Daily Papers

Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model's ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model training. By leveraging this approach, we develop ChemLLM, the first large language model dedicated to chemistry, capable of performing various tasks across chemical disciplines with smooth dialogue interaction. ChemLLM beats GPT-3.5 on all three principal tasks in chemistry, i.e., name conversion, molecular caption, and reaction prediction, and surpasses GPT-4 on two of them. Remarkably, ChemLLM also shows exceptional adaptability to related mathematical and physical tasks despite being trained mainly on chemical-centric corpora. Furthermore, ChemLLM demonstrates proficiency in specialized NLP tasks within chemistry, such as literature translation and cheminformatic programming. ChemLLM opens up a new avenue for exploration within chemical studies, while our method of integrating structured chemical knowledge into dialogue systems sets a new frontier for developing LLMs across various scientific fields. Codes, Datasets, and Model weights are publicly accessible at hf.co/AI4Chem/ChemLLM-7B-Chat.

Artificial intelligence systems are increasingly deployed in biomedical research. However, current evaluation frameworks may inadequately assess their effectiveness as research collaborators. This rapid review examines benchmarking practices for AI systems in preclinical biomedical research. Three major databases and two preprint servers were searched from January 1, 2018 to October 31, 2025, identifying 14 benchmarks that assess AI capabilities in literature understanding, experimental design, and hypothesis generation. The results revealed that all current benchmarks assess isolated component capabilities, including data analysis quality, hypothesis validity, and experimental protocol design. However, authentic research collaboration requires integrated workflows spanning multiple sessions, with contextual memory, adaptive dialogue, and constraint propagation. This gap implies that systems excelling on component benchmarks may fail as practical research co-pilots. A process-oriented evaluation framework is proposed that addresses four critical dimensions absent from current benchmarks: dialogue quality, workflow orchestration, session continuity, and researcher experience. These dimensions are essential for evaluating AI systems as research co-pilots rather than as isolated task executors.

The dominant paradigm for building LLM based agents is the Agent Loop, an iterative cycle where a single language model decides what to do next by reading an ever growing context window. This paradigm has three structural weaknesses: implicit dependencies between steps, unbounded recovery loops, and mutable execution history that complicates debugging. We characterize the Agent Loop as a single ready unit scheduler: at any moment, at most one executable unit is active, and the choice of which unit to activate comes from opaque LLM inference rather than an inspectable policy. This perspective places Agent Loops and graph based execution engines on a single semantic continuum. We propose SGH, Structured Graph Harness, which lifts control flow from implicit context into an explicit static DAG. SGH makes three commitments: execution plans are immutable within a plan version, planning execution and recovery are separated into three layers, and recovery follows a strict escalation protocol. These choices trade some expressiveness for controllability, verifiability, and implementability. Our contributions are fourfold: a scheduler unified framework that applies classical scheduling theory to LLM agent execution and identifies challenges introduced by non deterministic LLM nodes; a trade off analysis of controllability, expressiveness, and implementability across 70 surveyed systems; a formal specification including a node state machine with termination and soundness guarantees; and an attributable experimental framework with a seven group design for future validation. This is a position paper and design proposal. We provide a theoretical framework, design analysis, and experimental protocol, not a production implementation or empirical results.

The Model Context Protocol (MCP) standardizes how AI agents discover and invoke external tools, with over 10,000 active servers and 97 million monthly SDK downloads as of early 2026. Yet MCP does not yet standardize how agents safely operate those tools at production scale. Three protocol-level primitives remain missing: identity propagation, adaptive tool budgeting, and structured error semantics. This paper identifies these gaps through field lessons from an enterprise deployment of an AI agent platform integrated with a major cloud provider's MCP servers (client name redacted). We propose three mechanisms to fill them: (1) the Context-Aware Broker Protocol (CABP), which extends JSON-RPC with identity-scoped request routing via a six-stage broker pipeline; (2) Adaptive Timeout Budget Allocation (ATBA), which frames sequential tool invocation as a budget allocation problem over heterogeneous latency distributions; and (3) the Structured Error Recovery Framework (SERF), which provides machine-readable failure semantics that enable deterministic agent self-correction. We organize production failure modes into five design dimensions (server contracts, user context, timeouts, errors, and observability), document concrete failure vignettes, and present a production readiness checklist. All three algorithms are formalized as testable hypotheses with reproducible experimental methodology. Field observations demonstrate that while MCP provides a solid protocol foundation, reliable agent tool integration requires infrastructure-level mechanisms that the specification does not yet address.

There is a multitude of novel generative models for open-domain conversational systems; however, there is no systematic evaluation of different systems. Systematic comparisons require consistency in experimental design, evaluation sets, conversational systems and their outputs, and statistical analysis. We lay out a protocol for the evaluation of conversational models using head-to-head pairwise comparison. We analyze ten recent models that claim state-of-the-art performance using a paired head-to-head performance (win-loss-tie) on five evaluation datasets. Our findings show that DialoGPT and Blender are superior systems using Bradley-Terry model and TrueSkill ranking methods. These findings demonstrate the feasibility of our protocol to evaluate conversational agents and evaluation sets. Finally, we make all code and evaluations publicly available for researchers to compare their model to other state-of-the-art dialog models.

Large language models (LLMs) are increasingly used as simulated participants in social science experiments, but their behavior is often unstable and highly sensitive to design choices. Prior evaluations frequently conflate base-model capabilities with experimental instantiation, obscuring whether outcomes reflect the model itself or the agent setup. We instead frame participant simulation as an agent-design problem over full experimental protocols, where an agent is defined by a base model and a specification (e.g., participant attributes) that encodes behavioral assumptions. We introduce HUMANSTUDY-BENCH, a benchmark and execution engine that orchestrates LLM-based agents to reconstruct published human-subject experiments via a Filter--Extract--Execute--Evaluate pipeline, replaying trial sequences and running the original analysis pipeline in a shared runtime that preserves the original statistical procedures end to end. To evaluate fidelity at the level of scientific inference, we propose new metrics to quantify how much human and agent behaviors agree. We instantiate 12 foundational studies as an initial suite in this dynamic benchmark, spanning individual cognition, strategic interaction, and social psychology, and covering more than 6,000 trials with human samples ranging from tens to over 2,100 participants.

Speech deepfake source verification systems aims to determine whether two synthetic speech utterances originate from the same source generator, often assuming that the resulting source embeddings are independent of speaker traits. However, this assumption remains unverified. In this paper, we first investigate the impact of speaker factors on source verification. We propose a speaker-disentangled metric learning (SDML) framework incorporating two novel loss functions. The first leverages Chebyshev polynomial to mitigate gradient instability during disentanglement optimization. The second projects source and speaker embeddings into hyperbolic space, leveraging Riemannian metric distances to reduce speaker information and learn more discriminative source features. Experimental results on MLAAD benchmark, evaluated under four newly proposed protocols designed for source-speaker disentanglement scenarios, demonstrate the effectiveness of SDML framework. The code, evaluation protocols and demo website are available at https://github.com/xxuan-acoustics/RiemannSD-Net.

Keypoint detection & descriptors are foundational tech-nologies for computer vision tasks like image matching, 3D reconstruction and visual odometry. Hand-engineered methods like Harris corners, SIFT, and HOG descriptors have been used for decades; more recently, there has been a trend to introduce learning in an attempt to improve keypoint detectors. On inspection however, the results are difficult to interpret; recent learning-based methods employ a vast diversity of experimental setups and design choices: empirical results are often reported using different backbones, protocols, datasets, types of supervisions or tasks. Since these differences are often coupled together, it raises a natural question on what makes a good learned keypoint detector. In this work, we revisit the design of existing keypoint detectors by deconstructing their methodologies and identifying the key components. We re-design each component from first-principle and propose Simple Learned Keypoints (SiLK) that is fully-differentiable, lightweight, and flexible. Despite its simplicity, SiLK advances new state-of-the-art on Detection Repeatability and Homography Estimation tasks on HPatches and 3D Point-Cloud Registration task on ScanNet, and achieves competitive performance to state-of-the-art on camera pose estimation in 2022 Image Matching Challenge and ScanNet.

Our interest is in the design of software systems involving a human-expert interacting -- using natural language -- with a large language model (LLM) on data analysis tasks. For complex problems, it is possible that LLMs can harness human expertise and creativity to find solutions that were otherwise elusive. On one level, this interaction takes place through multiple turns of prompts from the human and responses from the LLM. Here we investigate a more structured approach based on an abstract protocol described in [3] for interaction between agents. The protocol is motivated by a notion of "two-way intelligibility" and is modelled by a pair of communicating finite-state machines. We provide an implementation of the protocol, and provide empirical evidence of using the implementation to mediate interactions between an LLM and a human-agent in two areas of scientific interest (radiology and drug design). We conduct controlled experiments with a human proxy (a database), and uncontrolled experiments with human subjects. The results provide evidence in support of the protocol's capability of capturing one- and two-way intelligibility in human-LLM interaction; and for the utility of two-way intelligibility in the design of human-machine systems. Our code is available at https://github.com/karannb/interact.

We evaluate existing foundation models video understanding capabilities using a carefully designed experiment protocol consisting of three hallmark tasks (action recognition, temporal localization, and spatiotemporal localization), eight datasets well received by the community, and four adaptation methods tailoring a foundation model (FM) for a downstream task. Moreover, we propose a scalar VideoGLUE score (VGS) to measure an FMs efficacy and efficiency when adapting to general video understanding tasks. Our main findings are as follows. First, task-specialized models significantly outperform the six FMs studied in this work, in sharp contrast to what FMs have achieved in natural language and image understanding. Second,video-native FMs, whose pretraining data contains the video modality, are generally better than image-native FMs in classifying motion-rich videos, localizing actions in time, and understanding a video of more than one action. Third, the video-native FMs can perform well on video tasks under light adaptations to downstream tasks(e.g., freezing the FM backbones), while image-native FMs win in full end-to-end finetuning. The first two observations reveal the need and tremendous opportunities to conduct research on video-focused FMs, and the last confirms that both tasks and adaptation methods matter when it comes to the evaluation of FMs.

As large-scale multi-agent systems evolve, the communication protocol layer has become a critical yet under-evaluated factor shaping performance and reliability. Despite the existence of diverse protocols (A2A, ACP, ANP, Agora, etc.), selection is often intuition-driven and lacks standardized guidance. We introduce ProtocolBench, a benchmark that systematically compares agent protocols along four measurable axes: task success, end-to-end latency, message or byte overhead, and robustness under failures. On ProtocolBench, protocol choice significantly influences system behavior. In the Streaming Queue scenario, overall completion time varies by up to 36.5% across protocols, and mean end-to-end latency differs by 3.48 s. Under Fail-Storm Recovery, resilience also differs consistently across protocols. Beyond evaluation, we present ProtocolRouter, a learnable protocol router that selects per-scenario (or per-module) protocols from requirement and runtime signals. ProtocolRouter reduces Fail-Storm recovery time by up to 18.1% versus the best single-protocol baseline, and achieves scenario-specific gains such as higher success in GAIA. We also release ProtocolRouterBench to standardize protocol evaluation and improve reliability at scale.

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

This position paper argues that computer science conferences should require tamper-evident, nonrepudiable attestations of experimental results. We name the underlying problem experiment nonrepudiation: a compliant protocol must bind the numbers in a paper to an actual executed computation in a way the author cannot later alter or deny. The current system relies on self-reported checklists, optional code sharing, and author-controlled logging. None of these mechanisms answer the question a reviewer cannot check: did the code the paper describes produce the numbers the paper reports? We define the problem formally, state the security properties any compliant protocol must satisfy, and describe a threat model that includes attacks current approaches do not prevent. To show that the problem is solvable, we built K-Veritas, a reference implementation in Go that produces signed reports without accessing training data. K-Veritas is a testbed, not a finished answer. We call on conferences and the community to treat nonrepudiation as a first-class requirement and to help build an open, independent standard for it.

Understanding causality should be a core requirement of any attempt to build real impact through AI. Due to the inherent unobservability of counterfactuals, large randomised trials (RCTs) are the standard for causal inference. But large experiments are generically expensive, and randomisation carries its own costs, e.g. when suboptimal decisions are trialed. Recent work has proposed more sample-efficient alternatives to RCTs, but these are not adaptable to the downstream application for which the causal effect is sought. In this work, we develop a task-specific approach to experimental design and derive sampling strategies customised to particular downstream applications. Across a range of important tasks, real-world datasets, and sample sizes, our method outperforms other benchmarks, e.g. requiring an order-of-magnitude less data to match RCT performance on targeted marketing tasks.

Indirect experiments provide a valuable framework for estimating treatment effects in situations where conducting randomized control trials (RCTs) is impractical or unethical. Unlike RCTs, indirect experiments estimate treatment effects by leveraging (conditional) instrumental variables, enabling estimation through encouragement and recommendation rather than strict treatment assignment. However, the sample efficiency of such estimators depends not only on the inherent variability in outcomes but also on the varying compliance levels of users with the instrumental variables and the choice of estimator being used, especially when dealing with numerous instrumental variables. While adaptive experiment design has a rich literature for direct experiments, in this paper we take the initial steps towards enhancing sample efficiency for indirect experiments by adaptively designing a data collection policy over instrumental variables. Our main contribution is a practical computational procedure that utilizes influence functions to search for an optimal data collection policy, minimizing the mean-squared error of the desired (non-linear) estimator. Through experiments conducted in various domains inspired by real-world applications, we showcase how our method can significantly improve the sample efficiency of indirect experiments.

This paper aims to provide a proof of concept of the accuracy of simulations for advanced networking study. The particular target technology is the Differentiated Services (DiffServ) architecture. The method has been to apply experimental activities conducted in a real network to a simulation environment, to gather the same performance parameters and to compare results. A worthy re-engineering of the DiffServ module of the deployed software program has been carried out and significant contribution have been made to overcome the encountered limitations and to enrich its modeling capabilities. Final results give useful suggestions for a more critical approach to simulations targeted for advanced networking study.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

Quantum cryptography is arguably the fastest growing area in quantum information science. Novel theoretical protocols are designed on a regular basis, security proofs are constantly improving, and experiments are gradually moving from proof-of-principle lab demonstrations to in-field implementations and technological prototypes. In this review, we provide both a general introduction and a state of the art description of the recent advances in the field, both theoretically and experimentally. We start by reviewing protocols of quantum key distribution based on discrete variable systems. Next we consider aspects of device independence, satellite challenges, and high rate protocols based on continuous variable systems. We will then discuss the ultimate limits of point-to-point private communications and how quantum repeaters and networks may overcome these restrictions. Finally, we will discuss some aspects of quantum cryptography beyond standard quantum key distribution, including quantum data locking and quantum digital signatures.

Interference is ubiquitous when conducting causal experiments over networks. Except for certain network structures, causal inference on the network in the presence of interference is difficult due to the entanglement between the treatment assignments and the interference levels. In this article, we conduct causal inference under interference on an observed, sparse but connected network, and we propose a novel design of experiments based on an independent set. Compared to conventional designs, the independent-set design focuses on an independent subset of data and controls their interference exposures through the assignments to the rest (auxiliary set). We provide a lower bound on the size of the independent set from a greedy algorithm , and justify the theoretical performance of estimators under the proposed design. Our approach is capable of estimating both spillover effects and treatment effects. We justify its superiority over conventional methods and illustrate the empirical performance through simulations.

Completely randomized experiments, originally developed by Fisher and Neyman in the 1930s, are still widely used in practice, even in online experimentation. However, such designs are of limited value for answering standard questions in marketplaces, where multiple populations of agents interact strategically, leading to complex patterns of spillover effects. In this paper, we derive the finite-sample properties of tractable estimators for "Simple Multiple Randomization Designs" (SMRDs), a new class of experimental designs which account for complex spillover effects in randomized experiments. Our derivations are obtained under a natural and general form of cross-unit interference, which we call "local interference". We discuss the estimation of main effects, direct effects, and spillovers, and present associated central limit theorems.

Biological protocols are fundamental to reproducible and safe life science research. While LLMs excel on general tasks, their systematic evaluation on these highly specialized, accuracy-critical, and inherently procedural texts remains limited. In this work, we present BioProBench, the first large-scale, integrated multi-task benchmark for biological protocol understanding and reasoning. While limited benchmarks have touched upon specific aspects like protocol QA, BioProBench provides a comprehensive suite of five core tasks: Protocol Question Answering, Step Ordering, Error Correction, Protocol Generation, and Protocol Reasoning, enabling a holistic evaluation of LLMs on procedural biological texts. Built upon 27K original protocols, it yields nearly 556K high-quality structured instances. We evaluate 12 mainstream open/closed-source LLMs on BioProBench. Experimental results reveal that while top models preform well on surface understanding tasks, struggle significantly with deep reasoning and structured generation tasks like ordering and generation. Furthermore, model comparisons reveal diverse performance: certain open-source models approach closed-source levels on some tasks, yet bio-specific small models lag behind general LLMs, indicating limitations on complex procedural content. Overall, our findings underscore that procedural reasoning within biological protocols represents a significant challenge for current LLMs. BioProBench serves as a standardized framework to diagnose these specific limitations and guide the development of AI systems better equipped for safely automating complex scientific procedures. The code and data are available at: https://github.com/YuyangSunshine/bioprotocolbench and https://huggingface.co/datasets/GreatCaptainNemo/BioProBench.

Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application remains constrained by rigid protocol design, limited adaptability to dynamic lab conditions, inadequate error handling, and high operational complexity. Here we introduce BioMARS (Biological Multi-Agent Robotic System), an intelligent platform that integrates LLMs, VLMs, and modular robotics to autonomously design, plan, and execute biological experiments. BioMARS uses a hierarchical architecture: the Biologist Agent synthesizes protocols via retrieval-augmented generation; the Technician Agent translates them into executable robotic pseudo-code; and the Inspector Agent ensures procedural integrity through multimodal perception and anomaly detection. The system autonomously conducts cell passaging and culture tasks, matching or exceeding manual performance in viability, consistency, and morphological integrity. It also supports context-aware optimization, outperforming conventional strategies in differentiating retinal pigment epithelial cells. A web interface enables real-time human-AI collaboration, while a modular backend allows scalable integration with laboratory hardware. These results highlight the feasibility of generalizable, AI-driven laboratory automation and the transformative role of language-based reasoning in biological research.

Randomized controlled trials (RCTs) are the benchmark for causal inference, yet field implementation can deviate. We here present a remote audit - a design-based, preregistrable diagnostic that uses only pre-treatment satellite imagery to test whether assignment is independent of local conditions. The conditional randomization test of the remote audit evaluates whether treatment assignment is more predictable from pre-treatment satellite features than expected under the experiment's registered mechanism, providing a finite-sample valid, design-based diagnostic that requires no parametric assumptions. The procedure is finite-sample valid, honors blocks and clusters, and controls multiplicity across image models and resolutions via a max-statistic. We illustrate with two RCTs: Uganda's Youth Opportunities Program, where the audit corroborates randomization and flags selection and missing-data risks; and a school-based trial in Bangladesh, where assignment is highly predictable from pre-treatment features relative to the stated design, consistent with independent concerns about irregularities. Remote audits complement balance tests, lower early-stage costs, and enable rapid design checks when baseline surveys are expensive or infeasible.

We study experiment design for unique identification of the causal graph of a simple SCM, where the graph may contain cycles. The presence of cycles in the structure introduces major challenges for experiment design as, unlike acyclic graphs, learning the skeleton of causal graphs with cycles may not be possible from merely the observational distribution. Furthermore, intervening on a variable in such graphs does not necessarily lead to orienting all the edges incident to it. In this paper, we propose an experiment design approach that can learn both cyclic and acyclic graphs and hence, unifies the task of experiment design for both types of graphs. We provide a lower bound on the number of experiments required to guarantee the unique identification of the causal graph in the worst case, showing that the proposed approach is order-optimal in terms of the number of experiments up to an additive logarithmic term. Moreover, we extend our result to the setting where the size of each experiment is bounded by a constant. For this case, we show that our approach is optimal in terms of the size of the largest experiment required for uniquely identifying the causal graph in the worst case.

Recent advances in quantum information science enabled the development of quantum communication network prototypes and created an opportunity to study full-stack quantum network architectures. This work develops SeQUeNCe, a comprehensive, customizable quantum network simulator. Our simulator consists of five modules: Hardware models, Entanglement Management protocols, Resource Management, Network Management, and Application. This framework is suitable for simulation of quantum network prototypes that capture the breadth of current and future hardware technologies and protocols. We implement a comprehensive suite of network protocols and demonstrate the use of SeQUeNCe by simulating a photonic quantum network with nine routers equipped with quantum memories. The simulation capabilities are illustrated in three use cases. We show the dependence of quantum network throughput on several key hardware parameters and study the impact of classical control message latency. We also investigate quantum memory usage efficiency in routers and demonstrate that redistributing memory according to anticipated load increases network capacity by 69.1% and throughput by 6.8%. We design SeQUeNCe to enable comparisons of alternative quantum network technologies, experiment planning, and validation and to aid with new protocol design. We are releasing SeQUeNCe as an open source tool and aim to generate community interest in extending it.

We study the problem of designing mechanisms for information acquisition scenarios. This setting models strategic interactions between an uniformed receiver and a set of informed senders. In our model the senders receive information about the underlying state of nature and communicate their observation (either truthfully or not) to the receiver, which, based on this information, selects an action. Our goal is to design mechanisms maximizing the receiver's utility while incentivizing the senders to report truthfully their information. First, we provide an algorithm that efficiently computes an optimal incentive compatible (IC) mechanism. Then, we focus on the online problem in which the receiver sequentially interacts in an unknown game, with the objective of minimizing the cumulative regret w.r.t. the optimal IC mechanism, and the cumulative violation of the incentive compatibility constraints. We investigate two different online scenarios, i.e., the full and bandit feedback settings. For the full feedback problem, we propose an algorithm that guarantees mathcal O(sqrt T) regret and violation, while for the bandit feedback setting we present an algorithm that attains mathcal O(T^{alpha}) regret and mathcal O(T^{1-alpha/2}) violation for any alphain[1/2, 1]. Finally, we complement our results providing a tight lower bound.

Network protocols are programs with inputs and outputs that follow predefined communication patterns to synchronize and exchange information. There are many protocols and each serves a different purpose, e.g., routing, transport, secure communication, etc. The functional and performance requirements for a protocol can be expressed using a formal specification, such as, a set of logical predicates over its traces. A protocol could be prevented from achieving its requirements due to a bug in its design or implementation, a component failure (e.g., a crash), or an attack. This dissertation shows that formal methods can feasibly characterize the functionality and performance of network protocols under normal conditions as well as when subjected to attacks.

Observational studies can yield clinically actionable evidence at scale, but executing them on real-world databases is open-ended and requires coherent decisions across cohort construction, analysis, and reporting. Prior evaluations of LLM agents emphasize isolated steps or single answers, missing the integrity and internal structure of the resulting evidence bundle. To address this gap, we introduce RWE-bench, a benchmark grounded in MIMIC-IV and derived from peer-reviewed observational studies. Each task provides the corresponding study protocol as the reference standard, requiring agents to execute experiments in a real database and iteratively generate tree-structured evidence bundles. We evaluate six LLMs (three open-source, three closed-source) under three agent scaffolds using both question-level correctness and end-to-end task metrics. Across 162 tasks, task success is low: the best agent reaches 39.9%, and the best open-source model reaches 30.4%. Agent scaffolds also matter substantially, causing over 30% variation in performance metrics. Furthermore, we implement an automated cohort evaluation method to rapidly localize errors and identify agent failure modes. Overall, the results highlight persistent limitations in agents' ability to produce end-to-end evidence bundles, and efficient validation remains an important direction for future work. Code and data are available at https://github.com/somewordstoolate/RWE-bench.

Standard evaluation protocols reveal a counterintuitive phenomenon: on 7.7% of benchmark problems spanning five datasets, larger language models underperform smaller ones by 28.4 percentage points despite 10-100x more parameters. Through systematic evaluation of 31 models (0.5B-405B parameters) across 1,485 problems, we identify the mechanism as spontaneous scale-dependent verbosity that introduces errors through overelaboration. Causal intervention experiments demonstrate this reflects correctable prompt design rather than fundamental capability limitations. Constraining large models to produce brief responses improves accuracy by 26 percentage points and reduces performance gaps by up to two-thirds. Most critically, brevity constraints completely reverse performance hierarchies on mathematical reasoning and scientific knowledge benchmarks, with large models achieving 7.7-15.9 percentage point advantages over small models -- direct inversions of the original gaps. These reversals prove large models possess superior latent capabilities that universal prompting masks. We validate findings through three independent contamination tests and demonstrate inverse scaling operates continuously across the full parameter spectrum, with dataset-specific optimal scales ranging from 0.5B to 3.0B parameters. Our results establish that maximizing large model performance requires scale-aware prompt engineering rather than universal evaluation protocols, with immediate implications for deployment: prompt adaptation simultaneously improves accuracy and reduces computational costs.

Foundation models are moving from response generation into operational roles. They plan across steps, call tools, request human input, coordinate with other agents, and increasingly carry responsibility for work that affects customers, claims, code, contracts, and clinical decisions. Production deployments are no longer one human supervising one model. They are multi-human, multi-agent collaborations that cross teams, time zones, and trust boundaries. The technical surface for this collaboration remains weakly specified. When an agent drafts a response and a human edits it before it ships, the moment of human judgement is the most valuable signal in the system. In current practice it is recorded, if at all, in application code, chat threads, ticket comments, and tribal memory. Two protocol standards address adjacent concerns: MCP standardises agent access to tools and data, and A2A standardises agent-to-agent interoperability. Neither defines the shared workspace in which humans and agents perform accountable work together. This paper presents CHAP, the Collaborative Human-Agent Protocol. Under CHAP, the override that used to vanish into a chat thread becomes a structured event carrying a diff, a rationale, and a content hash. The handoff between shifts becomes a portable envelope rather than a pinned message. The human approval of an agent's draft becomes a non-repudiable signed decision that can be replayed years later. The protocol achieves this through a small Core (workspaces, participants, tasks, artefacts, and an append-only evidence log) together with composable profiles that add review, modes, routing, deliberation, handoff, identity, signatures, and transparency-backed audit as deployments require them. Specification, reference implementation, conformance suite, and worked examples are available at: https://github.com/BrightbeamAI/chap

Recent machine learning papers often report 1-2 percentage point improvements from a single run on a benchmark. These gains are highly sensitive to random seeds, data ordering, and implementation details, yet are rarely accompanied by uncertainty estimates or significance tests. It is therefore unclear when a reported +1-2% reflects a real algorithmic advance versus noise. We revisit this problem under realistic compute budgets, where only a few runs are affordable. We propose a simple, PC-friendly evaluation protocol based on paired multi-seed runs, bias-corrected and accelerated (BCa) bootstrap confidence intervals, and a sign-flip permutation test on per-seed deltas. The protocol is intentionally conservative and is meant as a guardrail against over-claiming. We instantiate it on CIFAR-10, CIFAR-10N, and AG News using synthetic no-improvement, small-gain, and medium-gain scenarios. Single runs and unpaired t-tests often suggest significant gains for 0.6-2.0 point improvements, especially on text. With only three seeds, our paired protocol never declares significance in these settings. We argue that such conservative evaluation is a safer default for small gains under tight budgets.

Generating entanglement between distant quantum systems is at the core of quantum networking. In recent years, numerous theoretical protocols for remote entanglement generation have been proposed, of which many have been experimentally realized. Here, we provide a modular theoretical framework to elucidate the general mechanisms of photon-mediated entanglement generation between single spins in atomic or solid-state systems. Our framework categorizes existing protocols at various levels of abstraction and allows for combining the elements of different schemes in new ways. These abstraction layers make it possible to readily compare protocols for different quantum hardware. To enable the practical evaluation of protocols tailored to specific experimental parameters, we have devised numerical simulations based on the framework with our codes available online.

Recently, Agentic AI has become an increasingly popular research field. However, we argue that current agent research practices lack standardization and scientific rigor, making it hard to conduct fair comparisons among methods. As a result, it is still unclear how different design choices in agent frameworks affect effectiveness, and measuring their progress remains challenging. In this work, we conduct a systematic empirical study on GAIA benchmark and BrowseComp to examine the impact of popular design choices in key agent components in a fair and rigorous manner. We find that the lack of a standard evaluation protocol makes previous works, even open-sourced ones, non-reproducible, with significant variance between random runs. Therefore, we introduce a more robust evaluation protocol to stabilize comparisons. Our study reveals which components and designs are crucial for effective agents, while others are redundant, despite seeming logical. Based on our findings, we build and open-source OAgents, a new foundation agent framework that achieves state-of-the-art performance among open-source projects. OAgents offers a modular design for various agent components, promoting future research in Agentic AI.

LLM agents increasingly act after consuming ranked external information streams such as social feeds, search results, retrieval contexts, and email queues, yet safety evaluations almost always test the model or the user prompt in isolation, never the upstream ranker that decides what the agent reads just before it acts. We introduce a controlled protocol that holds the model, persona, topic, and final decision prompt fixed and varies only the composition and ordering of the posts an agent encounters during a preceding ten-turn "scrolling" phase, isolating the causal effect of feed curation on a downstream decision. Across 2,785 decision rollouts on four modern open instruct LLMs from three independent labs, we identify three response regimes: adversarial capitulation, default saturation, and a default-direction asymmetry in which a one-sided feed tips a decision the model was genuinely uncertain about (in the clearest cases from 5% to 100%; Fisher p as low as 3 x 10^-10) but cannot dislodge one it already favors or holds firmly. The effect follows a dose-response curve, survives a generator swap that rules out a writing-style artifact, generalizes across several decision domains including security-relevant choices such as removing a deployment approval gate or relaxing access controls, and is partly mitigated by two simple feed-level defenses; a frontier model retains its default. We characterize the recommender as a practical, default-bounded control surface for LLM agents, and argue that agent evaluations must audit the feed layer rather than the final prompt alone.

A Mamba state-space model trained only for next-step prediction appears to recover Granger-causal structure through a simple readout S = |W_{out} W_{in}|, with early experiments suggesting the phenomenon generalized across architectures and benefited from interventional data at p < 10^{-5}. We package the protocol used to test that claim -- standardized synthetic generators (VAR/Lorenz/CauseMe-style), three intervention semantics (do(X=c), soft-noise, random-forcing), edge-provenance cards on three real datasets, and size-matched control arms -- as a reusable falsification benchmark, and walk the claim through it in five stages. The method-level claim does not survive: (i) a plain linear bottleneck does as well or better; (ii) tuned Lasso beats the bottleneck on synthetic CauseMe-style benchmarks, and on Lorenz-96 (the only real benchmark with unambiguous ground truth) classical PCMCI and Granger lead a tight cluster in which the bottleneck trails; (iii) the headline intervention advantage is roughly 60% a sample-size confound, and the residual disappears under standard do(X=c) interventions, surviving only under a non-standard random-forcing scheme; (iv) even that residual reproduces, with a larger effect, in classical bivariate Granger -- the effect is method-agnostic. What survives is a narrow characterization result; the benchmark is the lasting artifact, and each stage above is one of its control arms.

Diagnosing 802.11 packet captures requires expert protocol knowledge, is slow, inconsistent across engineers, and unscalable. LLM-based approaches sound plausible but fabricate protocol events absent from captures (especially truncated traces), produce uncalibrated confidence scores, and suffer evaluation bias when golden references are co-produced by the model under test. We introduce PROBE (Protocol Reasoning Over evidence-Based Ensembles), a multi-stage pipeline addressing all three failures. It integrates (i) deterministic PCAP-to-text normalization with frame-level verifiability, (ii) multi-run, multi-candidate ensembles with optional cross-model second opinion and progressive obfuscation, (iii) a verdict-aware evidence framework treating absence of failure evidence as contributing evidence, and (iv) a fully deterministic composite reliability score from evidence validity, run-to-run stability, and cross-model agreement without LLM self-assessment. On 87 enterprise Wi-Fi captures (104 capture-reviewer pairs), single-pass LLM analysis raises weighted evidence F1 from 0.871 (expert baseline) to 0.912 but misses critical frames in 35% of cases. Naive ensemble voting drops below baseline (0.842) as majority voting amplifies conservative verdicts: 50% of confirmed failures are misclassified as 'no issue' or 'insufficient evidence.' Adding evidence-grounded reconciliation achieves 0.957 F1, a 96% auto-accept rate, and a worst-case floor above 0.70. LLM self-reported confidence clusters at 0.95 regardless of difficulty (71% report exactly 0.95), confirming it is uninformative. We also introduce a model-agnostic evaluation framework using per-field assertion matching, eliminating circular bias from model-co-produced golden references.

Autonomous research systems increasingly make the scientific workflow executable: agents can propose ideas, run code, inspect results, and draft papers. But executable workflows do not by themselves produce research judgment. We analyze where current systems lose trial experience: weak evidence becomes prose, pilot signals become broad claims, memory remains textual, and recurring process failures do not change later behavior. We introduce Sibyl-AutoResearch, a self-evolving AutoResearch framework built around Scientific Trial-and-Error Harnesses. A harness lets agents run bounded trials, preserve positive and negative outcomes, and route lessons into later planning, validation, claim scope, scheduling, critique, writing, and harness repair. We formalize this through two auditable conversion units: trial-to-behavior conversion, which links trial signals to later research actions, and trial-to-harness-behavior conversion, which links recurring process failures to system updates. We implement the framework in SIBYL, a file-backed autonomous research system that exposes the state, roles, memory, gates, and artifact traces needed to inspect these conversion paths. A retrospective audit identifies eight high-confidence conversion events, with a median latency of one iteration and a maximum latency of three iterations. A recovered-failure registry further shows how five naturally occurring failure classes, including duplicate results, stale numbers, and unsupported statistics, were blocked, downgraded, or routed into later repair. These traces do not establish a comparative performance claim; they show that the proposed conversion units are recoverable from realistic autonomous-research workspaces. The SIBYL framework and system are available at https://github.com/Sibyl-Research-Team/AutoResearch-SibylSystem.

We present the Consilium Protocol, a Byzantine Fault Tolerance-derived architecture for structured multi-model AI deliberation that treats inter-model disagreement as epistemic signal rather than error. The protocol assigns engineered cognitive personas to language models -- separating what a model is from how it reasons -- and introduces an In-Sample/Out-of-Sample validation framework adapted from quantitative finance to distinguish training-data consensus from empirically grounded conclusions. Across 1,478 deliberation sessions spanning 32 topics in 10 domain categories, we demonstrate that (1) the cognitive persona, not the underlying model, determines epistemic behavior: free edge-inference models costing 0.0002 USD per batch produced comparable analytical output to frontier models costing 10.69 USD; (2) RLHF alignment training creates measurable, domain-specific epistemic blind spots -- contested policy topics exhibit 12.3 percentage points less adversarial challenge than settled science topics, and AI safety topics show asymmetric bias (Δ=11.6%) where models challenge claims that AI is dangerous far more vigorously than claims that AI risk is overstated; (3) the protocol exhibits no directional bias of its own (immigration Δ=2.3%, renewables Δ=1.2%); and (4) out-of-sample evidence retrieval validated 239 claims with 100% evidence retrieval and surfaced 167 blind-spot discoveries invisible to training-data deliberation. Run-to-run reproducibility across randomized modeltimespersona assignments averages pm2.2% standard deviation. Total cost for the complete battery including all overhead: 217 USD. We release the protocol specification under MIT license to enable independent verification.

Traditional scientific discovery relies on an iterative hypothesise-experiment-refine cycle that has driven progress for centuries, but its intuitive, ad-hoc implementation often wastes resources, yields inefficient designs, and misses critical insights. This tutorial presents Bayesian Optimisation (BO), a principled probability-driven framework that formalises and automates this core scientific cycle. BO uses surrogate models (e.g., Gaussian processes) to model empirical observations as evolving hypotheses, and acquisition functions to guide experiment selection, balancing exploitation of known knowledge and exploration of uncharted domains to eliminate guesswork and manual trial-and-error. We first frame scientific discovery as an optimisation problem, then unpack BO's core components, end-to-end workflows, and real-world efficacy via case studies in catalysis, materials science, organic synthesis, and molecule discovery. We also cover critical technical extensions for scientific applications, including batched experimentation, heteroscedasticity, contextual optimisation, and human-in-the-loop integration. Tailored for a broad audience, this tutorial bridges AI advances in BO with practical natural science applications, offering tiered content to empower cross-disciplinary researchers to design more efficient experiments and accelerate principled scientific discovery.

SCTP is a transport protocol offering features such as multi-homing, multi-streaming, and message-oriented delivery. Its two main implementations were subjected to conformance tests using the PacketDrill tool. Conformance testing is not exhaustive and a recent vulnerability (CVE-2021-3772) showed SCTP is not immune to attacks. Changes addressing the vulnerability were implemented, but the question remains whether other flaws might persist in the protocol design. We study the security of the SCTP design, taking a rigorous approach rooted in formal methods. We create a formal Promela model of SCTP, and define 10 properties capturing the essential protocol functionality based on its RFC specification and consultation with the lead RFC author. Then we show using the Spin model checker that our model satisfies these properties. We define 4 attacker models - Off-Path, where the attacker is an outsider that can spoof the port and IP of a peer; Evil-Server, where the attacker is a malicious peer; Replay, where an attacker can capture and replay, but not modify, packets; and On-Path, where the attacker controls the channel between peers. We modify an attack synthesis tool designed for transport protocols, Korg, to support our SCTP model and four attacker models. We synthesize 14 unique attacks using the attacker models - including the CVE vulnerability in the Off-Path attacker model, 4 attacks in the Evil-Server attacker model, an opportunistic ABORT attack in the Replay attacker model, and eight connection manipulation attacks in the On-Path attacker model. We show that the proposed patch eliminates the vulnerability and does not introduce new ones according to our model and protocol properties. Finally, we identify and analyze an ambiguity in the RFC, which we show can be interpreted insecurely. We propose an erratum and show that it eliminates the ambiguity.

Data teams at frontier AI companies routinely train small proxy models to make critical decisions about pretraining data recipes for full-scale training runs. However, the community has a limited understanding of whether and when conclusions drawn from small-scale experiments reliably transfer to full-scale model training. In this work, we uncover a subtle yet critical issue in the standard experimental protocol for data recipe assessment: the use of identical small-scale model training configurations across all data recipes in the name of "fair" comparison. We show that the experiment conclusions about data quality can flip with even minor adjustments to training hyperparameters, as the optimal training configuration is inherently data-dependent. Moreover, this fixed-configuration protocol diverges from full-scale model development pipelines, where hyperparameter optimization is a standard step. Consequently, we posit that the objective of data recipe assessment should be to identify the recipe that yields the best performance under data-specific tuning. To mitigate the high cost of hyperparameter tuning, we introduce a simple patch to the evaluation protocol: using reduced learning rates for proxy model training. We show that this approach yields relative performance that strongly correlates with that of fully tuned large-scale LLM pretraining runs. Theoretically, we prove that for random-feature models, this approach preserves the ordering of datasets according to their optimal achievable loss. Empirically, we validate this approach across 23 data recipes covering four critical dimensions of data curation, demonstrating dramatic improvements in the reliability of small-scale experiments.

Distributed protocols should be robust to both benign malfunction (e.g. packet loss or delay) and attacks (e.g. message replay) from internal or external adversaries. In this paper we take a formal approach to the automated synthesis of attackers, i.e. adversarial processes that can cause the protocol to malfunction. Specifically, given a formal threat model capturing the distributed protocol model and network topology, as well as the placement, goals, and interface (inputs and outputs) of potential attackers, we automatically synthesize an attacker. We formalize four attacker synthesis problems - across attackers that always succeed versus those that sometimes fail, and attackers that attack forever versus those that do not - and we propose algorithmic solutions to two of them. We report on a prototype implementation called KORG and its application to TCP as a case-study. Our experiments show that KORG can automatically generate well-known attacks for TCP within seconds or minutes.

This study addresses the challenge of estimating average treatment effects (ATEs) for advertising campaigns in online marketplaces where complete randomized experimentation is infeasible. We propose two key innovations: (1) a shrinkage estimator that optimally combines observational and experimental data without assuming smooth treatment effects across campaigns, and (2) a Bayesian adaptive experimental design framework that efficiently selects campaigns for randomized evaluation that minimizes cumulative risk. Our shrinkage estimator achieves lower risk compared to existing methods by balancing bias-variance tradeoffs, while our adaptive design significantly reduces the costs of campaign randomization. We establish theoretical guarantees including asymptotic normality and regret bounds. In an application to Amazon Ads data analyzing 2,583 campaigns, our approach achieves equivalent estimation precision while requiring only half of the randomized experiments needed by random sampling, the standard method widely used in practice today. The proposed method serves as a practical solution for marketplace platforms to efficiently measure advertising effectiveness while managing experimentation costs.

The rapid development of large language models (LLMs) has led to the widespread deployment of LLM agents across diverse industries, including customer service, content generation, data analysis, and even healthcare. However, as more LLM agents are deployed, a major issue has emerged: there is no standard way for these agents to communicate with external tools or data sources. This lack of standardized protocols makes it difficult for agents to work together or scale effectively, and it limits their ability to tackle complex, real-world tasks. A unified communication protocol for LLM agents could change this. It would allow agents and tools to interact more smoothly, encourage collaboration, and triggering the formation of collective intelligence. In this paper, we provide the first comprehensive analysis of existing agent protocols, proposing a systematic two-dimensional classification that differentiates context-oriented versus inter-agent protocols and general-purpose versus domain-specific protocols. Additionally, we conduct a comparative performance analysis of these protocols across key dimensions such as security, scalability, and latency. Finally, we explore the future landscape of agent protocols by identifying critical research directions and characteristics necessary for next-generation protocols. These characteristics include adaptability, privacy preservation, and group-based interaction, as well as trends toward layered architectures and collective intelligence infrastructures. We expect this work to serve as a practical reference for both researchers and engineers seeking to design, evaluate, or integrate robust communication infrastructures for intelligent agents.

The Model Context Protocol (MCP) has emerged as a de facto standard for integrating Large Language Models with external tools, yet no formal security analysis of the protocol specification exists. We present the first rigorous security analysis of MCP's architectural design, identifying three fundamental protocol-level vulnerabilities: (1) absence of capability attestation allowing servers to claim arbitrary permissions, (2) bidirectional sampling without origin authentication enabling server-side prompt injection, and (3) implicit trust propagation in multi-server configurations. We implement MCPBench, a novel framework bridging existing agent security benchmarks to MCP-compliant infrastructure, enabling direct measurement of protocol-specific attack surfaces. Through controlled experiments on 847 attack scenarios across five MCP server implementations, we demonstrate that MCP's architectural choices amplify attack success rates by 23--41\% compared to equivalent non-MCP integrations. We propose MCPSec, a backward-compatible protocol extension adding capability attestation and message authentication, reducing attack success rates from 52.8\% to 12.4\% with median latency overhead of 8.3ms per message. Our findings establish that MCP's security weaknesses are architectural rather than implementation-specific, requiring protocol-level remediation.

The Model Context Protocol (MCP) has emerged as a universal standard that enables AI agents to seamlessly connect with external tools, significantly enhancing their functionality. However, while MCP brings notable benefits, it also introduces significant vulnerabilities, such as Tool Poisoning Attacks (TPA), where hidden malicious instructions exploit the sycophancy of large language models (LLMs) to manipulate agent behavior. Despite these risks, current academic research on MCP security remains limited, with most studies focusing on narrow or qualitative analyses that fail to capture the diversity of real-world threats. To address this gap, we present the MCP Attack Library (MCPLIB), which categorizes and implements 31 distinct attack methods under four key classifications: direct tool injection, indirect tool injection, malicious user attacks, and LLM inherent attack. We further conduct a quantitative analysis of the efficacy of each attack. Our experiments reveal key insights into MCP vulnerabilities, including agents' blind reliance on tool descriptions, sensitivity to file-based attacks, chain attacks exploiting shared context, and difficulty distinguishing external data from executable commands. These insights, validated through attack experiments, underscore the urgency for robust defense strategies and informed MCP design. Our contributions include 1) constructing a comprehensive MCP attack taxonomy, 2) introducing a unified attack framework MCPLIB, and 3) conducting empirical vulnerability analysis to enhance MCP security mechanisms. This work provides a foundational framework, supporting the secure evolution of MCP ecosystems.

Agent communication protocols are becoming critical infrastructure for large language model (LLM) systems that must use tools, coordinate with other agents, and operate across heterogeneous environments. This work presents a human-inspired perspective on this emerging landscape by organizing agent communication into three layers: communication, syntactic, and semantic. Under this framework, we systematically analyze 18 representative protocols and compare how they support reliable transport, structured interaction, and meaning-level coordination. Our analysis shows a clear imbalance in current protocol design. Most protocols provide increasingly mature support for transport, streaming, schema definition, and lifecycle management, but offer limited protocol-level mechanisms for clarification, context alignment, and verification. As a result, semantic responsibilities are often pushed into prompts, wrappers, or application-specific orchestration logic, creating hidden interoperability and maintenance costs. To make this gap actionable, we further identify major forms of technical debt in today's protocol ecosystem and distill practical guidance for selecting protocols under different deployment settings. We conclude by outlining a research agenda for interoperable, secure, and semantically robust agent ecosystems that move beyond message passing toward shared understanding.

Large language model (LLM)-powered agents are increasingly used to plan and execute scientific workflows, yet most research cyberinfrastructure (CI) exposes heterogeneous APIs and implements security models that present barriers for use by agents. We report on our experience using the Model Context Protocol (MCP) as a unifying interface that makes research capabilities discoverable, invokable, and composable. Our approach is pragmatic: we implement thin MCP servers over mature services, including Globus Transfer, Compute, and Search; status APIs exposed by computing facilities; Octopus event fabric; and domain-specific tools such as Garden and Galaxy. We use case studies in computational chemistry, bioinformatics, quantum chemistry, and filesystem monitoring to illustrate how this MCP-oriented architecture can be used in practice. We distill lessons learned and outline open challenges in evaluation and trust for agent-led science.

AI coding agents are increasingly used for scientific work, but their end-to-end autonomous research capability remains difficult to verify. We present ResearchClawBench, a benchmark for evaluating autonomous scientific research across 40 tasks from 10 scientific domains. Each task is grounded in a real published paper, provides related literature and raw data, and hides the target paper during evaluation. Expert-curated multimodal rubrics decompose the target scientific artifacts into weighted criteria, enabling evaluation of target-paper-level re-discovery while leaving room for new discovery. We evaluate seven autonomous research (auto-research) agents under a unified protocol and seventeen native LLMs through the lightweight ResearchHarness. Current systems remain far from reliable re-discovery: the strongest autonomous agent, Claude Code, averages 21.5, and the strongest ResearchHarness LLM, Claude-Opus-4.7, averages 20.7, with an LLM frontier mean of only 26.5. Error analysis shows that failures concentrate in experimental protocol mismatch, evidence mismatch, and missing scientific core. ResearchClawBench provides a reproducible evaluation frontier for measuring progress toward autonomous scientific research.

Benchmarks are necessary for healthcare evaluation, but are not sufficient for predicting deployment performance. Our position is that the evaluation--deployment gap arises not because of poorly designed benchmarks, but from implicit assumptions about how users interact with models that cannot be surfaced from benchmarks alone. To make this precise, we propose a classification of assumptions into two categories: task, which can be tested from conversation data alone, and outcome, which requires outcome data and behavioral studies for testing. Critically, outcome assumptions depend on human behavior, something that even well-designed benchmarks cannot directly observe. To demonstrate the operationality of this framework, we retrospectively analyze a healthcare RCT as a case study and find that the gap naturally separates into task and outcome gaps of roughly equal size. To address this, we make two contributions: first, we propose BenchmarkCards, an artifact that documents assumptions, and second, we propose staged evaluation, a procedure that systematically tests assumptions and evaluates performance.

Understanding the world and explaining it with scientific theories is a central aspiration of artificial intelligence research. Proposing theories, designing experiments to test them, and then revising them based on data are fundamental to scientific discovery. Despite the significant promise of LLM-based scientific agents, no benchmarks systematically test LLM's ability to propose scientific models, collect experimental data, and revise them in light of new data. We introduce BoxingGym, a benchmark with 10 environments for systematically evaluating both experimental design (e.g. collecting data to test a scientific theory) and model discovery (e.g. proposing and revising scientific theories). To enable tractable and quantitative evaluation, we implement each environment as a generative probabilistic model with which a scientific agent can run interactive experiments. These probabilistic models are drawn from various real-world scientific domains ranging from psychology to ecology. To quantitatively evaluate a scientific agent's ability to collect informative experimental data, we compute the expected information gain (EIG), an information-theoretic quantity which measures how much an experiment reduces uncertainty about the parameters of a generative model. A good scientific theory is a concise and predictive explanation. Therefore, to quantitatively evaluate model discovery, we ask a scientific agent to explain their model and then assess whether this explanation enables another scientific agent to make reliable predictions about this environment. In addition to this explanation-based evaluation, we compute standard model evaluation metrics such as prediction errors. We find that current LLMs, such as GPT-4o, struggle with both experimental design and model discovery. We find that augmenting the LLM-based agent with an explicit statistical model does not reliably improve these results.

We consider in this paper the problem of optimal experiment design where a decision maker can choose which points to sample to obtain an estimate hatβ of the hidden parameter β^{star} of an underlying linear model. The key challenge of this work lies in the heteroscedasticity assumption that we make, meaning that each covariate has a different and unknown variance. The goal of the decision maker is then to figure out on the fly the optimal way to allocate the total budget of T samples between covariates, as sampling several times a specific one will reduce the variance of the estimated model around it (but at the cost of a possible higher variance elsewhere). By trying to minimize the ell^2-loss E [lVerthatβ-β^{star}rVert^2] the decision maker is actually minimizing the trace of the covariance matrix of the problem, which corresponds then to online A-optimal design. Combining techniques from bandit and convex optimization we propose a new active sampling algorithm and we compare it with existing ones. We provide theoretical guarantees of this algorithm in different settings, including a O(T^{-2}) regret bound in the case where the covariates form a basis of the feature space, generalizing and improving existing results. Numerical experiments validate our theoretical findings.

As large language models (LLMs) become more powerful and are deployed more autonomously, it will be increasingly important to prevent them from causing harmful outcomes. Researchers have investigated a variety of safety techniques for this purpose, e.g. using models to review the outputs of other models, or red-teaming techniques to surface subtle failure modes. However, researchers have not evaluated whether such techniques still ensure safety if the model is itself intentionally trying to subvert them. In this paper, we develop and evaluate pipelines of safety techniques ("protocols") that are robust to intentional subversion. We investigate a scenario in which we want to solve a sequence of programming problems, using access to a powerful but untrusted model (in our case, GPT-4), access to a less powerful trusted model (in our case, GPT-3.5), and limited access to high-quality trusted labor. We investigate protocols that aim to never submit solutions containing backdoors, which we operationalize here as logical errors that are not caught by test cases. We investigate a range of protocols and test each against strategies that the untrusted model could use to subvert them. One protocol is what we call trusted editing. This protocol first asks GPT-4 to write code, and then asks GPT-3.5 to rate the suspiciousness of that code. If the code is below some suspiciousness threshold, it is submitted. Otherwise, GPT-3.5 edits the solution to remove parts that seem suspicious and then submits the edited code. Another protocol is untrusted monitoring. This protocol asks GPT-4 to write code, and then asks another instance of GPT-4 whether the code is backdoored, using various techniques to prevent the GPT-4 instances from colluding. These protocols improve substantially on simple baselines.

The rapid development of the AI agent communication protocols, including the Model Context Protocol (MCP), Agent2Agent (A2A), Agora, and Agent Network Protocol (ANP), is reshaping how AI agents communicate with tools, services, and each other. While these protocols support scalable multi-agent interaction and cross-organizational interoperability, their security principles remain understudied, and standardized threat modeling is limited; no protocol-centric risk assessment framework has been established yet. This paper presents a systematic security analysis of four emerging AI agent communication protocols. First, we develop a structured threat modeling analysis that examines protocol architectures, trust assumptions, interaction patterns, and lifecycle behaviors to identify protocol-specific and cross-protocol risk surfaces. Second, we introduce a qualitative risk assessment framework that identifies twelve protocol-level risks and evaluates security posture across the creation, operation, and update phases through systematic assessment of likelihood, impact, and overall protocol risk, with implications for secure deployment and future standardization. Third, we provide a measurement-driven case study on MCP that formalizes the risk of missing mandatory validation/attestation for executable components as a falsifiable security claim by quantifying wrong-provider tool execution under multi-server composition across representative resolver policies. Collectively, our results highlight key design-induced risk surfaces and provide actionable guidance for secure deployment and future standardization of agent communication ecosystems.

We introduce a gradient-based approach for the problem of Bayesian optimal experimental design to learn causal models in a batch setting -- a critical component for causal discovery from finite data where interventions can be costly or risky. Existing methods rely on greedy approximations to construct a batch of experiments while using black-box methods to optimize over a single target-state pair to intervene with. In this work, we completely dispose of the black-box optimization techniques and greedy heuristics and instead propose a conceptually simple end-to-end gradient-based optimization procedure to acquire a set of optimal intervention target-state pairs. Such a procedure enables parameterization of the design space to efficiently optimize over a batch of multi-target-state interventions, a setting which has hitherto not been explored due to its complexity. We demonstrate that our proposed method outperforms baselines and existing acquisition strategies in both single-target and multi-target settings across a number of synthetic datasets.

The diffusion MRI Neurite Exchange Imaging model offers a promising framework for probing gray matter microstructure by estimating parameters such as compartment sizes, diffusivities, and inter-compartmental water exchange time. However, existing protocols require long scan times. This study proposes a reduced acquisition scheme for the Connectome 2.0 scanner that preserves model accuracy while substantially shortening scan duration. We developed a data-driven framework using explainable artificial intelligence with a guided recursive feature elimination strategy to identify an optimal 8-feature subset from a 15-feature protocol. The performance of this optimized protocol was validated in vivo and benchmarked against the full acquisition and alternative reduction strategies. Parameter accuracy, preservation of anatomical contrast, and test-retest reproducibility were assessed. The reduced protocol yielded parameter estimates and cortical maps comparable to the full protocol, with low estimation errors in synthetic data and minimal impact on test-retest variability. Compared to theory-driven and heuristic reduction schemes, the optimized protocol demonstrated superior robustness, reducing the deviation in water exchange time estimates by over two-fold. In conclusion, this hybrid optimization framework enables viable imaging of neurite exchange in 14 minutes without loss of parameter fidelity. This approach supports the broader application of exchange-sensitive diffusion magnetic resonance imaging in neuroscience and clinical research, and offers a generalizable method for designing efficient acquisition protocols in biophysical parameter mapping.

We study auto research as a closed empirical loop driven by external measurement. Each submitted trial carries a hypothesis, an executable code edit, an evaluator-owned outcome, and feedback that shapes the next proposal. The output is not a generated paper or a single model checkpoint, but an auditable trajectory of proposals, code diffs, experiments, scores, and failure labels. We instantiate this loop with specialist agents that partition recipe surfaces and share measured lineage across trials. The central empirical finding is that lineage feedback lets agents turn evaluator outcomes, including crashes, budget overruns, size failures, and accuracy-gate misses, into later program-level recipe edits rather than one-shot suggestions. Across 1,197 headline-run trials plus 600 Parameter Golf control trials after one-time setup and launch, humans did not choose proposals, edit recipes, override scores, or repair failed trials during the search. In the three headline runs, the same submitted-trial loop reduces Parameter Golf validation bpb by 0.81%, raises NanoChat-D12 CORE by 38.7%, and reduces CIFAR-10 Airbench96 wallclock by 4.59%, with each task measured by its own external evaluator and legality checks. The trace includes a strict architecture-domain audit of 157 headline-run submissions and program rewrites such as a NanoChat attention-kernel path change. Within this scope the loop autonomously writes code, submits experiments, absorbs feedback, applies and combines known techniques inside each environment, and improves public starting recipes.

Many benchmarks for automated causal inference evaluate a system's performance based on a single numerical output, such as an Average Treatment Effect (ATE). This approach conflates two distinct steps in causal analysis: identification-formulating a valid research design under stated assumptions-and estimation-implementing that design numerically on finite data. We introduce CausalReasoningBenchmark, a benchmark of 173 queries across 138 real-world datasets, curated from 85 peer-reviewed research papers and four widely-used causal-inference textbooks. For each query a system must produce (i) a structured identification specification that names the strategy, the treatment, outcome, and control variables, and all design-specific elements, and (ii) a point estimate with a standard error. By scoring these two components separately, our benchmark enables granular diagnosis: it distinguishes failures in causal reasoning from errors in numerical execution. Baseline results with a state-of-the-art LLM show that, while the model correctly identifies the high-level strategy in 84 % of cases, full identification-specification correctness drops to only 30 %, revealing that the bottleneck lies in the nuanced details of research design rather than in computation. CausalReasoningBenchmark is publicly available on Hugging Face and is designed to foster the development of more robust automated causal-inference systems.

Access to the right evidence does not guarantee that large language models (LLMs) will reason with it correctly. This gap between retrieval and reasoning is especially concerning in clinical settings, where outputs must align with structured protocols. We study this gap using Written Exposure Therapy (WET) guidelines as a testbed. In evaluating model responses to curated clinician-vetted questions, we find that errors persist even when authoritative passages are provided. To address this, we propose an evaluation framework that measures accuracy, consistency, and fidelity of reasoning. Our results highlight both the potential and the risks: retrieval-augmented generation (RAG) can constrain outputs, but safe deployment requires assessing reasoning as rigorously as retrieval.

Evaluations are critical for understanding the capabilities of large language models (LLMs). Fundamentally, evaluations are experiments; but the literature on evaluations has largely ignored the literature from other sciences on experiment analysis and planning. This article shows researchers with some training in statistics how to think about and analyze data from language model evaluations. Conceptualizing evaluation questions as having been drawn from an unseen super-population, we present formulas for analyzing evaluation data, measuring differences between two models, and planning an evaluation experiment. We make a number of specific recommendations for running language model evaluations and reporting experiment results in a way that minimizes statistical noise and maximizes informativeness.

We consider the task of evaluating policies of algorithmic resource allocation through randomized controlled trials (RCTs). Such policies are tasked with optimizing the utilization of limited intervention resources, with the goal of maximizing the benefits derived. Evaluation of such allocation policies through RCTs proves difficult, notwithstanding the scale of the trial, because the individuals' outcomes are inextricably interlinked through resource constraints controlling the policy decisions. Our key contribution is to present a new estimator leveraging our proposed novel concept, that involves retrospective reshuffling of participants across experimental arms at the end of an RCT. We identify conditions under which such reassignments are permissible and can be leveraged to construct counterfactual trials, whose outcomes can be accurately ascertained, for free. We prove theoretically that such an estimator is more accurate than common estimators based on sample means -- we show that it returns an unbiased estimate and simultaneously reduces variance. We demonstrate the value of our approach through empirical experiments on synthetic, semi-synthetic as well as real case study data and show improved estimation accuracy across the board.

We present DPBench, a benchmark for evaluating coordination in multi-agent systems built from large language models. Existing benchmarks measure task-level success under a fixed protocol; the structural conditions under which coordination succeeds or fails at all have not been characterised. DPBench adapts the Dining Philosophers problem into a controlled testbed where the action protocol, the communication structure, and the group size each vary independently. We evaluate six agents: GPT-5.2, Claude Opus 4.5, Grok 4.1, Gemini 2.5 Flash, Llama 4 Maverick, and a uniform-random baseline. Under simultaneous action at N=5 with the default prompt, deadlock ranges from 25.0% (95% Wilson CI [11.2, 46.9]) for GPT-5.2 to 90.0% [74.4, 96.5] for Gemini 2.5 Flash; sequential action is solved by four of the six. Holding the model fixed at Gemini 2.5 Flash, three protocol variables drive deadlock from 90% to within CI of zero: three rounds of pre-commitment communication (0.0% vs. single-round 86.7%), a prompt encoding a classical concurrency primitive (0.0% for resource-ordering and symmetry-breaking, against 100% for the minimal prompt), or doubling the group from N=5 to N=10 (90.0% to 10.0%). Single-round messaging and memory of past timesteps do not change the rate at the sample size we ran. Whether the same model coordinates or deadlocks is determined by the protocol, not by the model's capability.

As large language models (LLMs) become increasingly capable, it is prudent to assess whether safety measures remain effective even if LLMs intentionally try to bypass them. Previous work introduced control evaluations, an adversarial framework for testing deployment strategies of untrusted models (i.e., models which might be trying to bypass safety measures). While prior work treats a single failure as unacceptable, we perform control evaluations in a "distributed threat setting" -- a setting where no single action is catastrophic and no single action provides overwhelming evidence of misalignment. We approach this problem with a two-level deployment framework that uses an adaptive macro-protocol to choose between micro-protocols. Micro-protocols operate on a single task, using a less capable, but extensively tested (trusted) model to harness and monitor the untrusted model. Meanwhile, the macro-protocol maintains an adaptive credence on the untrusted model's alignment based on its past actions, using it to pick between safer and riskier micro-protocols. We evaluate our method in a code generation testbed where a red team attempts to generate subtly backdoored code with an LLM whose deployment is safeguarded by a blue team. We plot Pareto frontiers of safety (# of non-backdoored solutions) and usefulness (# of correct solutions). At a given level of usefulness, our adaptive deployment strategy reduces the number of backdoors by 80% compared to non-adaptive baselines.

Large language model agents now act on codebases, browsers, operating systems, calendars, files, and tool ecosystems, but the benchmarks used to evaluate them are fragmented: each emphasizes a different unit of measurement (final task success, tool-call validity, repeated-pass consistency, trajectory safety, or attack robustness). A line of 2024-2025 work has converged on the diagnosis that a single accuracy column is no longer the right unit of comparison for deployable agents. AgentAtlas extends this line of work with four components: (i) a six-state control-decision taxonomy (Act / Ask / Refuse / Stop / Confirm / Recover); (ii) a nine-category trajectory-failure taxonomy with two orthogonal hierarchical labels (primary_error_source, impact); (iii) a taxonomy-aware vs. taxonomy-blind methodology that measures how much of a model's apparent capability comes from the supervision in the prompt; and (iv) a benchmark-coverage audit mapping fifteen agent benchmarks against six behavioral axes. To demonstrate the methodology we run a small fixed eight-model set (1,342 generated items, four frontier closed and four open-weight) under both prompt modes. Removing the explicit label menu drops every model's trajectory accuracy by 14-40 pp to a tight 0.54-0.62 floor regardless of family, and no single model wins on all three of control accuracy, trajectory diagnosis, and tool-context utility retention. We treat the synthetic run as a measurement-protocol demonstration, not a benchmark release.

Large language model (LLM)-based systems are increasingly deployed to conduct scientific research autonomously, yet whether their reasoning adheres to the epistemic norms that make scientific inquiry self-correcting is poorly understood. Here, we evaluate LLM-based scientific agents across eight domains, spanning workflow execution to hypothesis-driven inquiry, through more than 25,000 agent runs and two complementary lenses: (i) a systematic performance analysis that decomposes the contributions of the base model and the agent scaffold, and (ii) a behavioral analysis of the epistemological structure of agent reasoning. We observe that the base model is the primary determinant of both performance and behavior, accounting for 41.4% of explained variance versus 1.5% for the scaffold. Across all configurations, evidence is ignored in 68% of traces, refutation-driven belief revision occurs in 26%, and convergent multi-test evidence is rare. The same reasoning pattern appears whether the agent executes a computational workflow or conducts hypothesis-driven inquiry. They persist even when agents receive near-complete successful reasoning trajectories as context, and the resulting unreliability compounds across repeated trials in epistemically demanding domains. Thus, current LLM-based agents execute scientific workflows but do not exhibit the epistemic patterns that characterize scientific reasoning. Outcome-based evaluation cannot detect these failures, and scaffold engineering alone cannot repair them. Until reasoning itself becomes a training target, the scientific knowledge produced by such agents cannot be justified by the process that generated it.

The field of Deep Learning (DL) has undergone explosive growth during the last decade, with a substantial impact on Natural Language Processing (NLP) as well. Yet, compared to more established disciplines, a lack of common experimental standards remains an open challenge to the field at large. Starting from fundamental scientific principles, we distill ongoing discussions on experimental standards in NLP into a single, widely-applicable methodology. Following these best practices is crucial to strengthen experimental evidence, improve reproducibility and support scientific progress. These standards are further collected in a public repository to help them transparently adapt to future needs.

With an increasing number of replication studies performed in psychological science, the question of how to evaluate the outcome of a replication attempt deserves careful consideration. Bayesian approaches allow to incorporate uncertainty and prior information into the analysis of the replication attempt by their design. The Replication Bayes Factor, introduced by Verhagen & Wagenmakers (2014), provides quantitative, relative evidence in favor or against a successful replication. In previous work by Verhagen & Wagenmakers (2014) it was limited to the case of t-tests. In this paper, the Replication Bayes Factor is extended to F-tests in multi-group, fixed-effect ANOVA designs. Simulations and examples are presented to facilitate the understanding and to demonstrate the usefulness of this approach. Finally, the Replication Bayes Factor is compared to other Bayesian and frequentist approaches and discussed in the context of replication attempts. R code to calculate Replication Bayes factors and to reproduce the examples in the paper is available at https://osf.io/jv39h/.

The automatic evaluation of instruction following typically involves using large language models (LLMs) to assess response quality. However, there is a lack of comprehensive evaluation of these LLM-based evaluators across two dimensions: the base LLMs and the evaluation protocols. Therefore, we present a thorough meta-evaluation of instruction following, including 25 base LLMs and 15 recently proposed evaluation protocols, on 4 human-annotated datasets, assessing the evaluation accuracy of the LLM-evaluators. Our evaluation allows us to identify the best-performing base LLMs and evaluation protocols with a high degree of robustness. Moreover, our large-scale evaluation reveals: (1) Base LLM performance ranking remains largely consistent across evaluation protocols, with less capable LLMs showing greater improvement from protocol enhancements; (2) Robust evaluation of evaluation protocols requires many base LLMs with varying capability levels, as protocol effectiveness can depend on the base LLM used; (3) Evaluation results on different datasets are not always consistent, so a rigorous evaluation requires multiple datasets with distinctive features. We release our meta-evaluation suite ReIFE, which provides the codebase and evaluation result collection for more than 500 LLM-evaluator configurations, to support future research in instruction-following evaluation.

Limited large-scale evaluations exist for facilitation strategies of online discussions due to significant costs associated with human involvement. An effective solution is synthetic discussion simulations using Large Language Models (LLMs) to create initial pilot experiments. We propose a simple, generalizable, LLM-driven methodology to prototype the development of LLM facilitators, and produce high-quality synthetic data without human involvement. We use our methodology to test whether current facilitation strategies can improve the performance of LLM facilitators. We find that, while LLM facilitators significantly improve synthetic discussions, there is no evidence that the application of more elaborate facilitation strategies proposed in modern Social Science research lead to further improvements in discussion quality, compared to more basic approaches. Additionally, we find that small LLMs (such as Mistral Nemo 12B) can perform comparably to larger models (such as LLaMa 70B), and that special instructions must be used for instruction-tuned models to induce toxicity in synthetic discussions. We confirm that each component of our methodology contributes substantially to high quality data via an ablation study. We release an open-source framework, "SynDisco" (pip install syndisco), which implements our methodology. We also release the "Virtual Moderation Dataset" (https://paperswithcode.com/dataset/vmd), a large, publicly available dataset containing LLM-generated and LLM-annotated discussions using multiple open-source LLMs.

Hypothesis ranking is a crucial component of automated scientific discovery, particularly in natural sciences where wet-lab experiments are costly and throughput-limited. Existing approaches focus on pre-experiment ranking, relying solely on large language model's internal reasoning without incorporating empirical outcomes from experiments. We introduce the task of experiment-guided ranking, which aims to prioritize candidate hypotheses based on the results of previously tested ones. However, developing such strategies is challenging due to the impracticality of repeatedly conducting real experiments in natural science domains. To address this, we propose a simulator grounded in three domain-informed assumptions, modeling hypothesis performance as a function of similarity to a known ground truth hypothesis, perturbed by noise. We curate a dataset of 124 chemistry hypotheses with experimentally reported outcomes to validate the simulator. Building on this simulator, we develop a pseudo experiment-guided ranking method that clusters hypotheses by shared functional characteristics and prioritizes candidates based on insights derived from simulated experimental feedback. Experiments show that our method outperforms pre-experiment baselines and strong ablations.

Randomized controlled trials often do not represent the populations where decisions are made, and covariate shift across studies can invalidate standard IPD meta-analysis and transport estimators. We propose a placebo-anchored transport framework that treats source-trial outcomes as abundant proxy signals and target-trial placebo outcomes as scarce, high-fidelity gold labels to calibrate baseline risk. A low-complexity (sparse) correction anchors proxy outcome models to the target population, and the anchored models are embedded in a cross-fitted doubly robust learner, yielding a Neyman-orthogonal, target-site doubly robust estimator for patient-level heterogeneous treatment effects when target treated outcomes are available. We distinguish two regimes: in connected targets (with a treated arm), the method yields target-identified effect estimates; in disconnected targets (placebo-only), it reduces to a principled screen--then--transport procedure under explicit working-model transport assumptions. Experiments on synthetic data and a semi-synthetic IHDP benchmark evaluate pointwise CATE accuracy, ATE error, ranking quality for targeting, decision-theoretic policy regret, and calibration. Across connected settings, the proposed method is best or near-best and improves substantially over proxy-only, target-only, and transport baselines at small target sample sizes; in disconnected settings, it retains strong ranking performance for targeting while pointwise accuracy depends on the strength of the working transport condition.

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells in quantitative, predictive, and mechanistic ways. We discuss the role of mathematical models in the context of cell-fate decision making systems across the tree of life. Complex multi-cellular organisms have been a particular focus, but single celled organisms also have to sense and respond to their environment. We center our discussion around the idea of design principles which we can learn from observations and modeling, and exploit in order to (re)-design or guide cellular behavior.

Much has been said about observability in system theory and control; however, it has been recently that observability in complex networks has seriously attracted the attention of researchers. This paper examines the state-of-the-art and discusses some issues raised due to "complexity" and "stochasticity". These unresolved issues call for a new practical methodology. For stochastic systems, a degree of observability may be defined and the observability problem is not a binary (i.e., yes-no) question anymore. Here, we propose to employ a goal-seeking system to play a supervisory role in the network. Hence, improving the degree of observability would be a valid objective for the supervisory system. Towards this goal, the supervisor dynamically optimizes the observation process by reconfiguring the sensory parts in the network. A cognitive dynamic system is suggested as a proper choice for the supervisory system. In this framework, the network itself is viewed as the environment with which the cognitive dynamic system interacts. Computer experiments confirm the potential of the proposed approach for addressing some of the issues raised in networks due to complexity and stochasticity.

The ability of Large Language Models (LLMs) to mimic human behavior triggered a plethora of computational social science research, assuming that empirical studies of humans can be conducted with AI agents instead. Since there have been conflicting research findings on whether and when this hypothesis holds, there is a need to better understand the differences in their experimental designs. We focus on replicating the behavior of social network users with the use of LLMs for the analysis of communication on social networks. First, we provide a formal framework for the simulation of social networks, before focusing on the sub-task of imitating user communication. We empirically test different approaches to imitate user behavior on X in English and German. Our findings suggest that social simulations should be validated by their empirical realism measured in the setting in which the simulation components were fitted. With this paper, we argue for more rigor when applying generative-agent-based modeling for social simulation.

Large language models (LLMs) are increasingly used to take actions in the real world and support human decision-making, yet most agents rely on parametric knowledge, fixed post-training data, retrieval, or search. This paradigm breaks down in novel domains and for sophisticated queries that cannot be answered from prior knowledge alone. Knowing the laws of physics, for instance, does not by itself enable LLMs to answer queries or complete long-horizon tasks in a complex physical system. To address this, we introduce Hierarchical Experimentalist Agents (HExA), an in-context self-improvement framework to learn from active experimentation. HExA iteratively designs and refines query-relevant experiments, learns a reusable library of composable skills from experience, and integrates experimental evidence to answer queries or take actions. HExA is training-free, compatible with any black-box model, and does not require external supervision, oracles, or offline data. To evaluate active experimentation, we introduce Interphyre, a tool-calling benchmark built on the PHYRE 2D procedural physics environment, where agents propose interventions and test hypotheses through simulation APIs. Experiments show that current LLM agents struggle in these settings, especially on the hardest levels of Interphyre. Claude Sonnet 4.6 achieves only 2% success, while HExA improves the same model to up to 77% success. HExA also improves open-weight models and outperforms agentic baselines such as ReAct and Reflexion. Moreover, using only skills learned from easier levels and transferred without active experimentation, HExA achieves 44% success, demonstrating the reusability and generalization of its learned skills. Overall, HExA shows that learning through active experimentation can help agents discover useful knowledge, acquire reusable skills, and make efficient progress on novel long-horizon tasks.

In social sciences, researchers often face challenges when conducting large-scale experiments, particularly due to the simulations' complexity and the lack of technical expertise required to develop such frameworks. Agent-Based Modeling (ABM) is a computational approach that simulates agents' actions and interactions to evaluate how their behaviors influence the outcomes. However, the traditional implementation of ABM can be demanding and complex. Generative Agent-Based Modeling (GABM) offers a solution by enabling scholars to create simulations where AI-driven agents can generate complex behaviors based on underlying rules and interactions. This paper introduces a framework for designing reliable experiments using GABM, making sophisticated simulation techniques more accessible to researchers across various fields. We provide a step-by-step guide for selecting appropriate tools, designing the model, establishing experimentation protocols, and validating results.

Classical Internet evolved exceptionally during the last five decades, from a network comprising a few static nodes in the early days to a leviathan interconnecting billions of devices. This has been possible by the separation of concern principle, for which the network functionalities are organized as a stack of layers, each providing some communication functionalities through specific network protocols. In this survey, we aim at highlighting the impossibility of adapting the classical Internet protocol stack to the Quantum Internet, due to the marvels of quantum mechanics. Indeed, the design of the Quantum Internet requires a major paradigm shift of the whole protocol stack for harnessing the peculiarities of quantum entanglement and quantum information. In this context, we first overview the relevant literature about Quantum Internet protocol stack. Then, stemming from this, we sheds the light on the open problems and required efforts toward the design of an effective and complete Quantum Internet protocol stack. To the best of authors' knowledge, a survey of this type is the first of its own. What emerges from this analysis is that the Quantum Internet, though still in its infancy, is a disruptive technology whose design requires an inter-disciplinary effort at the border between quantum physics, computer and telecommunications engineering.

Null Hypothesis Significance Testing is the de facto tool for assessing effectiveness differences between Information Retrieval systems. Researchers use statistical tests to check whether those differences will generalise to online settings or are just due to the samples observed in the laboratory. Much work has been devoted to studying which test is the most reliable when comparing a pair of systems, but most of the IR real-world experiments involve more than two. In the multiple comparisons scenario, testing several systems simultaneously may inflate the errors committed by the tests. In this paper, we use a new approach to assess the reliability of multiple comparison procedures using simulated and real TREC data. Experiments show that Wilcoxon plus the Benjamini-Hochberg correction yields Type I error rates according to the significance level for typical sample sizes while being the best test in terms of statistical power.

Randomized controlled trials (RCTs) are considered the gold standard for estimating the average treatment effect (ATE) of interventions. One use of RCTs is to study the causes of global poverty -- a subject explicitly cited in the 2019 Nobel Memorial Prize awarded to Duflo, Banerjee, and Kremer "for their experimental approach to alleviating global poverty." Because the ATE is a population summary, anti-poverty experiments often seek to unpack the effect variation around the ATE by conditioning (CATE) on tabular variables such as age and ethnicity that were measured during the RCT data collection. Although such variables are key to unpacking CATE, using only such variables may fail to capture historical, geographical, or neighborhood-specific contributors to effect variation, as tabular RCT data are often only observed near the time of the experiment. In global poverty research, when the location of the experiment units is approximately known, satellite imagery can provide a window into such factors important for understanding heterogeneity. However, there is no method that specifically enables applied researchers to analyze CATE from images. In this paper, using a deep probabilistic modeling framework, we develop such a method that estimates latent clusters of images by identifying images with similar treatment effects distributions. Our interpretable image CATE model also includes a sensitivity factor that quantifies the importance of image segments contributing to the effect cluster prediction. We compare the proposed methods against alternatives in simulation; also, we show how the model works in an actual RCT, estimating the effects of an anti-poverty intervention in northern Uganda and obtaining a posterior predictive distribution over effects for the rest of the country where no experimental data was collected. We make all models available in open-source software.

A/B tests are typically analyzed via frequentist p-values and confidence intervals; but these inferences are wholly unreliable if users endogenously choose samples sizes by *continuously monitoring* their tests. We define *always valid* p-values and confidence intervals that let users try to take advantage of data as fast as it becomes available, providing valid statistical inference whenever they make their decision. Always valid inference can be interpreted as a natural interface for a sequential hypothesis test, which empowers users to implement a modified test tailored to them. In particular, we show in an appropriate sense that the measures we develop tradeoff sample size and power efficiently, despite a lack of prior knowledge of the user's relative preference between these two goals. We also use always valid p-values to obtain multiple hypothesis testing control in the sequential context. Our methodology has been implemented in a large scale commercial A/B testing platform to analyze hundreds of thousands of experiments to date.

Laboratory workflows in pharmaceutical and biomedical research encode substantial tacit knowledge -- expert judgment about failure conditions, decision branching logic, and contextual dependencies -- that remains inaccessible to protocol documents, sensor streams, and existing biomedical ontologies. We present a repeatable structured expert elicitation methodology and federated Semantic Knowledge Graph (SKG) architecture for capturing and querying this knowledge, demonstrated through deployment at the Biochemical and Cellular Pharmacology Department of Genentech. Knowledge is elicited via the Protocol Intelligence Co-pilot, a purpose-built AI interview agent that applies structured elicitation lenses to surface tacit procedural knowledge with expert-assigned confidence scores, producing graph representations across three tiers: program-level decision milestones, assay protocol knowledge, and physical execution infrastructure. Separately constructed subgraphs, exemplified by immunoassay (ELISA), quantitative mass spectrometry (LC-MS/PRM), and laboratory automation, are aligned through a shared upper ontology and queried as a single federated graph. Evaluation demonstrates seven query types structurally unavailable from any individual data source, including a cross-subgraph traversal that identifies automation-masked silent failures -- conditions where execution logs report success while scientific validity is compromised. Critically, the MASKED_BY graph relationship encodes a class of laboratory risk invisible to current informatics platforms -- the structural gap that prevents existing systems from reasoning about scientific validity. This architecture provides the semantic world model that AI laboratory agents currently lack: a queryable representation of where workflows fail silently, where human judgment is irreplaceable, and which execution assets mask rather than detect failure.

As Model Context Protocol (MCP) introduces an easy-to-use ecosystem for users and developers, it also brings underexplored safety risks. Its decentralized architecture, which separates clients and servers, poses unique challenges for systematic safety analysis. This paper proposes a novel framework to enhance MCP safety. Guided by the MAESTRO framework, we first analyze the missing safety mechanisms in MCP, and based on this analysis, we propose the Model Contextual Integrity Protocol (MCIP), a refined version of MCP that addresses these gaps. Next, we develop a fine-grained taxonomy that captures a diverse range of unsafe behaviors observed in MCP scenarios. Building on this taxonomy, we develop benchmark and training data that support the evaluation and improvement of LLMs' capabilities in identifying safety risks within MCP interactions. Leveraging the proposed benchmark and training data, we conduct extensive experiments on state-of-the-art LLMs. The results highlight LLMs' vulnerabilities in MCP interactions and demonstrate that our approach substantially improves their safety performance.

Survey data are self-reported data collected directly from respondents by a questionnaire or an interview and are commonly used in epidemiology. Such data are traditionally collected via a single mode (e.g. face-to-face interview alone), but use of mixed-mode designs (e.g. offering face-to-face interview or online survey) has become more common. This introduces two key challenges. First, individuals may respond differently to the same question depending on the mode; these differences due to measurement are known as 'mode effects'. Second, different individuals may participate via different modes; these differences in sample composition between modes are known as 'mode selection'. Where recognised, mode effects are often handled by straightforward approaches such as conditioning on survey mode. However, while reducing mode effects, this and other equivalent approaches may introduce collider bias in the presence of mode selection. The existence of mode effects and the consequences of na\"ive conditioning may be underappreciated in epidemiology. This paper offers a simple introduction to these challenges using directed acyclic graphs by exploring a range of possible data structures. We discuss the potential implications of using conditioning- or imputation-based approaches and outline the advantages of quantitative bias analyses for dealing with mode effects.

A Recurrent Neural Network (RNN) was used to perform video frame prediction of microbial growth for a population of two mutants of Pseudomonas aeruginosa. The RNN was trained on videos of 20 frames that were acquired using fluorescence microscopy and microfluidics. The network predicted the last 10 frames of each video, and the accuracy's of the predictions was assessed by comparing raw images, population curves, and the number and size of individual colonies. Overall, we found the predictions to be accurate using this approach. The implications this result has on designing autonomous experiments in microbiology, and the steps that can be taken to make the predictions even more accurate, are discussed.

In the development of science, accurate and reproducible documentation of the experimental process is crucial. Automatic recognition of the actions in experiments from videos would help experimenters by complementing the recording of experiments. Towards this goal, we propose FineBio, a new fine-grained video dataset of people performing biological experiments. The dataset consists of multi-view videos of 32 participants performing mock biological experiments with a total duration of 14.5 hours. One experiment forms a hierarchical structure, where a protocol consists of several steps, each further decomposed into a set of atomic operations. The uniqueness of biological experiments is that while they require strict adherence to steps described in each protocol, there is freedom in the order of atomic operations. We provide hierarchical annotation on protocols, steps, atomic operations, object locations, and their manipulation states, providing new challenges for structured activity understanding and hand-object interaction recognition. To find out challenges on activity understanding in biological experiments, we introduce baseline models and results on four different tasks, including (i) step segmentation, (ii) atomic operation detection (iii) object detection, and (iv) manipulated/affected object detection. Dataset and code are available from https://github.com/aistairc/FineBio.

As multi-agent AI systems grow in complexity, the protocols connecting them constrain their capabilities. Current protocols such as A2A and MCP do not expose model-level properties as first-class primitives, ignoring properties fundamental to effective delegation: model identity, reasoning profile, quality calibration, and cost characteristics. We present the LLM Delegate Protocol (LDP), an AI-native communication protocol introducing five mechanisms: (1) rich delegate identity cards with quality hints and reasoning profiles; (2) progressive payload modes with negotiation and fallback; (3) governed sessions with persistent context; (4) structured provenance tracking confidence and verification status; (5) trust domains enforcing security boundaries at the protocol level. We implement LDP as a plugin for the JamJet agent runtime and evaluate against A2A and random baselines using local Ollama models and LLM-as-judge evaluation. Identity-aware routing achieves ~12x lower latency on easy tasks through delegate specialization, though it does not improve aggregate quality in our small delegate pool; semantic frame payloads reduce token count by 37% (p=0.031) with no observed quality loss; governed sessions eliminate 39% token overhead at 10 rounds; and noisy provenance degrades synthesis quality below the no-provenance baseline, arguing that confidence metadata is harmful without verification. Simulated analyses show architectural advantages in attack detection (96% vs. 6%) and failure recovery (100% vs. 35% completion). This paper contributes a protocol design, reference implementation, and initial evidence that AI-native protocol primitives enable more efficient and governable delegation.

Progress in computer-aided synthesis planning (CASP) is obscured by the lack of standardized evaluation infrastructure and the reliance on metrics that prioritize topological completion over chemical validity. We introduce RetroCast, a unified evaluation suite that standardizes heterogeneous model outputs into a common schema to enable statistically rigorous, apples-to-apples comparison. The framework includes a reproducible benchmarking pipeline with stratified sampling and bootstrapped confidence intervals, accompanied by SynthArena, an interactive platform for qualitative route inspection. We utilize this infrastructure to evaluate leading search-based and sequence-based algorithms on a new suite of standardized benchmarks. Our analysis reveals a divergence between "solvability" (stock-termination rate) and route quality; high solvability scores often mask chemical invalidity or fail to correlate with the reproduction of experimental ground truths. Furthermore, we identify a "complexity cliff" in which search-based methods, despite high solvability rates, exhibit a sharp performance decay in reconstructing long-range synthetic plans compared to sequence-based approaches. We release the full framework, benchmark definitions, and a standardized database of model predictions to support transparent and reproducible development in the field.

When artificial agents are jointly trained to perform collaborative tasks using a communication channel, they develop opaque goal-oriented communication protocols. Good task performance is often considered sufficient evidence that meaningful communication is taking place, but existing empirical results show that communication strategies induced by common objectives can be counterintuitive whilst solving the task nearly perfectly. In this work, we identify a goal-agnostic prerequisite to meaningful communication, which we term semantic consistency, based on the idea that messages should have similar meanings across instances. We provide a formal definition for this idea, and use it to compare the two most common objectives in the field of emergent communication: discrimination and reconstruction. We prove, under mild assumptions, that semantically inconsistent communication protocols can be optimal solutions to the discrimination task, but not to reconstruction. We further show that the reconstruction objective encourages a stricter property, spatial meaningfulness, which also accounts for the distance between messages. Experiments with emergent communication games validate our theoretical results. These findings demonstrate an inherent advantage of distance-based communication goals, and contextualize previous empirical discoveries.

If you had an AI Whale-to-English translator, how could you validate whether or not it is working? Does one need to interact with the animals or rely on grounded observations such as temperature? We provide theoretical and proof-of-concept experimental evidence suggesting that interaction and even observations may not be necessary for sufficiently complex languages. One may be able to evaluate translators solely by their English outputs, offering potential advantages in terms of safety, ethics, and cost. This is an instance of machine translation quality evaluation (MTQE) without any reference translations available. A key challenge is identifying ``hallucinations,'' false translations which may appear fluent and plausible. We propose using segment-by-segment translation together with the classic NLP shuffle test to evaluate translators. The idea is to translate animal communication, turn by turn, and evaluate how often the resulting translations make more sense in order than permuted. Proof-of-concept experiments on data-scarce human languages and constructed languages demonstrate the potential utility of this evaluation methodology. These human-language experiments serve solely to validate our reference-free metric under data scarcity. It is found to correlate highly with a standard evaluation based on reference translations, which are available in our experiments. We also perform a theoretical analysis suggesting that interaction may not be necessary nor efficient in the early stages of learning to translate.

Large language models are increasingly used as agents in social, economic, and policy simulations. A common assumption is that stronger reasoning should improve simulation fidelity. We argue that this assumption can fail when the objective is not to solve a strategic problem, but to sample plausible boundedly rational behavior. In such settings, reasoning-enhanced models can become better solvers and worse simulators: they can over-optimize for strategically dominant actions, collapse compromise-oriented terminal behavior, and sometimes exhibit a diversity-without-fidelity pattern in which local variation survives without outcome-level fidelity. We study this solver-sampler mismatch in three multi-agent negotiation environments adapted from earlier simulation work: an ambiguous fragmented-authority trading-limits scenario, an ambiguous unified-opposition trading-limits scenario, and a new-domain grid-curtailment case in emergency electricity management. We compare three reflection conditions, no reflection, bounded reflection, and native reasoning, across two primary model families and then extend the same protocol to direct OpenAI runs with GPT-4.1 and GPT-5.2. Across all three experiments, bounded reflection produces substantially more diverse and compromise-oriented trajectories than either no reflection or native reasoning. In the direct OpenAI extension, GPT-5.2 native ends in authority decisions in 45 of 45 runs across the three experiments, while GPT-5.2 bounded recovers compromise outcomes in every environment. The contribution is not a claim that reasoning is generally harmful. It is a methodological warning: model capability and simulation fidelity are different objectives, and behavioral simulation should qualify models as samplers, not only as solvers.

This position paper argues that the field of LLM agents requires a unified, telecom-inspired communication protocol to ensure safety, interoperability, and scalability, especially within the context of Next Generation (NextG) networks. Current ad-hoc communication methods are creating a fragmented ecosystem, reminiscent of the early "protocol wars" in networking, which stifles innovation and poses significant risks. Drawing inspiration from the layered, standardized protocols that underpin modern telecommunications, we propose the LLM-Agent Communication Protocol (LACP). LACP establishes a three-layer architecture designed to ensure semantic clarity in communication, transactional integrity for complex tasks, and robust, built-in security. In this position paper, we argue that adopting a principled, universal protocol is not merely beneficial but essential for realizing the potential of distributed AI. Such a standard is critical for ensuring that multi-agent systems can operate safely and reliably in the complex, real-time applications envisioned for 6G and beyond.

We introduce CausaLab, a scalable environment for evaluating interactive causal discovery by LLM agents. Unlike prior evaluations, CausaLab evaluates both whether an agent can solve a problem using causal evidence and whether its answer is grounded in a faithful recovered causal mechanism. Each episode places an agent in a synthetic laboratory: it receives prior measurement records, intervenes on a manipulator crystal, and predicts the resonance frequency of a held-out reactor crystal governed by the same mechanism. The hidden data-generating process is a randomly sampled structural causal model (SCM), so success requires recovering both a causal graph and structural equations rather than recalling prior knowledge. Experiments show a persistent gap between prediction and mechanism recovery: in the purely observational 6-node setting, GPT-5.2-high reaches 92% task accuracy but only 0.471 all-edge F_1. Mixed observation-intervention strategies improve structural fidelity, while pure intervention remains difficult even for strong agents. We identify premature stopping as a major weakness and show that consistency verification mitigates it. CausaLab therefore separates predictive success from causal understanding and exposes current LLM agents' limits as experimental causal reasoners.

Reproducibility is central to research credibility, yet large-scale reanalysis of empricial data remains costly because replication packages vary widely in structure, software environment, and documentation. We develop and evaluate an agentic AI workflow that addresses this execution bottleneck while preserving scientific rigor. The system separates scientific reasoning from computational execution: researchers design fixed diagnostic templates, and the workflow automates the acquisition, harmonization, and execution of replication materials using pre-specified, version-controlled code. A structured knowledge layer records resolved failure patterns, enabling adaptation across heterogeneous studies while keeping each pipeline version transparent and stable. We evaluate this workflow on 92 instrumental variable (IV) studies, including 67 with manually verified reproducible 2SLS estimates and 25 newly published IV studies under identical criteria. For each paper, we analyze up to three two-stage least squares (2SLS) specifications, totaling 215. Across the 92 papers, the system achieves 87% end-to-end success overall. Conditional on accessible data and code, reproducibility is 100% at both the paper and specification levels. The framework substantially lowers the cost of executing established empirical protocols and can be adapted in empirical settings where analytic templates and norms of transparency are well established.

Combined electric power system and High-Altitude Electromagnetic Pulse (HEMP) models are being developed to determine the effect of a HEMP on the US power grid. The work relies primarily on deterministic methods; however, it is computationally untenable to evaluate the E1 HEMP response of large numbers of grid components distributed across a large interconnection. Further, the deterministic assessment of these components' failures are largely unachievable. E1 HEMP laboratory testing of the components is accomplished, but is expensive, leaving few data points to construct failure models of grid components exposed to E1 HEMP. The use of Bayesian priors, developed using the subject matter expertise, combined with the minimal test data in a Bayesian inference process, provides the basis for the development of more robust and cost-effective statistical component failure models. These can be used with minimal computational burden in a simulation environment such as sampling of Cumulative Distribution Functions (CDFs).

How many experimental studies would have come to different conclusions had they been run on larger samples? I show how to estimate the expected number of statistically significant results that a set of experiments would have reported had their sample sizes all been counterfactually increased. The proposed deconvolution estimator is asymptotically normal and adjusts for publication bias. Unlike related methods, this approach requires no assumptions of any kind about the distribution of true intervention treatment effects and allows for point masses. Simulations find good coverage even when the t-score is only approximately normal. An application to randomized trials (RCTs) published in economics journals finds that doubling every sample would increase the power of t-tests by 7.2 percentage points on average. This effect is smaller than for non-RCTs and comparable to systematic replications in laboratory psychology where previous studies enabled more accurate power calculations. This suggests that RCTs are on average relatively insensitive to sample size increases. Research funders who wish to raise power should generally consider sponsoring better-measured and higher quality experiments -- rather than only larger ones.

Multi-agent sequential decision-making powers many real-world systems, from autonomous vehicles and robotics to collaborative AI assistants. In dynamic, partially observable environments, communication is often what reduces uncertainty and makes collaboration possible. This survey reviews multi-agent communication (MA-Comm) through the Five Ws: who communicates with whom, what is communicated, when communication occurs, and why communication is beneficial. This framing offers a clean way to connect ideas across otherwise separate research threads. We trace how communication approaches have evolved across three major paradigms. In Multi-Agent Reinforcement Learning (MARL), early methods used hand-designed or implicit protocols, followed by end-to-end learned communication optimized for reward and control. While successful, these protocols are frequently task-specific and hard to interpret, motivating work on Emergent Language (EL), where agents can develop more structured or symbolic communication through interaction. EL methods, however, still struggle with grounding, generalization, and scalability, which has fueled recent interest in large language models (LLMs) that bring natural language priors for reasoning, planning, and collaboration in more open-ended settings. Across MARL, EL, and LLM-based systems, we highlight how different choices shape communication design, where the main trade-offs lie, and what remains unsolved. We distill practical design patterns and open challenges to support future hybrid systems that combine learning, language, and control for scalable and interpretable multi-agent collaboration.

AI control protocols serve as a defense mechanism to stop untrusted LLM agents from causing harm in autonomous settings. Prior work treats this as a security problem, stress testing with exploits that use the deployment context to subtly complete harmful side tasks, such as backdoor insertion. In practice, most AI control protocols are fundamentally based on LLM monitors, which can become a central point of failure. We study adaptive attacks by an untrusted model that knows the protocol and the monitor model, which is plausible if the untrusted model was trained with a later knowledge cutoff or can search for this information autonomously. We instantiate a simple adaptive attack vector by which the attacker embeds publicly known or zero-shot prompt injections in the model outputs. Using this tactic, frontier models consistently evade diverse monitors and complete malicious tasks on two main AI control benchmarks. The attack works universally against current protocols that rely on a monitor. Furthermore, the recent Defer-to-Resample protocol even backfires, as its resampling amplifies the prompt injection and effectively reframes it as a best-of-n attack. In general, adaptive attacks on monitor models represent a major blind spot in current control protocols and should become a standard component of evaluations for future AI control mechanisms.

Clinical trials or studies oftentimes require long-term and/or costly follow-up of participants to evaluate a novel treatment/drug/vaccine. There has been increasing interest in the past few decades in using short-term surrogate outcomes as a replacement of the primary outcome i.e., in using the surrogate outcome, which can potentially be observed sooner, to make inference about the treatment effect on the long-term primary outcome. Very few of the available statistical methods to evaluate a surrogate are applicable to settings where both the surrogate and the primary outcome are time-to-event outcomes subject to censoring. Methods that can handle this setting tend to require parametric assumptions or be limited to assessing only the restricted mean survival time. In this paper, we propose a non-parametric approach to evaluate a censored surrogate outcome, such as time to progression, when the primary outcome is also a censored time-to-event outcome, such as time to death, and the treatment effect of interest is the difference in overall survival. Specifically, we define the proportion of the treatment effect on the primary outcome that is explained (PTE) by the censored surrogate outcome in this context, and estimate this proportion by defining and deriving an optimal transformation of the surrogate information. Our approach provides the added advantage of relaxed assumptions to guarantee that the true PTE is within (0,1), along with being model-free. Finite sample performance of our estimators are illustrated via extensive simulation studies and a real data application examining progression-free survival as a surrogate for overall survival for patients with metastatic colorectal cancer.

Recent advances in large language models (LLMs) have led to their extensive global deployment, and ensuring their safety calls for comprehensive and multilingual toxicity evaluations. However, existing toxicity benchmarks are overwhelmingly focused on English, posing serious risks to deploying LLMs in other languages. We address this by introducing PolygloToxicityPrompts (PTP), the first large-scale multilingual toxicity evaluation benchmark of 425K naturally occurring prompts spanning 17 languages. We overcome the scarcity of naturally occurring toxicity in web-text and ensure coverage across languages with varying resources by automatically scraping over 100M web-text documents. Using PTP, we investigate research questions to study the impact of model size, prompt language, and instruction and preference-tuning methods on toxicity by benchmarking over 60 LLMs. Notably, we find that toxicity increases as language resources decrease or model size increases. Although instruction- and preference-tuning reduce toxicity, the choice of preference-tuning method does not have any significant impact. Our findings shed light on crucial shortcomings of LLM safeguarding and highlight areas for future research.

We revisit Wald's celebrated Sequential Probability Ratio Test for sequential tests of two simple hypotheses, under privacy constraints. We propose DP-SPRT, a wrapper that can be calibrated to achieve desired error probabilities and privacy constraints, addressing a significant gap in previous work. DP-SPRT relies on a private mechanism that processes a sequence of queries and stops after privately determining when the query results fall outside a predefined interval. This OutsideInterval mechanism improves upon naive composition of existing techniques like AboveThreshold, potentially benefiting other sequential algorithms. We prove generic upper bounds on the error and sample complexity of DP-SPRT that can accommodate various noise distributions based on the practitioner's privacy needs. We exemplify them in two settings: Laplace noise (pure Differential Privacy) and Gaussian noise (R\'enyi differential privacy). In the former setting, by providing a lower bound on the sample complexity of any epsilon-DP test with prescribed type I and type II errors, we show that DP-SPRT is near optimal when both errors are small and the two hypotheses are close. Moreover, we conduct an experimental study revealing its good practical performance.

Scientific publication compresses a branching, iterative research process into a linear narrative, discarding the majority of what was discovered along the way. This compilation imposes two structural costs: a Storytelling Tax, where failed experiments, rejected hypotheses, and the branching exploration process are discarded to fit a linear narrative; and an Engineering Tax, where the gap between reviewer-sufficient prose and agent-sufficient specification leaves critical implementation details unwritten. Tolerable for human readers, these costs become critical when AI agents must understand, reproduce, and extend published work. We introduce the Agent-Native Research Artifact (ARA), a protocol that replaces the narrative paper with a machine-executable research package structured around four layers: scientific logic, executable code with full specifications, an exploration graph that preserves the failures compilation discards, and evidence grounding every claim in raw outputs. Three mechanisms support the ecosystem: a Live Research Manager that captures decisions and dead ends during ordinary development; an ARA Compiler that translates legacy PDFs and repos into ARAs; and an ARA-native review system that automates objective checks so human reviewers can focus on significance, novelty, and taste. On PaperBench and RE-Bench, ARA raises question-answering accuracy from 72.4% to 93.7% and reproduction success from 57.4% to 64.4%. On RE-Bench's five open-ended extension tasks, preserved failure traces in ARA accelerate progress, but can also constrain a capable agent from stepping outside the prior-run box depending on the agent's capabilities.

Benchmarking is seen as critical to assessing progress in NLP. However, creating a benchmark involves many design decisions (e.g., which datasets to include, which metrics to use) that often rely on tacit, untested assumptions about what the benchmark is intended to measure or is actually measuring. There is currently no principled way of analyzing these decisions and how they impact the validity of the benchmark's measurements. To address this gap, we draw on evidence-centered design in educational assessments and propose Evidence-Centered Benchmark Design (ECBD), a framework which formalizes the benchmark design process into five modules. ECBD specifies the role each module plays in helping practitioners collect evidence about capabilities of interest. Specifically, each module requires benchmark designers to describe, justify, and support benchmark design choices -- e.g., clearly specifying the capabilities the benchmark aims to measure or how evidence about those capabilities is collected from model responses. To demonstrate the use of ECBD, we conduct case studies with three benchmarks: BoolQ, SuperGLUE, and HELM. Our analysis reveals common trends in benchmark design and documentation that could threaten the validity of benchmarks' measurements.

Activation patching is a popular mechanistic interpretability technique, but has many subtleties regarding how it is applied and how one may interpret the results. We provide a summary of advice and best practices, based on our experience using this technique in practice. We include an overview of the different ways to apply activation patching and a discussion on how to interpret the results. We focus on what evidence patching experiments provide about circuits, and on the choice of metric and associated pitfalls.

Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e.g., the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e.g., drugs or antibiotics). In such underspecified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

Observational studies of causal effects require adjustment for confounding factors. In the tabular setting, where these factors are well-defined, separate random variables, the effect of confounding is well understood. However, in public policy, ecology, and in medicine, decisions are often made in non-tabular settings, informed by patterns or objects detected in images (e.g., maps, satellite or tomography imagery). Using such imagery for causal inference presents an opportunity because objects in the image may be related to the treatment and outcome of interest. In these cases, we rely on the images to adjust for confounding but observed data do not directly label the existence of the important objects. Motivated by real-world applications, we formalize this challenge, how it can be handled, and what conditions are sufficient to identify and estimate causal effects. We analyze finite-sample performance using simulation experiments, estimating effects using a propensity adjustment algorithm that employs a machine learning model to estimate the image confounding. Our experiments also examine sensitivity to misspecification of the image pattern mechanism. Finally, we use our methodology to estimate the effects of policy interventions on poverty in African communities from satellite imagery.

Estimation of causal effects is critical to a range of scientific disciplines. Existing methods for this task either require interventional data, knowledge about the ground truth causal graph, or rely on assumptions such as unconfoundedness, restricting their applicability in real-world settings. In the domain of tabular machine learning, Prior-data fitted networks (PFNs) have achieved state-of-the-art predictive performance, having been pre-trained on synthetic data to solve tabular prediction problems via in-context learning. To assess whether this can be transferred to the harder problem of causal effect estimation, we pre-train PFNs on synthetic data drawn from a wide variety of causal structures, including interventions, to predict interventional outcomes given observational data. Through extensive experiments on synthetic case studies, we show that our approach allows for the accurate estimation of causal effects without knowledge of the underlying causal graph. We also perform ablation studies that elucidate Do-PFN's scalability and robustness across datasets with a variety of causal characteristics.

Practical identifiability is a critical concern in data-driven modeling of mathematical systems. In this paper, we propose a novel framework for practical identifiability analysis to evaluate parameter identifiability in mathematical models of biological systems. Starting with a rigorous mathematical definition of practical identifiability, we demonstrate its equivalence to the invertibility of the Fisher Information Matrix. Our framework establishes the relationship between practical identifiability and coordinate identifiability, introducing a novel metric that simplifies and accelerates the evaluation of parameter identifiability compared to the profile likelihood method. Additionally, we introduce new regularization terms to address non-identifiable parameters, enabling uncertainty quantification and improving model reliability. To guide experimental design, we present an optimal data collection algorithm that ensures all model parameters are practically identifiable. Applications to Hill functions, neural networks, and dynamic biological models demonstrate the feasibility and efficiency of the proposed computational framework in uncovering critical biological processes and identifying key observable variables.

In unmanned aerial vehicle (UAV) networks, communication protocols and algorithms are essential for cooperation and collaboration between UAVs. Simulation provides a cost-effective solution for prototyping, debugging, and analyzing protocols and algorithms, avoiding the prohibitive expenses of field experiments. In this paper, we present ``UavNetSim-v1'', an open-source Python-based simulation platform designed for rapid development, testing, and evaluating the protocols and algorithms in UAV networks. ``UavNetSim-v1'' provides most of the functionalities developers may need, including routing/medium access control (MAC) protocols, topology control algorithms and mobility/energy models, while maintaining ease of use. Furthermore, the platform supports comprehensive performance evaluation and features an interactive visualization interface for in-depth algorithm analysis. In short, ``UavNetSim-v1'' lends itself to both rapid prototyping and educational purposes, and can serve as a lightweight yet powerful alternative to mature network simulators for UAV communication research.

The development of large language models (LLMs) has entered in a experience-driven era, flagged by the emergence of environment feedback-driven learning via reinforcement learning and tool-using agents. This encourages the emergenece of model context protocol (MCP), which defines the standard on how should a LLM interact with external services, such as \api and data. However, as MCP becomes the de facto standard for LLM agent systems, it also introduces new safety risks. In particular, MCP introduces third-party services, which are not controlled by the LLM developers, into the agent systems. These third-party MCP services provider are potentially malicious and have the economic incentives to exploit vulnerabilities and sabotage user-agent interactions. In this position paper, we advocate the research community in LLM safety to pay close attention to the new safety risks issues introduced by MCP, and develop new techniques to build safe MCP-powered agent systems. To establish our position, we argue with three key parts. (1) We first construct \framework, a controlled framework to examine safety issues in MCP-powered agent systems. (2) We then conduct a series of pilot experiments to demonstrate the safety risks in MCP-powered agent systems is a real threat and its defense is not trivial. (3) Finally, we give our outlook by showing a roadmap to build safe MCP-powered agent systems. In particular, we would call for researchers to persue the following research directions: red teaming, MCP safe LLM development, MCP safety evaluation, MCP safety data accumulation, MCP service safeguard, and MCP safe ecosystem construction. We hope this position paper can raise the awareness of the research community in MCP safety and encourage more researchers to join this important research direction. Our code is available at https://github.com/littlelittlenine/SafeMCP.git.

In many natural and engineered systems, unknown quantum channels act on a subsystem that cannot be directly controlled and measured, but is instead learned through a controllable subsystem that weakly interacts with it. We study quantum channel discrimination (QCD) under these restrictions, which we call hidden system QCD (HQCD). We find that sequential protocols achieve perfect discrimination and saturate the Heisenberg limit. In contrast, depth-1 parallel and multi-shot protocols cannot solve HQCD. This suggests that sequential protocols are superior in experimentally realistic situations.

Large language models are being widely used across industries to generate content that contributes directly to key performance metrics, such as conversion rates. Pretrained models, however, often fall short when it comes to aligning with human preferences or optimizing for business objectives. As a result, fine-tuning with good-quality labeled data is essential to guide models to generate content that achieves better results. Controlled experiments, like A/B tests, can provide such data, but they are often expensive and come with significant engineering and logistical challenges. Meanwhile, companies have access to a vast amount of historical (observational) data that remains underutilized. In this work, we study the challenges and opportunities of fine-tuning LLMs using observational data. We show that while observational outcomes can provide valuable supervision, directly fine-tuning models on such data can lead them to learn spurious correlations. We present empirical evidence of this issue using various real-world datasets and propose DeconfoundLM, a method that explicitly removes the effect of known confounders from reward signals. Using simulation experiments, we demonstrate that DeconfoundLM improves the recovery of causal relationships and mitigates failure modes found in fine-tuning methods that ignore or naively incorporate confounding variables. Our findings highlight that while observational data presents risks, with the right causal corrections, it can be a powerful source of signal for LLM alignment. Please refer to the project page for code and related resources.

We consider the problem of performing Bayesian inference in probabilistic models where observations are accompanied by uncertainty, referred to as "uncertain evidence." We explore how to interpret uncertain evidence, and by extension the importance of proper interpretation as it pertains to inference about latent variables. We consider a recently-proposed method "distributional evidence" as well as revisit two older methods: Jeffrey's rule and virtual evidence. We devise guidelines on how to account for uncertain evidence and we provide new insights, particularly regarding consistency. To showcase the impact of different interpretations of the same uncertain evidence, we carry out experiments in which one interpretation is defined as "correct." We then compare inference results from each different interpretation illustrating the importance of careful consideration of uncertain evidence.

Scientific discovery workflows usually contain and rely heavily on lab notes, where researchers record observations, interpret uncertain results, and plan follow-up experiments. Such informative lab notes preserve evolving scientific reasoning and author uncertainty, rather than polished final results exhibited in publications, providing a valuable opportunity for AI to engage in scientific exploration at a more comprehensive and deeper level. However, most prior work on scientific text focuses on papers, protocols, or structured databases, leaving informal laboratory notes underexplored as inputs to AI agents for science. This gap matters because lab notes often intermingle validated observations, tentative judgments, and possible experimental next steps within the same passage. If these signals are conflated, an AI agent may mistake uncertain scientific judgments for confirmed conclusions or executable actions. To this end, we present Notes2Skills, a two-stage framework for turning lab notebooks into verifiable skills for scientific AI agents while preserving the author's certainty. Across seven conditions and three wet-lab sessions, Notes2Skills is the only configuration that neither mistakes uncertain notes for firm instructions nor discards firm ones. We show that certainty preservation is the missing piece between lab notebooks and reliable agent skills, opening a path toward safer AI co-scientist systems.

In this paper, we propose feedback designs for manipulating a quantum state to a target state by performing sequential measurements. In light of Belavkin's quantum feedback control theory, for a given set of (projective or non-projective) measurements and a given time horizon, we show that finding the measurement selection policy that maximizes the probability of successful state manipulation is an optimal control problem for a controlled Markovian process. The optimal policy is Markovian and can be solved by dynamical programming. Numerical examples indicate that making use of feedback information significantly improves the success probability compared to classical scheme without taking feedback. We also consider other objective functionals including maximizing the expected fidelity to the target state as well as minimizing the expected arrival time. The connections and differences among these objectives are also discussed.

Schema-guided reasoning pipelines ask LLMs to produce explicit intermediate structures -- rubrics, checklists, verification queries -- before committing to a final decision. But do these structures causally determine the output, or merely accompany it? We introduce a causal evaluation protocol that makes this directly measurable: by selecting tasks where a deterministic function maps intermediate structures to decisions, every controlled edit implies a unique correct output. Across eight models and three benchmarks, models appear self-consistent with their own intermediate structures but fail to update predictions after intervention in up to 60% of cases -- revealing that apparent faithfulness is fragile once the intermediate structure changes. When derivation of the final decision from the structure is delegated to an external tool, this fragility largely disappears; however, prompts which ask to prioritize the intermediate structure over the original input do not materially close the gap. Overall, intermediate structures in schema-guided pipelines function as influential context rather than stable causal mediators.

Decentralized reputation schemes present a promising area of experimentation in blockchain applications. These solutions aim to overcome the shortcomings of simple monetary incentive mechanisms of naive tokenomics. However, there is a significant research gap regarding the limitations and benefits of such solutions. We formulate these trade-offs as a conjecture on the irreconcilability of three desirable properties of the reputation system in this context. Such a system can not be simultaneously generalizable, trustless, and Sybil resistant. To handle the limitations of this trilemma, we propose MeritRank: Sybil tolerant feedback aggregation mechanism for reputation. Instead of preventing Sybil attacks, our approach successfully bounds the benefits of these attacks. Using a dataset of participants' interactions in MakerDAO, we run experiments to demonstrate Sybil tolerance of MeritRank. Decay parameters of reputation in MeritRank: transitivity decay and connectivity decay, allow for a fine-tuning of desirable levels of reputation utility and Sybil tolerance in different use contexts.

We study the problem of adaptively identifying patient subpopulations that benefit from a given treatment during a confirmatory clinical trial. This type of adaptive clinical trial has been thoroughly studied in biostatistics, but has been allowed only limited adaptivity so far. Here, we aim to relax classical restrictions on such designs and investigate how to incorporate ideas from the recent machine learning literature on adaptive and online experimentation to make trials more flexible and efficient. We find that the unique characteristics of the subpopulation selection problem -- most importantly that (i) one is usually interested in finding subpopulations with any treatment benefit (and not necessarily the single subgroup with largest effect) given a limited budget and that (ii) effectiveness only has to be demonstrated across the subpopulation on average -- give rise to interesting challenges and new desiderata when designing algorithmic solutions. Building on these findings, we propose AdaGGI and AdaGCPI, two meta-algorithms for subpopulation construction. We empirically investigate their performance across a range of simulation scenarios and derive insights into their (dis)advantages across different settings.

Early warning signals have been proposed to forecast the possibility of a critical transition, such as the eutrophication of a lake, the collapse of a coral reef, or the end of a glacial period. Because such transitions often unfold on temporal and spatial scales that can be difficult to approach by experimental manipulation, research has often relied on historical observations as a source of natural experiments. Here we examine a critical difference between selecting systems for study based on the fact that we have observed a critical transition and those systems for which we wish to forecast the approach of a transition. This difference arises by conditionally selecting systems known to experience a transition of some sort and failing to account for the bias this introduces -- a statistical error often known as the Prosecutor's Fallacy. By analysing simulated systems that have experienced transitions purely by chance, we reveal an elevated rate of false positives in common warning signal statistics. We further demonstrate a model-based approach that is less subject to this bias than these more commonly used summary statistics. We note that experimental studies with replicates avoid this pitfall entirely.

Large language models are increasingly being used to assess and forecast research ideas, yet we lack scalable ways to evaluate the quality of models' judgments about these scientific ideas. Towards this goal, we introduce PoT, a semi-verifiable benchmarking framework that links scientific idea judgments to downstream signals that become observable later (e.g., citations and shifts in researchers' agendas). PoT freezes a pre-cutoff snapshot of evidence in an offline sandbox and asks models to forecast post-cutoff outcomes, enabling verifiable evaluation when ground truth arrives, scalable benchmarking without exhaustive expert annotation, and analysis of human-model misalignment against signals such as peer-review awards. In addition, PoT provides a controlled testbed for agent-based research judgments that evaluate scientific ideas, comparing tool-using agents to non-agent baselines under prompt ablations and budget scaling. Across 30,000+ instances spanning four benchmark domains, we find that, compared with non-agent baselines, higher interaction budgets generally improve agent performance, while the benefit of tool use is strongly task-dependent. By combining time-partitioned, future-verifiable targets with an offline sandbox for tool use, PoT supports scalable evaluation of agents on future-facing scientific idea judgment tasks.

Building language models (LMs), especially small and medium ones, remains more art than science. While large LMs often improve by sheer scale, it is still unclear why many design choices work. For small LMs, this uncertainty is more limiting: tight parameter budgets make each decision critical, yet researchers still lack systematic, scientific ways to test and refine new ideas. We introduce Pico, a lightweight, modular framework that enables systematic, hypothesis-driven research for small and medium-scale language model development. Pico consists of two libraries that together provide a practical sandbox where researchers can make targeted changes to a model's architecture or training procedures and directly observe their effects on the model's behavior. To support reproducible experimentation, we also release a suite of baseline models, pico-decoder, trained under standardized conditions and open-sourced for the community. Case studies highlight how Pico can support iterative small LM design and analysis.