execution-based tests, enabling controlled paired evaluation with and without the skill. Our results show that skill injection benefits are far more limited than rapid adoption suggests: 39 of 49 skills yield zero pass-rate improvement, and the average gain is only +1.2%. Token overhead varies from modest savings to a 451% increase while pass rates remain unchanged. Only seven specialized skills produce meaningful gains (up to +30%), while three degrade performance (up to -10%) due to version-mismatched guidance conflicting with project context. These findings suggest that agent skills are a narrow intervention whose utility depends strongly on domain fit, abstraction level, and contextual compatibility. SWE-Skills-Bench provides a testbed for evaluating the design, selection, and deployment of skills in software engineering agents. SWE-Skills-Bench is available at https://github.com/GeniusHTX/SWE-Skills-Bench.

We present RAG Playground, an open-source framework for systematic evaluation of Retrieval-Augmented Generation (RAG) systems. The framework implements and compares three retrieval approaches: naive vector search, reranking, and hybrid vector-keyword search, combined with ReAct agents using different prompting strategies. We introduce a comprehensive evaluation framework with novel metrics and provide empirical results comparing different language models (Llama 3.1 and Qwen 2.5) across various retrieval configurations. Our experiments demonstrate significant performance improvements through hybrid search methods and structured self-evaluation prompting, achieving up to 72.7% pass rate on our multi-metric evaluation framework. The results also highlight the importance of prompt engineering in RAG systems, with our custom-prompted agents showing consistent improvements in retrieval accuracy and response quality.

While "Intent-oriented programming" (or "Vibe Coding") redefines software engineering, existing code agents remain tethered to static code snapshots. Consequently, they struggle to model the critical information embedded in the temporal evolution of projects, failing to leverage the "reasoning trajectories" implicit in past successful practices. This limitation results in rigid behavioral logic and a lack of autonomous adaptability, ultimately hindering their ability to tackle complex, repository-level problems. To bridge this static-dynamic mismatch, we propose MemCoder, a framework designed to enable continual human-AI co-evolution. MemCoder first structures historical human experience to distill latent intent-to-code mappings from past commits. It then employs a self-refinement mechanism driven by verification feedback to correct agent behavior in real-time. Crucially, an experience self-internalization mechanism is introduced to crystallize human-validated solutions into long-term knowledge, thereby supporting sustained evolution. Experimental results on SWE-bench Verified demonstrate that MemCoder not only achieves State-of-the-Art (SOTA) performance but also delivers a 9.4% improvement in resolved rate over the general foundation model DeepSeek-V3.2. These findings indicate that equipping agents with the capability to co-evolve with humans via project history and real-time feedback effectively unlocks the potential of general models in complex software engineering tasks.

Decades of engineering drawings and technical records remain locked in legacy archives with inconsistent or missing metadata, making retrieval difficult and often manual. We present Blueprint, a layout-aware multimodal retrieval system designed for large-scale engineering repositories. Blueprint detects canonical drawing regions, applies region-restricted VLM-based OCR, normalizes identifiers (e.g., DWG, part, facility), and fuses lexical and dense retrieval with a lightweight region-level reranker. Deployed on ~770k unlabeled files, it automatically produces structured metadata suitable for cross-facility search. We evaluate Blueprint on a 5k-file benchmark with 350 expert-curated queries using pooled, graded (0/1/2) relevance judgments. Blueprint delivers a 10.1% absolute gain in Success@3 and an 18.9% relative improvement in nDCG@3 over the strongest vision-language baseline}, consistently outperforming across vision, text, and multimodal intents. Oracle ablations reveal substantial headroom under perfect region detection and OCR. We release all queries, runs, annotations, and code to facilitate reproducible evaluation on legacy engineering archives.

Large Language Models, particularly decoder-only generative models such as GPT, are increasingly used to automate Software Engineering tasks. These models are primarily guided through natural language prompts, making prompt engineering a critical factor in system performance and behavior. Despite their growing role in SE research, prompt-related decisions are rarely documented in a systematic or transparent manner, hindering reproducibility and comparability across studies. To address this gap, we conducted a two-phase empirical study. First, we analyzed nearly 300 papers published at the top-3 SE conferences since 2022 to assess how prompt design, testing, and optimization are currently reported. Second, we surveyed 105 program committee members from these conferences to capture their expectations for prompt reporting in LLM-driven research. Based on the findings, we derived a structured guideline that distinguishes essential, desirable, and exceptional reporting elements. Our results reveal significant misalignment between current practices and reviewer expectations, particularly regarding version disclosure, prompt justification, and threats to validity. We present our guideline as a step toward improving transparency, reproducibility, and methodological rigor in LLM-based SE research.

Handwritten STEM exams capture open-ended reasoning and diagrams, but manual grading is slow and difficult to scale. We present an end-to-end workflow for grading scanned handwritten engineering quizzes with multimodal large language models (LLMs) that preserves the standard exam process (A4 paper, unconstrained student handwriting). The lecturer provides only a handwritten reference solution (100%) and a short set of grading rules; the reference is converted into a text-only summary that conditions grading without exposing the reference scan. Reliability is achieved through a multi-stage design with a format/presence check to prevent grading blank answers, an ensemble of independent graders, supervisor aggregation, and rigid templates with deterministic validation to produce auditable, machine-parseable reports. We evaluate the frozen pipeline in a clean-room protocol on a held-out real course quiz in Slovenian, including hand-drawn circuit schematics. With state-of-the-art backends (GPT-5.2 and Gemini-3 Pro), the full pipeline achieves approx8-point mean absolute difference to lecturer grades with low bias and an estimated manual-review trigger rate of approx17% at D_{max}=40. Ablations show that trivial prompting and removing the reference solution substantially degrade accuracy and introduce systematic over-grading, confirming that structured prompting and reference grounding are essential.

Vision-language foundation models (VLMs) show promise for diverse imaging tasks but often underperform on medical benchmarks. Prior efforts to improve performance include model finetuning, which requires large domain-specific datasets and significant compute, or manual prompt engineering, which is hard to generalize and often inaccessible to medical institutions seeking to deploy these tools. These challenges motivate interest in approaches that draw on a model's embedded knowledge while abstracting away dependence on human-designed prompts to enable scalable, weight-agnostic performance improvements. To explore this, we adapt the Declarative Self-improving Python (DSPy) framework for structured automated prompt optimization in medical vision-language systems through a comprehensive, formal evaluation. We implement prompting pipelines for five medical imaging tasks across radiology, gastroenterology, and dermatology, evaluating 10 open-source VLMs with four prompt optimization techniques. Optimized pipelines achieved a median relative improvement of 53% over zero-shot prompting baselines, with the largest gains ranging from 300% to 3,400% on tasks where zero-shot performance is low. These results highlight the substantial potential of applying automated prompt optimization to medical AI systems, demonstrating significant gains for vision-based applications requiring accurate clinical image interpretation. By reducing dependence on prompt design to elicit intended outputs, these techniques allow clinicians to focus on patient care and clinical decision-making. Furthermore, our experiments offer scalability and preserve data privacy, demonstrating performance improvement on open-source VLMs. We publicly release our evaluation pipelines to support reproducible research on specialized medical tasks, available at https://github.com/DaneshjouLab/prompt-triage-lab.

Access to real-world medical data is often restricted due to privacy regulations, posing a significant barrier to the advancement of healthcare research. Synthetic data offers a promising alternative; however, generating realistic, clinically valid, and privacy-conscious records remains a major challenge. Recent advancements in Large Language Models (LLMs) offer new opportunities for structured data generation; however, existing approaches frequently lack systematic prompting strategies and comprehensive, multi-dimensional evaluation frameworks. In this paper, we present SynLLM, a modular framework for generating high-quality synthetic medical tabular data using 20 state-of-the-art open-source LLMs, including LLaMA, Mistral, and GPT variants, guided by structured prompts. We propose four distinct prompt types, ranging from example-driven to rule-based constraints, that encode schema, metadata, and domain knowledge to control generation without model fine-tuning. Our framework features a comprehensive evaluation pipeline that rigorously assesses generated data across statistical fidelity, clinical consistency, and privacy preservation. We evaluate SynLLM across three public medical datasets, including Diabetes, Cirrhosis, and Stroke, using 20 open-source LLMs. Our results show that prompt engineering significantly impacts data quality and privacy risk, with rule-based prompts achieving the best privacy-quality balance. SynLLM establishes that, when guided by well-designed prompts and evaluated with robust, multi-metric criteria, LLMs can generate synthetic medical data that is both clinically plausible and privacy-aware, paving the way for safer and more effective data sharing in healthcare research.

Structured pruning and quantization are fundamental techniques used to reduce the size of deep neural networks (DNNs) and typically are applied independently. Applying these techniques jointly via co-optimization has the potential to produce smaller, high-quality models. However, existing joint schemes are not widely used because of (1) engineering difficulties (complicated multi-stage processes), (2) black-box optimization (extensive hyperparameter tuning to control the overall compression), and (3) insufficient architecture generalization. To address these limitations, we present the framework GETA, which automatically and efficiently performs joint structured pruning and quantization-aware training on any DNNs. GETA introduces three key innovations: (i) a quantization-aware dependency graph (QADG) that constructs a pruning search space for generic quantization-aware DNN, (ii) a partially projected stochastic gradient method that guarantees layerwise bit constraints are satisfied, and (iii) a new joint learning strategy that incorporates interpretable relationships between pruning and quantization. We present numerical experiments on both convolutional neural networks and transformer architectures that show that our approach achieves competitive (often superior) performance compared to existing joint pruning and quantization methods.

System logs record detailed runtime information of software systems and are used as the main data source for many tasks around software engineering. As modern software systems are evolving into large scale and complex structures, logs have become one type of fast-growing big data in industry. In particular, such logs often need to be stored for a long time in practice (e.g., a year), in order to analyze recurrent problems or track security issues. However, archiving logs consumes a large amount of storage space and computing resources, which in turn incurs high operational cost. Data compression is essential to reduce the cost of log storage. Traditional compression tools (e.g., gzip) work well for general texts, but are not tailed for system logs. In this paper, we propose a novel and effective log compression method, namely logzip. Logzip is capable of extracting hidden structures from raw logs via fast iterative clustering and further generating coherent intermediate representations that allow for more effective compression. We evaluate logzip on five large log datasets of different system types, with a total of 63.6 GB in size. The results show that logzip can save about half of the storage space on average over traditional compression tools. Meanwhile, the design of logzip is highly parallel and only incurs negligible overhead. In addition, we share our industrial experience of applying logzip to Huawei's real products.

Autonomous AI research has advanced rapidly, but long-horizon ML research engineering remains difficult: agents must sustain coherent progress across task comprehension, environment setup, implementation, experimentation, and debugging over hours or days. We introduce AiScientist, a system for autonomous long-horizon engineering for ML research built on a simple principle: strong long-horizon performance requires both structured orchestration and durable state continuity. To this end, AiScientist combines hierarchical orchestration with a permission-scoped File-as-Bus workspace: a top-level Orchestrator maintains stage-level control through concise summaries and a workspace map, while specialized agents repeatedly re-ground on durable artifacts such as analyses, plans, code, and experimental evidence rather than relying primarily on conversational handoffs, yielding thin control over thick state. Across two complementary benchmarks, AiScientist improves PaperBench score by 10.54 points on average over the best matched baseline and achieves 81.82 Any Medal% on MLE-Bench Lite. Ablation studies further show that File-as-Bus protocol is a key driver of performance, reducing PaperBench by 6.41 points and MLE-Bench Lite by 31.82 points when removed. These results suggest that long-horizon ML research engineering is a systems problem of coordinating specialized work over durable project state, rather than a purely local reasoning problem.

We introduce **SWE-Flow**, a novel data synthesis framework grounded in Test-Driven Development (TDD). Unlike existing software engineering data that rely on human-submitted issues, **SWE-Flow** automatically infers incremental development steps directly from unit tests, which inherently encapsulate high-level requirements. The core of **SWE-Flow** is the construction of a Runtime Dependency Graph (RDG), which precisely captures function interactions, enabling the generation of a structured, step-by-step *development schedule*. At each step, **SWE-Flow** produces a partial codebase, the corresponding unit tests, and the necessary code modifications, resulting in fully verifiable TDD tasks. With this approach, we generated 16,061 training instances and 2,020 test instances from real-world GitHub projects, creating the **SWE-Flow-Eval** benchmark. Our experiments show that fine-tuning open model on this dataset significantly improves performance in TDD-based coding. To facilitate further research, we release all code, datasets, models, and Docker images at [Github](https://github.com/Hambaobao/SWE-Flow).

AI agents have become increasingly capable at isolated software engineering (SWE) tasks such as resolving issues on Github. Yet long-horizon tasks involving multiple interdependent subtasks still pose challenges both with respect to accuracy, and with respect to timely completion. A natural approach to solving these long-horizon tasks in a timely manner is asynchronous multi-agent collaboration, where multiple agents work on different parts of the task at the same time. But effective application of multi-agent systems has proven surprisingly difficult: concurrent edits by multiple agents interfere with each other, dependencies are difficult to synchronize, and combining partial progress into a coherent whole is challenging. On the other hand, human developers have long relied on mature collaboration infrastructure to manage these challenges in large software projects. Inspired by these collaboration primitives, we introduce Centralized Asynchronous Isolated Delegation (CAID), a structured multi-agent coordination paradigm grounded in three core SWE primitives: centralized task delegation, asynchronous execution, and isolated workspaces. CAID constructs dependency-aware task plans through a central manager, executes subtasks concurrently in isolated workspaces, and consolidates progress via structured integration with executable test-based verification. In empirical evaluation, we find that CAID improves accuracy over single-agent baselines by 26.7% absolute on paper reproduction tasks (PaperBench) and 14.3% on Python library development tasks (Commit0). Through systematic analysis, we find that branch-and-merge is a central coordination mechanism for multi-agent collaboration, and that SWE primitives such as git worktree, git commit, and git merge enable it to be realized in a reliable and executable manner.

As model families, training recipes, and compute budgets become increasingly standardized, further gains in machine learning systems depend increasingly on data. Yet data engineering remains largely manual and ad hoc: practitioners repeatedly search for external datasets, adapt them to existing pipelines, validate candidate data through downstream training, and carry forward lessons from prior attempts. We study task-conditioned autonomous data engineering, where an autonomous agent improves a fixed learning algorithm by optimizing only the data side, including external data discovery, data selection and composition, cleaning and transformation. The goal is to obtain a stronger downstream solution while leaving the learning algorithm unchanged. To address the open-ended search space, branch-dependent refinement, and delayed validation inherent in autonomous data engineering, we propose DataMaster, a data-agent framework that integrates tree-structured search, shared candidate data, and cumulative memory. DataMaster consists of three key components: a DataTree that organizes alternative data-engineering branches, a shared Data Pool that stores discovered external data sources for reuse, and a Global Memory that records node outcomes, artifacts, and reusable findings. Together, these components allow the agent to discover candidate data, construct executable training inputs, evaluate them through downstream feedback, and carry useful evidence across branches. We evaluate DataMaster on two types of benchmarks, MLE-Bench Lite and PostTrainBench. On MLE-Bench Lite, it improves medal rate by 32.27% over the initial score; on PostTrainBench, it surpasses the instruct model on GPQA (31.02% vs 30.35%).

The future of software engineering--SE 3.0--is unfolding with the rise of AI teammates: autonomous, goal-driven systems collaborating with human developers. Among these, autonomous coding agents are especially transformative, now actively initiating, reviewing, and evolving code at scale. This paper introduces AIDev, the first large-scale dataset capturing how such agents operate in the wild. Spanning over 456,000 pull requests by five leading agents--OpenAI Codex, Devin, GitHub Copilot, Cursor, and Claude Code--across 61,000 repositories and 47,000 developers, AIDev provides an unprecedented empirical foundation for studying autonomous teammates in software development. Unlike prior work that has largely theorized the rise of AI-native software engineering, AIDev offers structured, open data to support research in benchmarking, agent readiness, optimization, collaboration modeling, and AI governance. The dataset includes rich metadata on PRs, authorship, review timelines, code changes, and integration outcomes--enabling exploration beyond synthetic benchmarks like SWE-bench. For instance, although agents often outperform humans in speed, their PRs are accepted less frequently, revealing a trust and utility gap. Furthermore, while agents accelerate code submission--one developer submitted as many PRs in three days as they had in three years--these are structurally simpler (via code complexity metrics). We envision AIDev as a living resource: extensible, analyzable, and ready for the SE and AI communities. Grounding SE 3.0 in real-world evidence, AIDev enables a new generation of research into AI-native workflows and supports building the next wave of symbiotic human-AI collaboration. The dataset is publicly available at https://github.com/SAILResearch/AI_Teammates_in_SE3. > AI Agent, Agentic AI, Coding Agent, Agentic Coding, Software Engineering Agent

Proteins power a vast array of functional processes in living cells. The capability to create new proteins with designed structures and functions would thus enable the engineering of cellular behavior and development of protein-based therapeutics and materials. Structure-based protein design aims to find structures that are designable (can be realized by a protein sequence), novel (have dissimilar geometry from natural proteins), and diverse (span a wide range of geometries). While advances in protein structure prediction have made it possible to predict structures of novel protein sequences, the combinatorially large space of sequences and structures limits the practicality of search-based methods. Generative models provide a compelling alternative, by implicitly learning the low-dimensional structure of complex data distributions. Here, we leverage recent advances in denoising diffusion probabilistic models and equivariant neural networks to develop Genie, a generative model of protein structures that performs discrete-time diffusion using a cloud of oriented reference frames in 3D space. Through in silico evaluations, we demonstrate that Genie generates protein backbones that are more designable, novel, and diverse than existing models. This indicates that Genie is capturing key aspects of the distribution of protein structure space and facilitates protein design with high success rates. Code for generating new proteins and training new versions of Genie is available at https://github.com/aqlaboratory/genie.

This paper introduces a multi-agent framework guided by Large Language Models (LLMs) to assist in the early stages of engineering design, a phase often characterized by vast parameter spaces and inherent uncertainty. Operating under a human-in-the-loop paradigm and demonstrated on the canonical problem of aerodynamic airfoil design, the framework employs a team of specialized agents: a Coding Assistant, a Design Agent, a Systems Engineering Agent, and an Analyst Agent - all coordinated by a human Manager. Integrated within a set-based design philosophy, the process begins with a collaborative phase where the Manager and Coding Assistant develop a suite of validated tools, after which the agents execute a structured workflow to systematically explore and prune a large set of initial design candidates. A key contribution of this work is the explicit integration of formal risk management, employing the Conditional Value-at-Risk (CVaR) as a quantitative metric to filter designs that exhibit a high probability of failing to meet performance requirements, specifically the target coefficient of lift. The framework automates labor-intensive initial exploration through a global sensitivity analysis conducted by the Analyst agent, which generates actionable heuristics to guide the other agents. The process culminates by presenting the human Manager with a curated final set of promising design candidates, augmented with high-fidelity Computational Fluid Dynamics (CFD) simulations. This approach effectively leverages AI to handle high-volume analytical tasks, thereby enhancing the decision-making capability of the human expert in selecting the final, risk-assessed design.

Large language models (LLMs) exhibit strong performance on self-contained programming tasks. However, they still struggle with repository-level software engineering (SWE), which demands (1) deep codebase navigation with effective context management for accurate localization, and (2) systematic approaches for iterative, test-driven code modification to resolve issues. To address these challenges, we propose SWE-Adept, an LLM-based two-agent framework where a localization agent identifies issue-relevant code locations and a resolution agent implements the corresponding fixes. For issue localization, we introduce agent-directed depth-first search that selectively traverses code dependencies. This minimizes issue-irrelevant content in the agent's context window and improves localization accuracy. For issue resolution, we employ adaptive planning and structured problem solving. We equip the agent with specialized tools for progress tracking and Git-based version control. These tools interface with a shared working memory that stores code-state checkpoints indexed by execution steps, facilitating precise checkpoint retrieval. This design enables reliable agent-driven version-control operations for systematic issue resolution, including branching to explore alternative solutions and reverting failed edits. Experiments on SWE-Bench Lite and SWE-Bench Pro demonstrate that SWE-Adept consistently outperforms prior approaches in both issue localization and resolution, improving the end-to-end resolve rate by up to 4.7%.

Autonomous agents based on Large Language Models (LLMs) have evolved from reactive assistants to systems capable of planning, executing actions via tools, and iterating over environment observations. However, they remain vulnerable to structural limitations: lack of native state, context degradation over long horizons, and the gap between probabilistic generation and deterministic execution requirements. This paper presents the ESAA (Event Sourcing for Autonomous Agents) architecture, which separates the agent's cognitive intention from the project's state mutation, inspired by the Event Sourcing pattern. In ESAA, agents emit only structured intentions in validated JSON (agent.result or issue.report); a deterministic orchestrator validates, persists events in an append-only log (activity.jsonl), applies file-writing effects, and projects a verifiable materialized view (roadmap.json). The proposal incorporates boundary contracts (AGENT_CONTRACT.yaml), metaprompting profiles (PARCER), and replay verification with hashing (esaa verify), ensuring the immutability of completed tasks and forensic traceability. Two case studies validate the architecture: (i) a landing page project (9 tasks, 49 events, single-agent composition) and (ii) a clinical dashboard system (50 tasks, 86 events, 4 concurrent agents across 8 phases), both concluding with run.status=success and verify_status=ok. The multi-agent case study demonstrates real concurrent orchestration with heterogeneous LLMs (Claude Sonnet 4.6, Codex GPT-5, Antigravity/Gemini 3 Pro, and Claude Opus 4.6), providing empirical evidence of the architecture's scalability beyond single-agent scenarios.

Hand-drawn sketches are a natural and efficient medium for capturing and conveying ideas. Despite significant advancements in controllable natural image generation, translating freehand sketches into structured, machine-readable diagrams remains a labor-intensive and predominantly manual task. The primary challenge stems from the inherent ambiguity of sketches, which lack the structural constraints and semantic precision required for automated diagram generation. To address this challenge, we introduce SketchAgent, a multi-agent system designed to automate the transformation of hand-drawn sketches into structured diagrams. SketchAgent integrates sketch recognition, symbolic reasoning, and iterative validation to produce semantically coherent and structurally accurate diagrams, significantly reducing the need for manual effort. To evaluate the effectiveness of our approach, we propose the Sketch2Diagram Benchmark, a comprehensive dataset and evaluation framework encompassing eight diverse diagram categories, such as flowcharts, directed graphs, and model architectures. The dataset comprises over 6,000 high-quality examples with token-level annotations, standardized preprocessing, and rigorous quality control. By streamlining the diagram generation process, SketchAgent holds great promise for applications in design, education, and engineering, while offering a significant step toward bridging the gap between intuitive sketching and machine-readable diagram generation. The benchmark is released at https://huggingface.co/datasets/DiagramAgent/Sketch2Diagram-Benchmark.

Programming language processing (similar to natural language processing) is a hot research topic in the field of software engineering; it has also aroused growing interest in the artificial intelligence community. However, different from a natural language sentence, a program contains rich, explicit, and complicated structural information. Hence, traditional NLP models may be inappropriate for programs. In this paper, we propose a novel tree-based convolutional neural network (TBCNN) for programming language processing, in which a convolution kernel is designed over programs' abstract syntax trees to capture structural information. TBCNN is a generic architecture for programming language processing; our experiments show its effectiveness in two different program analysis tasks: classifying programs according to functionality, and detecting code snippets of certain patterns. TBCNN outperforms baseline methods, including several neural models for NLP.

We introduce Agent K v1.0, an end-to-end autonomous data science agent designed to automate, optimise, and generalise across diverse data science tasks. Fully automated, Agent K v1.0 manages the entire data science life cycle by learning from experience. It leverages a highly flexible structured reasoning framework to enable it to dynamically process memory in a nested structure, effectively learning from accumulated experience stored to handle complex reasoning tasks. It optimises long- and short-term memory by selectively storing and retrieving key information, guiding future decisions based on environmental rewards. This iterative approach allows it to refine decisions without fine-tuning or backpropagation, achieving continuous improvement through experiential learning. We evaluate our agent's apabilities using Kaggle competitions as a case study. Following a fully automated protocol, Agent K v1.0 systematically addresses complex and multimodal data science tasks, employing Bayesian optimisation for hyperparameter tuning and feature engineering. Our new evaluation framework rigorously assesses Agent K v1.0's end-to-end capabilities to generate and send submissions starting from a Kaggle competition URL. Results demonstrate that Agent K v1.0 achieves a 92.5\% success rate across tasks, spanning tabular, computer vision, NLP, and multimodal domains. When benchmarking against 5,856 human Kaggle competitors by calculating Elo-MMR scores for each, Agent K v1.0 ranks in the top 38\%, demonstrating an overall skill level comparable to Expert-level users. Notably, its Elo-MMR score falls between the first and third quartiles of scores achieved by human Grandmasters. Furthermore, our results indicate that Agent K v1.0 has reached a performance level equivalent to Kaggle Grandmaster, with a record of 6 gold, 3 silver, and 7 bronze medals, as defined by Kaggle's progression system.

Compressing a predefined deep neural network (DNN) into a compact sub-network with competitive performance is crucial in the efficient machine learning realm. This topic spans various techniques, from structured pruning to neural architecture search, encompassing both pruning and erasing operators perspectives. Despite advancements, existing methods suffers from complex, multi-stage processes that demand substantial engineering and domain knowledge, limiting their broader applications. We introduce the third-generation Only-Train-Once (OTOv3), which first automatically trains and compresses a general DNN through pruning and erasing operations, creating a compact and competitive sub-network without the need of fine-tuning. OTOv3 simplifies and automates the training and compression process, minimizes the engineering efforts required from users. It offers key technological advancements: (i) automatic search space construction for general DNNs based on dependency graph analysis; (ii) Dual Half-Space Projected Gradient (DHSPG) and its enhanced version with hierarchical search (H2SPG) to reliably solve (hierarchical) structured sparsity problems and ensure sub-network validity; and (iii) automated sub-network construction using solutions from DHSPG/H2SPG and dependency graphs. Our empirical results demonstrate the efficacy of OTOv3 across various benchmarks in structured pruning and neural architecture search. OTOv3 produces sub-networks that match or exceed the state-of-the-arts. The source code will be available at https://github.com/tianyic/only_train_once.