Daily Papers

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

Retrieval-Augmented Generation (RAG) improves factual accuracy by grounding responses in external knowledge. However, existing methods typically rely on a single source, either unstructured text or structured knowledge. Moreover, they lack cognitively inspired mechanisms for activating relevant knowledge. To address these issues, we propose KG-Infused RAG, a framework that integrates KGs into RAG systems to implement spreading activation, a cognitive process that enables concept association and inference. KG-Infused RAG retrieves KG facts, expands the query accordingly, and enhances generation by combining corpus passages with structured facts, enabling interpretable, multi-source retrieval grounded in semantic structure. We further improve KG-Infused RAG via preference learning on sampled key stages in the pipeline. Experiments on five QA benchmarks show that KG-Infused RAG consistently outperforms vanilla RAG (by 3.8% to 13.8%). Additionally, when integrated into Self-RAG, KG-Infused RAG brings further performance gains, demonstrating its effectiveness and versatility as a plug-and-play enhancement module for corpus-based RAG methods.

Clinical predictive models often rely on patients' electronic health records (EHR), but integrating medical knowledge to enhance predictions and decision-making is challenging. This is because personalized predictions require personalized knowledge graphs (KGs), which are difficult to generate from patient EHR data. To address this, we propose GraphCare, an open-world framework that uses external KGs to improve EHR-based predictions. Our method extracts knowledge from large language models (LLMs) and external biomedical KGs to build patient-specific KGs, which are then used to train our proposed Bi-attention AugmenTed (BAT) graph neural network (GNN) for healthcare predictions. On two public datasets, MIMIC-III and MIMIC-IV, GraphCare surpasses baselines in four vital healthcare prediction tasks: mortality, readmission, length of stay (LOS), and drug recommendation. On MIMIC-III, it boosts AUROC by 17.6\% and 6.6\% for mortality and readmission, and F1-score by 7.9\% and 10.8\% for LOS and drug recommendation, respectively. Notably, GraphCare demonstrates a substantial edge in scenarios with limited data availability. Our findings highlight the potential of using external KGs in healthcare prediction tasks and demonstrate the promise of GraphCare in generating personalized KGs for promoting personalized medicine.

Large language models (LLMs) have demonstrated remarkable capabilities in various complex tasks, yet they still suffer from hallucinations. Introducing external knowledge, such as knowledge graph, can enhance the LLMs' ability to provide factual answers. LLMs have the ability to interactively explore knowledge graphs. However, most approaches have been affected by insufficient internal knowledge excavation in LLMs, limited generation of trustworthy knowledge reasoning paths, and a vague integration between internal and external knowledge. Therefore, we propose KnowPath, a knowledge-enhanced large model framework driven by the collaboration of internal and external knowledge. It relies on the internal knowledge of the LLM to guide the exploration of interpretable directed subgraphs in external knowledge graphs, better integrating the two knowledge sources for more accurate reasoning. Extensive experiments on multiple real-world datasets confirm the superiority of KnowPath.

Conversational recommender systems (CRS) aim to recommend relevant items to users by eliciting user preference through natural language conversation. Prior work often utilizes external knowledge graphs for items' semantic information, a language model for dialogue generation, and a recommendation module for ranking relevant items. This combination of multiple components suffers from a cumbersome training process, and leads to semantic misalignment issues between dialogue generation and item recommendation. In this paper, we represent items in natural language and formulate CRS as a natural language processing task. Accordingly, we leverage the power of pre-trained language models to encode items, understand user intent via conversation, perform item recommendation through semantic matching, and generate dialogues. As a unified model, our PECRS (Parameter-Efficient CRS), can be optimized in a single stage, without relying on non-textual metadata such as a knowledge graph. Experiments on two benchmark CRS datasets, ReDial and INSPIRED, demonstrate the effectiveness of PECRS on recommendation and conversation. Our code is available at: https://github.com/Ravoxsg/efficient_unified_crs.

Although large language models (LLMs) have achieved significant success in various tasks, they often struggle with hallucination problems, especially in scenarios requiring deep and responsible reasoning. These issues could be partially addressed by introducing external knowledge graphs (KG) in LLM reasoning. In this paper, we propose a new LLM-KG integrating paradigm ``LLMotimesKG'' which treats the LLM as an agent to interactively explore related entities and relations on KGs and perform reasoning based on the retrieved knowledge. We further implement this paradigm by introducing a new approach called Think-on-Graph (ToG), in which the LLM agent iteratively executes beam search on KG, discovers the most promising reasoning paths, and returns the most likely reasoning results. We use a number of well-designed experiments to examine and illustrate the following advantages of ToG: 1) compared with LLMs, ToG has better deep reasoning power; 2) ToG has the ability of knowledge traceability and knowledge correctability by leveraging LLMs reasoning and expert feedback; 3) ToG provides a flexible plug-and-play framework for different LLMs, KGs and prompting strategies without any additional training cost; 4) the performance of ToG with small LLM models could exceed large LLM such as GPT-4 in certain scenarios and this reduces the cost of LLM deployment and application. As a training-free method with lower computational cost and better generality, ToG achieves overall SOTA in 6 out of 9 datasets where most previous SOTAs rely on additional training.

The chit-chat-based conversational recommendation systems (CRS) provide item recommendations to users through natural language interactions. To better understand user's intentions, external knowledge graphs (KG) have been introduced into chit-chat-based CRS. However, existing chit-chat-based CRS usually generate repetitive item recommendations, and they cannot properly infuse knowledge from KG into CRS to generate informative responses. To remedy these issues, we first reformulate the conversational recommendation task to highlight that the recommended items should be new and possibly interested by users. Then, we propose the Knowledge-Enriched Conversational Recommendation System (KECRS). Specifically, we develop the Bag-of-Entity (BOE) loss and the infusion loss to better integrate KG with CRS for generating more diverse and informative responses. BOE loss provides an additional supervision signal to guide CRS to learn from both human-written utterances and KG. Infusion loss bridges the gap between the word embeddings and entity embeddings by minimizing distances of the same words in these two embeddings. Moreover, we facilitate our study by constructing a high-quality KG, \ie The Movie Domain Knowledge Graph (TMDKG). Experimental results on a large-scale dataset demonstrate that KECRS outperforms state-of-the-art chit-chat-based CRS, in terms of both recommendation accuracy and response generation quality.

GraphRAG enhances large language models (LLMs) to generate quality answers for user questions by retrieving related facts from external knowledge graphs. Existing GraphRAG methods adopt a fixed graph traversal strategy for fact retrieval but we observe that user questions come in different types and require different graph traversal strategies. As such, existing GraphRAG methods are limited in effectiveness (i.e., quality of the generated answers) and/or efficiency (i.e., response time or the number of used tokens). In this paper, we propose to classify the questions according to a complete four-class taxonomy and adaptively select the appropriate graph traversal strategy for each type of questions. Our system PolyG is essentially a query planner for GraphRAG and can handle diverse questions with an unified interface and execution engine. Compared with SOTA GraphRAG methods, PolyG achieves an overall win rate of 75% on generation quality and a speedup up to 4x on response time.

We introduce PersonalAI 2.0 (PAI-2), a novel framework, designed to enhance large language model (LLM) based systems through integration of external knowledge graphs (KG). The proposed approach addresses key limitations of existing Graph Retrieval-Augmented Generation (GraphRAG) methods by incorporating a dynamic, multistage query processing pipeline. The central point of PAI-2 design is its ability to perform adaptive, iterative information search, guided by extracted entities, matched graph vertices and generated clue-queries. Conducted evaluation over six benchmarks (Natural Questions, TriviaQA, HotpotQA, 2WikiMultihopQA, MuSiQue and DiaASQ) demonstrates improvement in factual correctness of generating answers compared to analogues methods (LightRAG, RAPTOR, and HippoRAG 2). PAI-2 achieves 4% average gain by LLM-as-a-Judge across four benchmarks, reflecting its effectiveness in reducing hallucination rates and increasing precision. We show that use of graph traversal algorithms (e.g. BeamSearch, WaterCircles) gain superior results compared to standard flatten retriever on average 6%, while enabled search plan enhancement mechanism gain 18% boost compared to disabled one by LLM-as-a-Judge across six datasets. In addition, ablation study reveals that PAI-2 achieves the SOTA result on MINE-1 benchmark, achieving 89% information-retention score, using LLMs from 7-14B tiers. Collectively, these findings underscore the potential of PAI-2 to serve as a foundational model for next-generation personalized AI applications, requiring scalable, context-aware knowledge representation and reasoning capabilities.

Question Answering (QA) systems are increasingly deployed in applications where they support real-world decisions. However, state-of-the-art models rely on deep neural networks, which are difficult to interpret by humans. Inherently interpretable models or post hoc explainability methods can help users to comprehend how a model arrives at its prediction and, if successful, increase their trust in the system. Furthermore, researchers can leverage these insights to develop new methods that are more accurate and less biased. In this paper, we introduce SQuARE v2, the new version of SQuARE, to provide an explainability infrastructure for comparing models based on methods such as saliency maps and graph-based explanations. While saliency maps are useful to inspect the importance of each input token for the model's prediction, graph-based explanations from external Knowledge Graphs enable the users to verify the reasoning behind the model prediction. In addition, we provide multiple adversarial attacks to compare the robustness of QA models. With these explainability methods and adversarial attacks, we aim to ease the research on trustworthy QA models. SQuARE is available on https://square.ukp-lab.de.

Causal graphs provide a high-level language for making mechanisms transparent. Recent work uses Large Language Models (LLMs) to recover causal graphs of external-world processes. Instead, in this paper, we use causal graphs to model LLM inference itself, providing stakeholders with a transparent view of how the model perceives and organizes high-level concepts to produce a prediction. We propose a four-phase method for constructing such graphs. Given a target LLM and a set of textual examples, our method discovers class-discriminative, human-interpretable concepts and maps each input to LLM-perceived concept states. We then introduce an MCMC-inspired counterfactual augmentation procedure that expands the sparse observational data through chains of counterfactuals. This enables stable causal discovery with σ-CG, yielding informative, interpretable graphs. We apply our method to three LLMs across disease diagnosis, sentiment analysis, and LLM-as-a-judge classification tasks. We evaluate the learned graphs for predictive fidelity and structural stability, and the MCMC-inspired augmentation for convergence and downstream utility. Our results show that the discovered causal graphs capture meaningful dependencies consistent with LLMs' reasoning. Together, this paper provides a foundation for concept-level explainability of LLMs.

Large Language Models (LLMs) have achieved exceptional capabilities in open generation across various domains, yet they encounter difficulties with tasks that require intensive knowledge. To address these challenges, methods for integrating knowledge have been developed, which augment LLMs with domain-specific knowledge graphs through external modules. These approaches, however, face data inefficiency issues as they necessitate the processing of both known and unknown knowledge for fine-tuning. Thus, our research focuses on a novel problem: efficiently integrating unknown knowledge into LLMs without unnecessary overlap of known knowledge. A risk of introducing new knowledge is the potential forgetting of existing knowledge. To mitigate this risk, we propose the innovative {\method} framework. This framework employs transformer internal states to determine when to enrich LLM outputs with additional information, effectively preventing knowledge forgetting. Performance evaluations using the UMLS-2.5k and MetaQA domain knowledge graphs reveal that {\method} not only successfully integrates new knowledge but also outperforms state-of-the-art baselines, reducing knowledge forgetting by 9\% and 6\%, respectively.

Retrieval-Augmented Generation (RAG) improves large language models by retrieving external knowledge, often truncated into smaller chunks due to the input context window, which leads to information loss, resulting in response hallucinations and broken reasoning chains. Moreover, traditional RAG retrieves unstructured knowledge, introducing irrelevant details that hinder accurate reasoning. To address these issues, we propose TAdaRAG, a novel RAG framework for on-the-fly task-adaptive knowledge graph construction from external sources. Specifically, we design an intent-driven routing mechanism to a domain-specific extraction template, followed by supervised fine-tuning and a reinforcement learning-based implicit extraction mechanism, ensuring concise, coherent, and non-redundant knowledge integration. Evaluations on six public benchmarks and a real-world business benchmark (NowNewsQA) across three backbone models demonstrate that TAdaRAG outperforms existing methods across diverse domains and long-text tasks, highlighting its strong generalization and practical effectiveness.

Traditional similarity-based schema matching methods are incapable of resolving semantic ambiguities and conflicts in domain-specific complex mapping scenarios due to missing commonsense and domain-specific knowledge. The hallucination problem of large language models (LLMs) also makes it challenging for LLM-based schema matching to address the above issues. Therefore, we propose a Knowledge Graph-based Retrieval-Augmented Generation model for Schema Matching, referred to as the KG-RAG4SM. In particular, KG-RAG4SM introduces novel vector-based, graph traversal-based, and query-based graph retrievals, as well as a hybrid approach and ranking schemes that identify the most relevant subgraphs from external large knowledge graphs (KGs). We showcase that KG-based retrieval-augmented LLMs are capable of generating more accurate results for complex matching cases without any re-training. Our experimental results show that KG-RAG4SM outperforms the LLM-based state-of-the-art (SOTA) methods (e.g., Jellyfish-8B) by 35.89% and 30.50% in terms of precision and F1 score on the MIMIC dataset, respectively; KG-RAG4SM with GPT-4o-mini outperforms the pre-trained language model (PLM)-based SOTA methods (e.g., SMAT) by 69.20% and 21.97% in terms of precision and F1 score on the Synthea dataset, respectively. The results also demonstrate that our approach is more efficient in end-to-end schema matching, and scales to retrieve from large KGs. Our case studies on the dataset from the real-world schema matching scenario exhibit that the hallucination problem of LLMs for schema matching is well mitigated by our solution.

Multi-label text classification (MLTC) tasks in the medical domain often face the long-tail label distribution problem. Prior works have explored hierarchical label structures to find relevant information for few-shot classes, but mostly neglected to incorporate external knowledge from medical guidelines. This paper presents DKEC, Domain Knowledge Enhanced Classification for diagnosis prediction with two innovations: (1) automated construction of heterogeneous knowledge graphs from external sources to capture semantic relations among diverse medical entities, (2) incorporating the heterogeneous knowledge graphs in few-shot classification using a label-wise attention mechanism. We construct DKEC using three online medical knowledge sources and evaluate it on a real-world Emergency Medical Services (EMS) dataset and a public electronic health record (EHR) dataset. Results show that DKEC outperforms the state-of-the-art label-wise attention networks and transformer models of different sizes, particularly for the few-shot classes. More importantly, it helps the smaller language models achieve comparable performance to large language models.

We study the problem of imposing conversational goals/keywords on open-domain conversational agents, where the agent is required to lead the conversation to a target keyword smoothly and fast. Solving this problem enables the application of conversational agents in many real-world scenarios, e.g., recommendation and psychotherapy. The dominant paradigm for tackling this problem is to 1) train a next-turn keyword classifier, and 2) train a keyword-augmented response retrieval model. However, existing approaches in this paradigm have two limitations: 1) the training and evaluation datasets for next-turn keyword classification are directly extracted from conversations without human annotations, thus, they are noisy and have low correlation with human judgements, and 2) during keyword transition, the agents solely rely on the similarities between word embeddings to move closer to the target keyword, which may not reflect how humans converse. In this paper, we assume that human conversations are grounded on commonsense and propose a keyword-guided neural conversational model that can leverage external commonsense knowledge graphs (CKG) for both keyword transition and response retrieval. Automatic evaluations suggest that commonsense improves the performance of both next-turn keyword prediction and keyword-augmented response retrieval. In addition, both self-play and human evaluations show that our model produces responses with smoother keyword transition and reaches the target keyword faster than competitive baselines.

The contributions of model complexity, data volume, and feature modalities to knowledge graph-based drug repurposing remain poorly quantified under rigorous temporal validation. We constructed a pharmacology knowledge graph from ChEMBL 36 comprising 5,348 entities including 3,127 drugs, 1,156 proteins, and 1,065 indications. A strict temporal split was enforced with training data up to 2022 and testing data from 2023 to 2025, together with biologically verified hard negatives mined from failed assays and clinical trials. We benchmarked five knowledge graph embedding models and a standard graph neural network with 3.44 million parameters that incorporates drug chemical structure using a graph attention encoder and ESM-2 protein embeddings. Scaling experiments ranging from 0.78 to 9.75 million parameters and from 25 to 100 percent of the data, together with feature ablation studies, were used to isolate the contributions of model capacity, graph density, and node feature modalities. Removing the graph attention based drug structure encoder and retaining only topological embeddings combined with ESM-2 protein features improved drug protein PR-AUC from 0.5631 to 0.5785 while reducing VRAM usage from 5.30 GB to 353 MB. Replacing the drug encoder with Morgan fingerprints further degraded performance, indicating that explicit chemical structure representations can be detrimental for predicting pharmacological network interactions. Increasing model size beyond 2.44 million parameters yielded diminishing returns, whereas increasing training data consistently improved performance. External validation confirmed 6 of the top 14 novel predictions as established therapeutic indications. These results show that drug pharmacological behavior can be accurately predicted using target-centric information and drug network topology alone, without requiring explicit chemical structure representations.

Large Language Models (LLMs) excel at code generation but struggle with complex problems. Retrieval-Augmented Generation (RAG) mitigates this issue by integrating external knowledge, yet retrieval models often miss relevant context, and generation models hallucinate with irrelevant data. We propose Programming Knowledge Graph (PKG) for semantic representation and fine-grained retrieval of code and text. Our approach enhances retrieval precision through tree pruning and mitigates hallucinations via a re-ranking mechanism that integrates non-RAG solutions. Structuring external data into finer-grained nodes improves retrieval granularity. Evaluations on HumanEval and MBPP show up to 20% pass@1 accuracy gains and a 34% improvement over baselines on MBPP. Our findings demonstrate that our proposed PKG approach along with re-ranker effectively address complex problems while maintaining minimal negative impact on solutions that are already correct without RAG. The replication package is published at https://github.com/iamshahd/ProgrammingKnowledgeGraph

The computer vision domain has greatly benefited from an abundance of data across many modalities to improve on various visual tasks. Recently, there has been a lot of focus on self-supervised pre-training methods through Masked Autoencoders (MAE) he2022masked,bachmann2022multimae, usually used as a first step before optimizing for a downstream task, such as classification or regression. This is very useful as it doesn't require any manually labeled data. In this work, we introduce Probabilistic Hyper-Graphs using Masked Autoencoders (PHG-MAE): a novel model that unifies the classical work on neural graphs leordeanu2021semi with the modern approach of masked autoencoders under a common theoretical framework. Through random masking of entire modalities, not just patches, the model samples from the distribution of hyper-edges on each forward pass. Additionally, the model adapts the standard MAE algorithm by combining pre-training and fine-tuning into a single training loop. Moreover, our approach enables the creation of inference-time ensembles which, through aggregation, boost the final prediction performance and consistency. Lastly, we show that we can apply knowledge distillation on top of the ensembles with little loss in performance, even with models that have fewer than 1M parameters. While our work mostly focuses on outdoor UAV scenes that contain multiple world interpretations and modalities, the same steps can be followed in other similar domains, such as autonomous driving or indoor robotics. In order to streamline the process of integrating external pre-trained experts for computer vision multi-modal multi-task learning (MTL) scenarios, we developed a data-pipeline software. Using this tool, we have created and released a fully-automated extension of the Dronescapes dataset. All the technical details, code and reproduction steps are publicly released.

The 7-point checklist (7PCL) is a widely used diagnostic tool in dermoscopy for identifying malignant melanoma by assigning point values to seven specific attributes. However, the traditional 7PCL is limited to distinguishing between malignant melanoma and melanocytic Nevi, and falls short in scenarios where multiple skin diseases with appearances similar to melanoma coexist. To address this limitation, we propose a novel diagnostic framework that integrates a clinical knowledge-based topological graph (CKTG) with a gradient diagnostic strategy featuring a data-driven weighting system (GD-DDW). The CKTG captures both the internal and external relationships among the 7PCL attributes, while the GD-DDW emulates dermatologists' diagnostic processes, prioritizing visual observation before making predictions. Additionally, we introduce a multimodal feature extraction approach leveraging a dual-attention mechanism to enhance feature extraction through cross-modal interaction and unimodal collaboration. This method incorporates meta-information to uncover interactions between clinical data and image features, ensuring more accurate and robust predictions. Our approach, evaluated on the EDRA dataset, achieved an average AUC of 88.6%, demonstrating superior performance in melanoma detection and feature prediction. This integrated system provides data-driven benchmarks for clinicians, significantly enhancing the precision of melanoma diagnosis.

Digital Twins are digital representations of systems in the Internet of Things (IoT) that are often based on AI models that are trained on data from those systems. Semantic models are used increasingly to link these datasets from different stages of the IoT systems life-cycle together and to automatically configure the AI modelling pipelines. This combination of semantic models with AI pipelines running on external datasets raises unique challenges particular if rolled out at scale. Within this paper we will discuss the unique requirements of applying semantic graphs to automate Digital Twins in different practical use cases. We will introduce the benchmark dataset DTBM that reflects these characteristics and look into the scaling challenges of different knowledge graph technologies. Based on these insights we will propose a reference architecture that is in-use in multiple products in IBM and derive lessons learned for scaling knowledge graphs for configuring AI models for Digital Twins.

Knowledge is inherently time-sensitive and continuously evolves over time. Although current Retrieval-Augmented Generation (RAG) systems enrich LLMs with external knowledge, they largely ignore this temporal nature. This raises two challenges for RAG. First, current RAG methods lack effective time-aware representations. Same facts of different time are difficult to distinguish with vector embeddings or conventional knowledge graphs. Second, most RAG evaluations assume a static corpus, leaving a blind spot regarding update costs and retrieval stability as knowledge evolves. To make RAG time-aware, we propose Temporal GraphRAG (TG-RAG), which models external corpora as a bi-level temporal graph consisting of a temporal knowledge graph with timestamped relations and a hierarchical time graph. Multi-granularity temporal summaries are generated for each time node to capture both key events and broader trends at that time. The design supports incremental updates by extracting new temporal facts from the incoming corpus and merging them into the existing graph. The temporal graph explicitly represents identical facts at different times as distinct edges to avoid ambiguity, and the time hierarchy graph allows only generating reports for new leaf time nodes and their ancestors, ensuring effective and efficient updates. During inference, TG-RAG dynamically retrieves a subgraph within the temporal and semantic scope of the query, enabling precise evidence gathering. Moreover, we introduce ECT-QA, a time-sensitive question-answering dataset featuring both specific and abstract queries, along with a comprehensive evaluation protocol designed to assess incremental update capabilities of RAG systems. Extensive experiments show that TG-RAG significantly outperforms existing baselines, demonstrating the effectiveness of our method in handling temporal knowledge and incremental updates.

Large language models (LLMs), such as ChatGPT and GPT4, are making new waves in the field of natural language processing and artificial intelligence, due to their emergent ability and generalizability. However, LLMs are black-box models, which often fall short of capturing and accessing factual knowledge. In contrast, Knowledge Graphs (KGs), Wikipedia and Huapu for example, are structured knowledge models that explicitly store rich factual knowledge. KGs can enhance LLMs by providing external knowledge for inference and interpretability. Meanwhile, KGs are difficult to construct and evolving by nature, which challenges the existing methods in KGs to generate new facts and represent unseen knowledge. Therefore, it is complementary to unify LLMs and KGs together and simultaneously leverage their advantages. In this article, we present a forward-looking roadmap for the unification of LLMs and KGs. Our roadmap consists of three general frameworks, namely, 1) KG-enhanced LLMs, which incorporate KGs during the pre-training and inference phases of LLMs, or for the purpose of enhancing understanding of the knowledge learned by LLMs; 2) LLM-augmented KGs, that leverage LLMs for different KG tasks such as embedding, completion, construction, graph-to-text generation, and question answering; and 3) Synergized LLMs + KGs, in which LLMs and KGs play equal roles and work in a mutually beneficial way to enhance both LLMs and KGs for bidirectional reasoning driven by both data and knowledge. We review and summarize existing efforts within these three frameworks in our roadmap and pinpoint their future research directions.

Many machine learning tasks can benefit from external knowledge. Large knowledge graphs store such knowledge, and embedding methods can be used to distill it into ready-to-use vector representations for downstream applications. For this purpose, current models have however two limitations: they are primarily optimized for link prediction, via local contrastive learning, and they struggle to scale to the largest graphs due to GPU memory limits. To address these, we introduce SEPAL: a Scalable Embedding Propagation ALgorithm for large knowledge graphs designed to produce high-quality embeddings for downstream tasks at scale. The key idea of SEPAL is to enforce global embedding alignment by optimizing embeddings only on a small core of entities, and then propagating them to the rest of the graph via message passing. We evaluate SEPAL on 7 large-scale knowledge graphs and 46 downstream machine learning tasks. Our results show that SEPAL significantly outperforms previous methods on downstream tasks. In addition, SEPAL scales up its base embedding model, enabling fitting huge knowledge graphs on commodity hardware.

Retrieval-augmented generation (RAG) is critical for reducing hallucinations and incorporating external knowledge into Large Language Models (LLMs). However, advanced RAG systems face a trade-off between performance and efficiency. Multi-round RAG approaches achieve strong reasoning but incur excessive LLM calls and token costs, while Graph RAG methods suffer from computationally expensive, error-prone graph construction and retrieval redundancy. To address these challenges, we propose T^2RAG, a novel framework that operates on a simple, graph-free knowledge base of atomic triplets. T^2RAG leverages an LLM to decompose questions into searchable triplets with placeholders, which it then iteratively resolves by retrieving evidence from the triplet database. Empirical results show that T^2RAG significantly outperforms state-of-the-art multi-round and Graph RAG methods, achieving an average performance gain of up to 11\% across six datasets while reducing retrieval costs by up to 45\%. Our code is available at https://github.com/rockcor/T2RAG

Recent advances in search-augmented large reasoning models (LRMs) enable the retrieval of external knowledge to reduce hallucinations in multistep reasoning. However, their ability to operate on graph-structured data, prevalent in domains such as e-commerce, social networks, and scientific citations, remains underexplored. Unlike plain text corpora, graphs encode rich topological signals that connect related entities and can serve as valuable priors for retrieval, enabling more targeted search and improved reasoning efficiency. Yet, effectively leveraging such structure poses unique challenges, including the difficulty of generating graph-expressive queries and ensuring reliable retrieval that balances structural and semantic relevance. To address this gap, we introduce GraphSearch, the first framework that extends search-augmented reasoning to graph learning, enabling zero-shot graph learning without task-specific fine-tuning. GraphSearch combines a Graph-aware Query Planner, which disentangles search space (e.g., 1-hop, multi-hop, or global neighbors) from semantic queries, with a Graph-aware Retriever, which constructs candidate sets based on topology and ranks them using a hybrid scoring function. We further instantiate two traversal modes: GraphSearch-R, which recursively expands neighborhoods hop by hop, and GraphSearch-F, which flexibly retrieves across local and global neighborhoods without hop constraints. Extensive experiments across diverse benchmarks show that GraphSearch achieves competitive or even superior performance compared to supervised graph learning methods, setting state-of-the-art results in zero-shot node classification and link prediction. These findings position GraphSearch as a flexible and generalizable paradigm for agentic reasoning over graphs.

Large Language Models (LLMs) have significantly advanced medical question-answering by leveraging extensive clinical data and medical literature. However, the rapid evolution of medical knowledge and the labor-intensive process of manually updating domain-specific resources pose challenges to the reliability of these systems. To address this, we introduce Agentic Medical Graph-RAG (AMG-RAG), a comprehensive framework that automates the construction and continuous updating of medical knowledge graphs, integrates reasoning, and retrieves current external evidence, such as PubMed and WikiSearch. By dynamically linking new findings and complex medical concepts, AMG-RAG not only improves accuracy but also enhances interpretability in medical queries. Evaluations on the MEDQA and MEDMCQA benchmarks demonstrate the effectiveness of AMG-RAG, achieving an F1 score of 74.1 percent on MEDQA and an accuracy of 66.34 percent on MEDMCQA, outperforming both comparable models and those 10 to 100 times larger. Notably, these improvements are achieved without increasing computational overhead, highlighting the critical role of automated knowledge graph generation and external evidence retrieval in delivering up-to-date, trustworthy medical insights.

Recent advancements in large language models (LLMs) have enabled their use as agents for planning complex tasks. Existing methods typically rely on a thought-action-observation (TAO) process to enhance LLM performance, but these approaches are often constrained by the LLMs' limited knowledge of complex tasks. Retrieval-augmented generation (RAG) offers new opportunities by leveraging external databases to ground generation in retrieved information. In this paper, we identify two key challenges (enlargability and transferability) in applying RAG to task planning. We propose InstructRAG, a novel solution within a multi-agent meta-reinforcement learning framework, to address these challenges. InstructRAG includes a graph to organize past instruction paths (sequences of correct actions), an RL-Agent with Reinforcement Learning to expand graph coverage for enlargability, and an ML-Agent with Meta-Learning to improve task generalization for transferability. The two agents are trained end-to-end to optimize overall planning performance. Our experiments on four widely used task planning datasets demonstrate that InstructRAG significantly enhances performance and adapts efficiently to new tasks, achieving up to a 19.2% improvement over the best existing approach.

Large Language Models (LLMs) and Code-LLMs (CLLMs) have significantly improved code generation, but, they frequently face difficulties when dealing with challenging and complex problems. Retrieval-Augmented Generation (RAG) addresses this issue by retrieving and integrating external knowledge at the inference time. However, retrieval models often fail to find most relevant context, and generation models, with limited context capacity, can hallucinate when given irrelevant data. We present a novel framework that leverages a Programming Knowledge Graph (PKG) to semantically represent and retrieve code. This approach enables fine-grained code retrieval by focusing on the most relevant segments while reducing irrelevant context through a tree-pruning technique. PKG is coupled with a re-ranking mechanism to reduce even more hallucinations by selectively integrating non-RAG solutions. We propose two retrieval approaches-block-wise and function-wise-based on the PKG, optimizing context granularity. Evaluations on the HumanEval and MBPP benchmarks show our method improves pass@1 accuracy by up to 20%, and outperforms state-of-the-art models by up to 34% on MBPP. Our contributions include PKG-based retrieval, tree pruning to enhance retrieval precision, a re-ranking method for robust solution selection and a Fill-in-the-Middle (FIM) enhancer module for automatic code augmentation with relevant comments and docstrings.

Knowledge graphs (KGs) have the advantage of providing fine-grained detail for question-answering systems. Unfortunately, building a reliable KG is time-consuming and expensive as it requires human intervention. To overcome this issue, we propose a novel framework to automatically construct a KG from unstructured documents that does not require external alignment. We first extract surface-form knowledge tuples from unstructured documents and encode them with contextual information. Entities with similar context semantics are then linked through internal alignment to form a graph structure. This allows us to extract the desired information from multiple documents by traversing the generated KG without a manual process. We examine its performance in retrieval based QA systems by reformulating the WikiMovies and MetaQA datasets into a tuple-level retrieval task. The experimental results show that our method outperforms traditional retrieval methods by a large margin.

Current paradigms for code verification rely heavily on external mechanisms-such as execution-based unit tests or auxiliary LLM judges-which are often labor-intensive or limited by the judging model's own capabilities. This raises a fundamental, yet unexplored question: Can an LLM's functional correctness be assessed purely from its internal computational structure? Our primary objective is to investigate whether the model's neural dynamics encode internally decodable signals that are predictive of logical validity during code generation. Inspired by mechanistic interpretability, we propose to treat code verification as a mechanistic diagnostic task, mapping the model's explicit algorithmic trajectory into line-level attribution graphs. By decomposing complex residual flows, we aim to identify the structural signatures that distinguish sound reasoning from logical failure within the model's internal circuits. Analysis across Python, C++, and Java confirms that intrinsic correctness signals are robust across diverse syntaxes. Topological features from these internal graphs predict correctness more reliably than surface heuristics and enable targeted causal interventions to fix erroneous logic. These findings establish internal introspection as a decodable property for verifying generated code. Our code is at https:// github.com/bruno686/CodeCircuit.

Graph retrieval-augmented generation (GraphRAG) has emerged as a powerful paradigm for enhancing large language models (LLMs) with external knowledge. It leverages graphs to model the hierarchical structure between specific concepts, enabling more coherent and effective knowledge retrieval for accurate reasoning.Despite its conceptual promise, recent studies report that GraphRAG frequently underperforms vanilla RAG on many real-world tasks. This raises a critical question: Is GraphRAG really effective, and in which scenarios do graph structures provide measurable benefits for RAG systems? To address this, we propose GraphRAG-Bench, a comprehensive benchmark designed to evaluate GraphRAG models onboth hierarchical knowledge retrieval and deep contextual reasoning. GraphRAG-Bench features a comprehensive dataset with tasks of increasing difficulty, coveringfact retrieval, complex reasoning, contextual summarization, and creative generation, and a systematic evaluation across the entire pipeline, from graph constructionand knowledge retrieval to final generation. Leveraging this novel benchmark, we systematically investigate the conditions when GraphRAG surpasses traditional RAG and the underlying reasons for its success, offering guidelines for its practical application. All related resources and analyses are collected for the community at https://github.com/GraphRAG-Bench/GraphRAG-Benchmark.

Large language models (LLMs), such as ChatGPT and GPT-4, are versatile and can solve different tasks due to their emergent ability and generalizability. However, LLMs sometimes lack domain-specific knowledge to perform tasks, which would also cause hallucination during inference. In some previous works, additional modules like graph neural networks (GNNs) are trained on retrieved knowledge from external knowledge bases, aiming to mitigate the problem of lacking domain-specific knowledge. However, incorporating additional modules: 1) would need retraining additional modules when encountering novel domains; 2) would become a bottleneck since LLMs' strong abilities are not fully utilized for retrieval. In this paper, we propose a paradigm, termed Knowledge Solver (KSL), to teach LLMs to search for essential knowledge from external knowledge bases by harnessing their own strong generalizability. Specifically, we design a simple yet effective prompt to transform retrieval into a multi-hop decision sequence, which empowers LLMs with searching knowledge ability in zero-shot manner. Additionally, KSL is able to provide complete retrieval paths and therefore increase explainability of LLMs' reasoning processes. We conduct experiments on three datasets: CommonsenseQA, OpenbookQA, and MedQA-USMLE, and found that our approach improves LLM baseline performance by a relatively large margin.

Retrieval-augmented generation (RAG) has shown some success in augmenting large language models (LLMs) with external knowledge. However, as a non-parametric knowledge integration paradigm for LLMs, RAG methods heavily rely on external retrieval modules and the retrieved textual context prior. Especially for very large scale knowledge augmentation, they would introduce substantial inference latency due to expensive searches and much longer relevant context. In this paper, we propose a parametric knowledge integration method, called AtlasKV, a scalable, effective, and general way to augment LLMs with billion-scale knowledge graphs (KGs) (e.g. 1B triples) using very little GPU memory cost (e.g. less than 20GB VRAM). In AtlasKV, we introduce KG2KV and HiKVP to integrate KG triples into LLMs at scale with sub-linear time and memory complexity. It maintains strong knowledge grounding and generalization performance using the LLMs' inherent attention mechanism, and requires no external retrievers, long context priors, or retraining when adapting to new knowledge.

Recent advancements in large language models (LLMs) have shown impressive versatility across various tasks. To eliminate its hallucinations, retrieval-augmented generation (RAG) has emerged as a powerful approach, leveraging external knowledge sources like knowledge graphs (KGs). In this paper, we study the task of KG-driven RAG and propose a novel Similar Graph Enhanced Retrieval-Augmented Generation (SimGRAG) method. It effectively addresses the challenge of aligning query texts and KG structures through a two-stage process: (1) query-to-pattern, which uses an LLM to transform queries into a desired graph pattern, and (2) pattern-to-subgraph, which quantifies the alignment between the pattern and candidate subgraphs using a graph semantic distance (GSD) metric. We also develop an optimized retrieval algorithm that efficiently identifies the top-k subgraphs within 1-second latency on a 10-million-scale KG. Extensive experiments show that SimGRAG outperforms state-of-the-art KG-driven RAG methods in both question answering and fact verification, offering superior plug-and-play usability and scalability.

Large language models (LLMs), while exhibiting exceptional performance, suffer from hallucinations, especially on knowledge-intensive tasks. Existing works propose to augment LLMs with individual text units retrieved from external knowledge corpora to alleviate the issue. However, in many domains, texts are interconnected (e.g., academic papers in a bibliographic graph are linked by citations and co-authorships) which form a (text-attributed) graph. The knowledge in such graphs is encoded not only in single texts/nodes but also in their associated connections. To facilitate the research of augmenting LLMs with graphs, we manually construct a Graph Reasoning Benchmark dataset called GRBench, containing 1,740 questions that can be answered with the knowledge from 10 domain graphs. Then, we propose a simple and effective framework called Graph Chain-of-thought (Graph-CoT) to augment LLMs with graphs by encouraging LLMs to reason on the graph iteratively. Each Graph-CoT iteration consists of three sub-steps: LLM reasoning, LLM-graph interaction, and graph execution. We conduct systematic experiments with three LLM backbones on GRBench, where Graph-CoT outperforms the baselines consistently. The code is available at https://github.com/PeterGriffinJin/Graph-CoT.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

Improving the performance of large language models (LLMs) in complex question-answering (QA) scenarios has always been a research focal point. Recent studies have attempted to enhance LLMs' performance by combining step-wise planning with external retrieval. While effective for advanced models like GPT-3.5, smaller LLMs face challenges in decomposing complex questions, necessitating supervised fine-tuning. Previous work has relied on manual annotation and knowledge distillation from teacher LLMs, which are time-consuming and not accurate enough. In this paper, we introduce a novel framework for enhancing LLMs' planning capabilities by using planning data derived from knowledge graphs (KGs). LLMs fine-tuned with this data have improved planning capabilities, better equipping them to handle complex QA tasks that involve retrieval. Evaluations on multiple datasets, including our newly proposed benchmark, highlight the effectiveness of our framework and the benefits of KG-derived planning data.

Tabular data in knowledge-rich domains often carries a latent prior in the form of Boolean implication relationships (BIRs) between pairs of features. We mine such relationships with a sparse-exception binomial test. The mined implications form a typed directed graph, equivalent to a propositional rule base of 2-literal clauses. We encode this graph as the connectivity of a layered neural network, called BIRDNet, in which each hidden unit corresponds to one mined rule and binds only to its two features. We show two consequences of this design: First, the architecture is sparse by construction: at most 2/d of the weights in each BIR layer are active, where d is the input dimension. Second, the model is interpretable: every trained unit keeps a stable symbolic identity, so rules can be read off the network without surrogate models. Unlike most neurosymbolic models, BIRDNet does not consume an external rule base; its structural prior is mined from the data. We evaluate BIRDNet on six transcriptomic and proteomic benchmarks. Our results show that BIRDNet stays within 0.02 AUROC of the strongest dense baseline, at a small accuracy cost, while using up to 96times fewer active parameters than an architecture-matched dense MLP. First-layer rules recover known biological signatures across multiple cancer subtypes and tissue types, including canonical amplicons, lineage-defining co-expression modules, and immune-infiltration markers. Data and code are available at: https://github.com/MAHI-Group/BIRDNet.

Retrieval-Augmented Generation (RAG) and Graph-based RAG has become the important paradigm for enhancing Large Language Models (LLMs) with external knowledge. However, existing approaches face a fundamental trade-off. While graph-based methods are inherently dependent on high-quality graph structures, they face significant practical constraints: manually constructed knowledge graphs are prohibitively expensive to scale, while automatically extracted graphs from corpora are limited by the performance of the underlying LLM extractors, especially when using smaller, local-deployed models. This paper presents Think-on-Graph 3.0 (ToG-3), a novel framework that introduces Multi-Agent Context Evolution and Retrieval (MACER) mechanism to overcome these limitations. Our core innovation is the dynamic construction and refinement of a Chunk-Triplets-Community heterogeneous graph index, which pioneeringly incorporates a dual-evolution mechanism of Evolving Query and Evolving Sub-Graph for precise evidence retrieval. This approach addresses a critical limitation of prior Graph-based RAG methods, which typically construct a static graph index in a single pass without adapting to the actual query. A multi-agent system, comprising Constructor, Retriever, Reflector, and Responser agents, collaboratively engages in an iterative process of evidence retrieval, answer generation, sufficiency reflection, and, crucially, evolving query and subgraph. This dual-evolving multi-agent system allows ToG-3 to adaptively build a targeted graph index during reasoning, mitigating the inherent drawbacks of static, one-time graph construction and enabling deep, precise reasoning even with lightweight LLMs. Extensive experiments demonstrate that ToG-3 outperforms compared baselines on both deep and broad reasoning benchmarks, and ablation studies confirm the efficacy of the components of MACER framework.

As multimodal LLM-driven agents continue to advance in autonomy and generalization, evaluation based on static datasets can no longer adequately assess their true capabilities in dynamic environments and diverse tasks. Existing LLM-based synthetic data methods are largely designed for LLM training and evaluation, and thus cannot be directly applied to agent tasks that require tool use and interactive capabilities. While recent studies have explored automatic agent task generation with LLMs, most efforts remain limited to text or image analysis, without systematically modeling multi-step interactions in web environments. To address these challenges, we propose Graph2Eval, a knowledge graph-based framework that automatically generates both multimodal document comprehension tasks and web interaction tasks, enabling comprehensive evaluation of agents' reasoning, collaboration, and interactive capabilities. In our approach, knowledge graphs constructed from multi-source external data serve as the task space, where we translate semantic relations into structured multimodal tasks using subgraph sampling, task templates, and meta-paths. A multi-stage filtering pipeline based on node reachability, LLM scoring, and similarity analysis is applied to guarantee the quality and executability of the generated tasks. Furthermore, Graph2Eval supports end-to-end evaluation of multiple agent types (Single-Agent, Multi-Agent, Web Agent) and measures reasoning, collaboration, and interaction capabilities. We instantiate the framework with Graph2Eval-Bench, a curated dataset of 1,319 tasks spanning document comprehension and web interaction scenarios. Experiments show that Graph2Eval efficiently generates tasks that differentiate agent and model performance, revealing gaps in reasoning, collaboration, and web interaction across different settings and offering a new perspective for agent evaluation.

LLMs and AI chatbots have improved people's efficiency in various fields. However, the necessary knowledge for answering the question may be beyond the models' knowledge boundaries. To mitigate this issue, many researchers try to introduce external knowledge, such as knowledge graphs and Internet contents, into LLMs for up-to-date information. However, the external information from the Internet may include counterfactual information that will confuse the model and lead to an incorrect response. Thus there is a pressing need for LLMs to possess the ability to distinguish reliable information from external knowledge. Therefore, to evaluate the ability of LLMs to discern the reliability of external knowledge, we create a benchmark from existing knowledge bases. Our benchmark consists of two tasks, Question Answering and Text Generation, and for each task, we provide models with a context containing counterfactual information. Evaluation results show that existing LLMs are susceptible to interference from unreliable external knowledge with counterfactual information, and simple intervention methods make limited contributions to the alleviation of this issue.

Large language model (LLM)-based agents have demonstrated strong capabilities in complex reasoning and problem solving through multi-step interactions, yet most deployed agents remain behaviorally static, with knowledge acquired during execution rarely translating into systematic improvement over time. In response, a growing line of work on self-evolving agents explores how agents can improve through experience during deployment, but most existing approaches either rely on ad hoc reflection limited to single-task correction or adopt unstructured memory that accumulates fragmented experience with delayed usability. To address this limitation, we introduce EXG, an experience graph framework for self-evolving agents that explicitly organizes accumulated successes and failures into a structured, relational representation. EXG is the first experience graph designed for self-evolving agents, supporting both online, real-time graph growth during execution for immediate cross-task experience reuse, and offline reuse of a consolidated experience graph as an external memory module. This design also enables EXG to serve as a plug-and-play component for existing self-evolving agents, organizing prior experience into a unified experience graph and improving both solution quality and resource efficiency as deployment progresses. Extensive experiments across code generation and reasoning benchmarks show that EXG attains more favorable performance-efficiency trade-offs than reflection- and memory-based baselines in both online and offline evaluations. Our results suggest that structuring experience as a graph provides a principled foundation for scalable and transferable self-evolving agent behavior.

Large language models (LLMs) show promise in medical diagnosis, but real-world deployment remains challenging due to high-stakes clinical decisions and imperfect reasoning reliability. As a result, careful inspection of model behavior is essential for assessing whether diagnostic reasoning is reliable and clinically grounded. However, debugging medical LLMs remains difficult. First, developers often lack sufficient medical domain expertise to interpret model errors in clinically meaningful terms. Second, models can fail across a large and diverse set of instances involving different input types, tasks, and reasoning steps, making it challenging for developers to prioritize which errors deserve focused inspection. Third, developers struggle to identify recurring error patterns across cases, as existing debugging practices are largely instance-centric and rely on manual inspection of isolated failures. To address these challenges, we present VeriLLMed, a visual analytics system that integrates external biomedical knowledge to audit and debug medical LLM diagnostic reasoning. VeriLLMed transforms model outputs into comparable reasoning paths, constructs knowledge graph-grounded reference paths, and identifies three recurring classes of diagnosis errors: relation errors, branch errors, and missing errors. Case studies and expert evaluation demonstrate that VeriLLMed helps developers identify clinically implausible reasoning and generate actionable insights that can inform the improvement of medical LLMs.

Recent advancements have highlighted that Large Language Models (LLMs) are prone to hallucinations when solving complex reasoning problems, leading to erroneous results. To tackle this issue, researchers incorporate Knowledge Graphs (KGs) to improve the reasoning ability of LLMs. However, existing methods face two limitations: 1) they typically assume that all answers to the questions are contained in KGs, neglecting the incompleteness issue of KGs, and 2) they treat the KG as a static repository and overlook the implicit logical reasoning structures inherent in KGs. In this paper, we introduce SymAgent, an innovative neural-symbolic agent framework that achieves collaborative augmentation between KGs and LLMs. We conceptualize KGs as dynamic environments and transform complex reasoning tasks into a multi-step interactive process, enabling KGs to participate deeply in the reasoning process. SymAgent consists of two modules: Agent-Planner and Agent-Executor. The Agent-Planner leverages LLM's inductive reasoning capability to extract symbolic rules from KGs, guiding efficient question decomposition. The Agent-Executor autonomously invokes predefined action tools to integrate information from KGs and external documents, addressing the issues of KG incompleteness. Furthermore, we design a self-learning framework comprising online exploration and offline iterative policy updating phases, enabling the agent to automatically synthesize reasoning trajectories and improve performance. Experimental results demonstrate that SymAgent with weak LLM backbones (i.e., 7B series) yields better or comparable performance compared to various strong baselines. Further analysis reveals that our agent can identify missing triples, facilitating automatic KG updates.

The extraction of aspect terms is a critical step in fine-grained sentiment analysis of text. Existing approaches for this task have yielded impressive results when the training and testing data are from the same domain. However, these methods show a drastic decrease in performance when applied to cross-domain settings where the domain of the testing data differs from that of the training data. To address this lack of extensibility and robustness, we propose a novel approach for automatically constructing domain-specific knowledge graphs that contain information relevant to the identification of aspect terms. We introduce a methodology for injecting information from these knowledge graphs into Transformer models, including two alternative mechanisms for knowledge insertion: via query enrichment and via manipulation of attention patterns. We demonstrate state-of-the-art performance on benchmark datasets for cross-domain aspect term extraction using our approach and investigate how the amount of external knowledge available to the Transformer impacts model performance.

Large Language Models (LLMs) are often challenged by generating erroneous or hallucinated responses, especially in complex reasoning tasks. Leveraging Knowledge Graphs (KGs) as external knowledge sources has emerged as a viable solution. However, existing KG-enhanced methods, either retrieval-based or agent-based, encounter difficulties in accurately retrieving knowledge and efficiently traversing KGs at scale. In this paper, we propose a unified framework, FiDeLiS, designed to improve the factuality of LLM responses by anchoring answers to verifiable reasoning steps retrieved from KGs. To achieve this, we leverage step-wise beam search with a deductive scoring function, allowing the LLM to validate reasoning process step by step, and halt the search once the question is deducible. In addition, we propose a Path-RAG module to pre-select a smaller candidate set for each beam search step, reducing computational costs by narrowing the search space. Extensive experiments show that our method, as a training-free framework, not only improve the performance but also enhance the factuality and interpretability across different benchmarks. Code is released at https://github.com/Y-Sui/FiDeLiS.

Retrieval-Augmented Generation (RAG) has become a powerful and widely used approach for improving large language models by grounding generation in retrieved evidence. However, RAG systems still produce incorrect answers in many cases. Why RAG fails despite having access to external information remains poorly understood. We present a model-internal study of retrieval-augmented generation that examines how retrieved evidence influences answer generation. Using circuit tracing, we construct attribution graphs that model the flow of information through transformer layers during decoding. These graphs represent interactions among retrieved context, intermediate model activations, and generated tokens, providing a graph, circuit-level view of how external evidence is integrated into the model's reasoning process across multiple question answering benchmarks, we observe consistent structural differences: correct predictions exhibit deeper reasoning paths, more distributed evidence flow, and a more structured pattern of local connectivity, while failed predictions show shallower, fragmented, and overly concentrated evidence flow. Building on these findings, we develop a graph-based error detection framework that uses attribution-graph topology features. Furthermore, we show that attribution graphs enable targeted interventions. By reinforcing question-constrained evidence grounding, we reshape internal routing so that answer generation remains guided by the question, leading to more effective integration of retrieved information and fewer errors.

Large language models (LLMs) continue to struggle with knowledge-intensive questions that require up-to-date information and multi-hop reasoning. Augmenting LLMs with hybrid external knowledge, such as unstructured text and structured knowledge graphs, offers a promising alternative to costly continual pretraining. As such, reliable evaluation of their retrieval and reasoning capabilities becomes critical. However, many existing benchmarks increasingly overlap with LLM pretraining data, which means answers or supporting knowledge may already be encoded in model parameters, making it difficult to distinguish genuine retrieval and reasoning from parametric recall. We introduce HybridRAG-Bench, a framework for constructing benchmarks to evaluate retrieval-intensive, multi-hop reasoning over hybrid knowledge. HybridRAG-Bench automatically couples unstructured text and structured knowledge graph representations derived from recent scientific literature on arXiv, and generates knowledge-intensive question-answer pairs grounded in explicit reasoning paths. The framework supports flexible domain and time-frame selection, enabling contamination-aware and customizable evaluation as models and knowledge evolve. Experiments across three domains (artificial intelligence, governance and policy, and bioinformatics) demonstrate that HybridRAG-Bench rewards genuine retrieval and reasoning rather than parametric recall, offering a principled testbed for evaluating hybrid knowledge-augmented reasoning systems. We release our code and data at github.com/junhongmit/HybridRAG-Bench.

Hallucination mitigation remains a persistent challenge for large language models (LLMs), even as model scales grow. Existing approaches often rely on external knowledge sources, such as structured databases or knowledge graphs, accessed through prompting or retrieval. However, prompt-based grounding is fragile and domain-sensitive, while symbolic knowledge integration incurs heavy retrieval and formatting costs. Motivated by knowledge graphs, we introduce Graph-Retrieved Adaptive Decoding (GRAD), a decoding-time method that grounds generation in corpus-derived evidence without retraining. GRAD constructs a sparse token transition graph by accumulating next-token logits across a small retrieved corpus in a single forward pass. During decoding, graph-retrieved logits are max-normalized and adaptively fused with model logits to favor high-evidence continuations while preserving fluency. Across three models and a range of question-answering benchmarks spanning intrinsic, extrinsic hallucination, and factuality tasks, GRAD consistently surpasses baselines, achieving up to 9.7% higher intrinsic accuracy, 8.6% lower hallucination rates, and 6.9% greater correctness compared to greedy decoding, while attaining the highest truth--informativeness product score among all methods. GRAD offers a lightweight, plug-and-play alternative to contrastive decoding and knowledge graph augmentation, demonstrating that statistical evidence from corpus-level token transitions can effectively steer generation toward more truthful and verifiable outputs.

Clinical natural language processing requires methods that can address domain-specific challenges, such as complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation using LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 7 clinical NLP tasks and 16 datasets reveals that ClinGen consistently enhances performance across various tasks, effectively aligning the distribution of real datasets and significantly enriching the diversity of generated training instances. We will publish our code and all the generated data in https://github.com/ritaranx/ClinGen.

Conversational recommendation systems (CRS) aim to recommend suitable items to users through natural language conversation. However, most CRS approaches do not effectively utilize the signal provided by these conversations. They rely heavily on explicit external knowledge e.g., knowledge graphs to augment the models' understanding of the items and attributes, which is quite hard to scale. To alleviate this, we propose an alternative information retrieval (IR)-styled approach to the CRS item recommendation task, where we represent conversations as queries and items as documents to be retrieved. We expand the document representation used for retrieval with conversations from the training set. With a simple BM25-based retriever, we show that our task formulation compares favorably with much more complex baselines using complex external knowledge on a popular CRS benchmark. We demonstrate further improvements using user-centric modeling and data augmentation to counter the cold start problem for CRSs.

Large Language Models (LLMs) often struggle with producing factually consistent answers due to limitations in their parametric memory. Retrieval-Augmented Generation (RAG) paradigms mitigate this issue by incorporating external knowledge at inference time. However, such methods typically handle knowledge as unstructured text, which reduces retrieval accuracy, hinders compositional reasoning, and amplifies the influence of irrelevant information on the factual consistency of LLM outputs. To overcome these limitations, we propose a novel framework that dynamically constructs and expands knowledge graphs (KGs) during inference, integrating both internal knowledge extracted from LLMs and external knowledge retrieved from external sources. Our method begins by extracting a seed KG from the question via prompting, followed by iterative expansion using the LLM's internal knowledge. The KG is then selectively refined through external retrieval, enhancing factual coverage and correcting inaccuracies. We evaluate our approach on three diverse Factual QA benchmarks, demonstrating consistent gains in factual accuracy over baselines. Our findings reveal that inference-time KG construction is a promising direction for enhancing LLM factuality in a structured, interpretable, and scalable manner.

Large Language Models (LLMs) are proficient at generating coherent and contextually relevant text but face challenges when addressing knowledge-intensive queries in domain-specific and factual question-answering tasks. Retrieval-augmented generation (RAG) systems mitigate this by incorporating external knowledge sources, such as structured knowledge graphs (KGs). However, LLMs often struggle to produce accurate answers despite access to KG-extracted information containing necessary facts. Our study investigates this dilemma by analyzing error patterns in existing KG-based RAG methods and identifying eight critical failure points. We observed that these errors predominantly occur due to insufficient focus on discerning the question's intent and adequately gathering relevant context from the knowledge graph facts. Drawing on this analysis, we propose the Mindful-RAG approach, a framework designed for intent-based and contextually aligned knowledge retrieval. This method explicitly targets the identified failures and offers improvements in the correctness and relevance of responses provided by LLMs, representing a significant step forward from existing methods.

Large Language Models (LLMs) have recently demonstrated remarkable reasoning abilities, yet hallucinate on knowledge-intensive tasks. Retrieval-augmented generation (RAG) mitigates this issue by grounding answers in external sources, e.g., knowledge graphs (KGs). However, existing KG-based RAG approaches rely on semantics-unaware path sampling and are weakly aligned with KG reasoning objectives, which limits further accuracy gains. They also feed retrieved paths directly into the reasoner without organizing them into answer-centered reasoning paths, hindering small LLMs' ability to leverage the retrieved knowledge. Furthermore, prior works predominantly rely on large LLMs (e.g., ChatGPT/GPT-4) or assume backbones above 7B parameters, leaving sub-7B models underexplored. We address this gap with RPO-RAG, the first KG-based RAG framework specifically designed for small LLMs, to the best of our knowledge. RPO-RAG introduces three key innovations: (1) a query-path semantic sampling strategy that provides informative supervisory signals; (2) a relation-aware preference optimization that aligns training with intermediate KG reasoning signals (e.g., relation); and (3) an answer-centered prompt design that organizes entities and reasoning paths in an interpretable format. Extensive experiments on two benchmark Knowledge Graph Question Answering (KGQA) datasets, WebQSP and CWQ, demonstrate that RPO-RAG effectively bridges the performance gap between small and large language models. On WebQSP, it improves F1 by up to 8.8%, reflecting enhanced answer precision, while on CWQ it achieves new state-of-the-art results among models under 8B parameters in both Hit and F1. Overall, RPO-RAG substantially improves the reasoning capability of small LLMs, even under 3B parameters-highlighting their potential for resource-efficient and practical on-device KGQA applications.

Graph Retrieval-Augmented Generation (GraphRAG) has emerged as a promising paradigm that organizes external knowledge into structured graphs of entities and relations, enabling large language models (LLMs) to perform complex reasoning beyond text-chunk retrieval. Recent advances have integrated reinforcement learning (RL) into agentic GraphRAG approaches, enabling iterative interactions with knowledge graphs during training. However, existing RL-based methods suffer from two key limitations: (1) they primarily depend on semantic similarity for retrieval, often overlooking the underlying graph topology, and (2) they rely on sparse, outcome-level rewards that fail to capture the quality of intermediate retrieval steps and their dependencies. To address these limitations, we propose HyperGraphPro, a progress-aware agentic framework for graph-based retrieval and multi-step reasoning. HyperGraphPro introduces a structure-aware hypergraph retrieval mechanism that jointly considers semantic relevance and graph connectivity, promoting coherent traversal along multi-hop reasoning paths. Furthermore, we design a progress-based stepwise policy optimization that provides dense learning signals by modulating advantages according to intermediate reasoning progress within a graph, rather than relying solely on final outcomes. Experiments on multi-hop question answering benchmarks demonstrate that HyperGraphPro consistently improves reasoning accuracy and generation quality over existing GraphRAG methods.

To understand a document with multiple events, event-event relation extraction (ERE) emerges as a crucial task, aiming to discern how natural events temporally or structurally associate with each other. To achieve this goal, our work addresses the problems of temporal event relation extraction (TRE) and subevent relation extraction (SRE). The latest methods for such problems have commonly built document-level event graphs for global reasoning across sentences. However, the edges between events are usually derived from external tools heuristically, which are not always reliable and may introduce noise. Moreover, they are not capable of preserving logical constraints among event relations, e.g., coreference constraint, symmetry constraint and conjunction constraint. These constraints guarantee coherence between different relation types,enabling the generation of a uniffed event evolution graph. In this work, we propose a novel method named LogicERE, which performs high-order event relation reasoning through modeling logic constraints. Speciffcally, different from conventional event graphs, we design a logic constraint induced graph (LCG) without any external tools. LCG involves event nodes where the interactions among them can model the coreference constraint, and event pairs nodes where the interactions among them can retain the symmetry constraint and conjunction constraint. Then we perform high-order reasoning on LCG with relational graph transformer to obtain enhanced event and event pair embeddings. Finally, we further incorporate logic constraint information via a joint logic learning module. Extensive experiments demonstrate the effectiveness of the proposed method with state-of-the-art performance on benchmark datasets.

Unsupervised commonsense reasoning (UCR) is becoming increasingly popular as the construction of commonsense reasoning datasets is expensive, and they are inevitably limited in their scope. A popular approach to UCR is to fine-tune language models with external knowledge (e.g., knowledge graphs), but this usually requires a large number of training examples. In this paper, we propose to transform the downstream multiple choice question answering task into a simpler binary classification task by ranking all candidate answers according to their reasonableness. To this end, for training the model, we convert the knowledge graph triples into reasonable and unreasonable texts. Extensive experimental results show the effectiveness of our approach on various multiple choice question answering benchmarks. Furthermore, compared with existing UCR approaches using KGs, ours is less data hungry. Our code is available at https://github.com/probe2/BUCA.

In this survey, we review methods that retrieve multimodal knowledge to assist and augment generative models. This group of works focuses on retrieving grounding contexts from external sources, including images, codes, tables, graphs, and audio. As multimodal learning and generative AI have become more and more impactful, such retrieval augmentation offers a promising solution to important concerns such as factuality, reasoning, interpretability, and robustness. We provide an in-depth review of retrieval-augmented generation in different modalities and discuss potential future directions. As this is an emerging field, we continue to add new papers and methods.

Text classification is an important and classical problem in natural language processing. There have been a number of studies that applied convolutional neural networks (convolution on regular grid, e.g., sequence) to classification. However, only a limited number of studies have explored the more flexible graph convolutional neural networks (convolution on non-grid, e.g., arbitrary graph) for the task. In this work, we propose to use graph convolutional networks for text classification. We build a single text graph for a corpus based on word co-occurrence and document word relations, then learn a Text Graph Convolutional Network (Text GCN) for the corpus. Our Text GCN is initialized with one-hot representation for word and document, it then jointly learns the embeddings for both words and documents, as supervised by the known class labels for documents. Our experimental results on multiple benchmark datasets demonstrate that a vanilla Text GCN without any external word embeddings or knowledge outperforms state-of-the-art methods for text classification. On the other hand, Text GCN also learns predictive word and document embeddings. In addition, experimental results show that the improvement of Text GCN over state-of-the-art comparison methods become more prominent as we lower the percentage of training data, suggesting the robustness of Text GCN to less training data in text classification.

Graph-based retrieval-augmented generation (RAG) enriches large language models (LLMs) with external knowledge for long-context understanding and multi-hop reasoning, but existing methods face a granularity dilemma: fine-grained entity-level graphs incur high token costs and lose context, while coarse document-level graphs fail to capture nuanced relations. We introduce QCG-RAG, a query-centric graph RAG framework that enables query-granular indexing and multi-hop chunk retrieval. Our query-centric approach leverages Doc2Query and Doc2Query{-}{-} to construct query-centric graphs with controllable granularity, improving graph quality and interpretability. A tailored multi-hop retrieval mechanism then selects relevant chunks via the generated queries. Experiments on LiHuaWorld and MultiHop-RAG show that QCG-RAG consistently outperforms prior chunk-based and graph-based RAG methods in question answering accuracy, establishing a new paradigm for multi-hop reasoning.

Retrieval-Augmented Generation (RAG) mitigates hallucination in Large Language Models (LLMs) by incorporating external data, with Knowledge Graphs (KGs) offering crucial information for question answering. Traditional Knowledge Graph Question Answering (KGQA) methods rely on semantic parsing, which typically retrieves knowledge strictly necessary for answer generation, thus often suffer from low coverage due to rigid schema requirements and semantic ambiguity. We present KERAG, a novel KG-based RAG pipeline that enhances QA coverage by retrieving a broader subgraph likely to contain relevant information. Our retrieval-filtering-summarization approach, combined with fine-tuned LLMs for Chain-of-Thought reasoning on knowledge sub-graphs, reduces noises and improves QA for both simple and complex questions. Experiments demonstrate that KERAG surpasses state-of-the-art solutions by about 7% in quality and exceeds GPT-4o (Tool) by 10-21%.

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.

Network embedding has been widely used in social recommendation and network analysis, such as recommendation systems and anomaly detection with graphs. However, most of previous approaches cannot handle large graphs efficiently, due to that (i) computation on graphs is often costly and (ii) the size of graph or the intermediate results of vectors could be prohibitively large, rendering it difficult to be processed on a single machine. In this paper, we propose an efficient and effective distributed algorithm for network embedding on large graphs using Apache Spark, which recursively partitions a graph into several small-sized subgraphs to capture the internal and external structural information of nodes, and then computes the network embedding for each subgraph in parallel. Finally, by aggregating the outputs on all subgraphs, we obtain the embeddings of nodes in a linear cost. After that, we demonstrate in various experiments that our proposed approach is able to handle graphs with billions of edges within a few hours and is at least 4 times faster than the state-of-the-art approaches. Besides, it achieves up to 4.25% and 4.27% improvements on link prediction and node classification tasks respectively. In the end, we deploy the proposed algorithms in two online games of Tencent with the applications of friend recommendation and item recommendation, which improve the competitors by up to 91.11% in running time and up to 12.80% in the corresponding evaluation metrics.

In this study, we introduced a new benchmark consisting of a curated dataset and a defined evaluation process to assess the compositional reasoning capabilities of large language models within the chemistry domain. We designed and validated a fully automated pipeline, verified by subject matter experts, to facilitate this task. Our approach integrates OpenAI reasoning models with named entity recognition (NER) systems to extract chemical entities from recent literature, which are then augmented with external knowledge bases to form a comprehensive knowledge graph. By generating multi-hop questions across these graphs, we assess LLM performance in both context-augmented and non-context augmented settings. Our experiments reveal that even state-of-the-art models face significant challenges in multi-hop compositional reasoning. The results reflect the importance of augmenting LLMs with document retrieval, which can have a substantial impact on improving their performance. However, even perfect retrieval accuracy with full context does not eliminate reasoning errors, underscoring the complexity of compositional reasoning. This work not only benchmarks and highlights the limitations of current LLMs but also presents a novel data generation pipeline capable of producing challenging reasoning datasets across various domains. Overall, this research advances our understanding of reasoning in computational linguistics.

To facilitate the research on intelligent and human-like chatbots with multi-modal context, we introduce a new video-based multi-modal dialogue dataset, called TikTalk. We collect 38K videos from a popular video-sharing platform, along with 367K conversations posted by users beneath them. Users engage in spontaneous conversations based on their multi-modal experiences from watching videos, which helps recreate real-world chitchat context. Compared to previous multi-modal dialogue datasets, the richer context types in TikTalk lead to more diverse conversations, but also increase the difficulty in capturing human interests from intricate multi-modal information to generate personalized responses. Moreover, external knowledge is more frequently evoked in our dataset. These facts reveal new challenges for multi-modal dialogue models. We quantitatively demonstrate the characteristics of TikTalk, propose a video-based multi-modal chitchat task, and evaluate several dialogue baselines. Experimental results indicate that the models incorporating large language models (LLM) can generate more diverse responses, while the model utilizing knowledge graphs to introduce external knowledge performs the best overall. Furthermore, no existing model can solve all the above challenges well. There is still a large room for future improvements, even for LLM with visual extensions. Our dataset is available at https://ruc-aimind.github.io/projects/TikTalk/.

Incorporating external knowledge to Visual Question Answering (VQA) has become a vital practical need. Existing methods mostly adopt pipeline approaches with different components for knowledge matching and extraction, feature learning, etc.However, such pipeline approaches suffer when some component does not perform well, which leads to error propagation and poor overall performance. Furthermore, the majority of existing approaches ignore the answer bias issue -- many answers may have never appeared during training (i.e., unseen answers) in real-word application. To bridge these gaps, in this paper, we propose a Zero-shot VQA algorithm using knowledge graphs and a mask-based learning mechanism for better incorporating external knowledge, and present new answer-based Zero-shot VQA splits for the F-VQA dataset. Experiments show that our method can achieve state-of-the-art performance in Zero-shot VQA with unseen answers, meanwhile dramatically augment existing end-to-end models on the normal F-VQA task.

In this work we address the problem of argument search. The purpose of argument search is the distillation of pro and contra arguments for requested topics from large text corpora. In previous works, the usual approach is to use a standard search engine to extract text parts which are relevant to the given topic and subsequently use an argument recognition algorithm to select arguments from them. The main challenge in the argument recognition task, which is also known as argument mining, is that often sentences containing arguments are structurally similar to purely informative sentences without any stance about the topic. In fact, they only differ semantically. Most approaches use topic or search term information only for the first search step and therefore assume that arguments can be classified independently of a topic. We argue that topic information is crucial for argument mining, since the topic defines the semantic context of an argument. Precisely, we propose different models for the classification of arguments, which take information about a topic of an argument into account. Moreover, to enrich the context of a topic and to let models understand the context of the potential argument better, we integrate information from different external sources such as Knowledge Graphs or pre-trained NLP models. Our evaluation shows that considering topic information, especially in connection with external information, provides a significant performance boost for the argument mining task.

Semantic representation and inference is essential for Natural Language Processing (NLP). The state of the art for semantic representation and inference is deep learning, and particularly Recurrent Neural Networks (RNNs), Convolutional Neural Networks (CNNs), and transformer Self-Attention models. This thesis investigates the use of deep learning for novel semantic representation and inference, and makes contributions in the following three areas: creating training data, improving semantic representations and extending inference learning. In terms of creating training data, we contribute the largest publicly available dataset of real-life factual claims for the purpose of automatic claim verification (MultiFC), and we present a novel inference model composed of multi-scale CNNs with different kernel sizes that learn from external sources to infer fact checking labels. In terms of improving semantic representations, we contribute a novel model that captures non-compositional semantic indicators. By definition, the meaning of a non-compositional phrase cannot be inferred from the individual meanings of its composing words (e.g., hot dog). Motivated by this, we operationalize the compositionality of a phrase contextually by enriching the phrase representation with external word embeddings and knowledge graphs. Finally, in terms of inference learning, we propose a series of novel deep learning architectures that improve inference by using syntactic dependencies, by ensembling role guided attention heads, incorporating gating layers, and concatenating multiple heads in novel and effective ways. This thesis consists of seven publications (five published and two under review).

Classifying patents by their relevance to the UN Sustainable Development Goals (SDGs) is crucial for tracking how innovation addresses global challenges. However, the absence of a large, labeled dataset limits the use of supervised learning. Existing methods, such as keyword searches, transfer learning, and citation-based heuristics, lack scalability and generalizability. This paper frames patent-to-SDG classification as a weak supervision problem, using citations from patents to SDG-tagged scientific publications (NPL citations) as a noisy initial signal. To address its sparsity and noise, we develop a composite labeling function (LF) that uses large language models (LLMs) to extract structured concepts, namely functions, solutions, and applications, from patents and SDG papers based on a patent ontology. Cross-domain similarity scores are computed and combined using a rank-based retrieval approach. The LF is calibrated via a custom positive-only loss that aligns with known NPL-SDG links without penalizing discovery of new SDG associations. The result is a silver-standard, soft multi-label dataset mapping patents to SDGs, enabling the training of effective multi-label regression models. We validate our approach through two complementary strategies: (1) internal validation against held-out NPL-based labels, where our method outperforms several baselines including transformer-based models, and zero-shot LLM; and (2) external validation using network modularity in patent citation, co-inventor, and co-applicant graphs, where our labels reveal greater thematic, cognitive, and organizational coherence than traditional technological classifications. These results show that weak supervision and semantic alignment can enhance SDG classification at scale.

External knowledge (a.k.a. side information) plays a critical role in zero-shot learning (ZSL) which aims to predict with unseen classes that have never appeared in training data. Several kinds of external knowledge, such as text and attribute, have been widely investigated, but they alone are limited with incomplete semantics. Some very recent studies thus propose to use Knowledge Graph (KG) due to its high expressivity and compatibility for representing kinds of knowledge. However, the ZSL community is still in short of standard benchmarks for studying and comparing different external knowledge settings and different KG-based ZSL methods. In this paper, we proposed six resources covering three tasks, i.e., zero-shot image classification (ZS-IMGC), zero-shot relation extraction (ZS-RE), and zero-shot KG completion (ZS-KGC). Each resource has a normal ZSL benchmark and a KG containing semantics ranging from text to attribute, from relational knowledge to logical expressions. We have clearly presented these resources including their construction, statistics, data formats and usage cases w.r.t. different ZSL methods. More importantly, we have conducted a comprehensive benchmarking study, with two general and state-of-the-art methods, two setting-specific methods and one interpretable method. We discussed and compared different ZSL paradigms w.r.t. different external knowledge settings, and found that our resources have great potential for developing more advanced ZSL methods and more solutions for applying KGs for augmenting machine learning. All the resources are available at https://github.com/China-UK-ZSL/Resources_for_KZSL.

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

In this paper, we aim to develop a large language model (LLM) with the reasoning ability on complex graph data. Currently, LLMs have achieved very impressive performance on various natural language learning tasks, extensions of which have also been applied to study the vision tasks with multi-modal data. However, when it comes to the graph learning tasks, existing LLMs present very serious flaws due to their several inherited weaknesses in performing {multi-step logic reasoning}, {precise mathematical calculation} and {perception about the spatial and temporal factors}. To address such challenges, in this paper, we will investigate the principles, methodologies and algorithms to empower existing LLMs with graph reasoning ability, which will have tremendous impacts on the current research of both LLMs and graph learning. Inspired by the latest ChatGPT and Toolformer models, we propose the Graph-ToolFormer (Graph Reasoning oriented Toolformer) framework to teach LLMs themselves with prompts augmented by ChatGPT to use external graph reasoning API tools. Specifically, we will investigate to teach Graph-ToolFormer to handle various graph data reasoning tasks in this paper, including both (1) very basic graph data loading and graph property reasoning tasks, ranging from simple graph order and size to the graph diameter and periphery, and (2) more advanced reasoning tasks on real-world graph data, such as bibliographic networks, protein molecules, sequential recommender systems, social networks and knowledge graphs.

Graphs are ubiquitous structures found in numerous real-world applications, such as drug discovery, recommender systems, and social network analysis. To model graph-structured data, graph neural networks (GNNs) have become a popular tool. However, existing GNN architectures encounter challenges in cross-graph learning where multiple graphs have different feature spaces. To address this, recent approaches introduce text-attributed graphs (TAGs), where each node is associated with a textual description, which can be projected into a unified feature space using textual encoders. While promising, this method relies heavily on the availability of text-attributed graph data, which is difficult to obtain in practice. To bridge this gap, we propose a novel method named Topology-Aware Node description Synthesis (TANS), leveraging large language models (LLMs) to convert existing graphs into text-attributed graphs. The key idea is to integrate topological information into LLMs to explain how graph topology influences node semantics. We evaluate our TANS on text-rich, text-limited, and text-free graphs, demonstrating its applicability. Notably, on text-free graphs, our method significantly outperforms existing approaches that manually design node features, showcasing the potential of LLMs for preprocessing graph-structured data in the absence of textual information. The code and data are available at https://github.com/Zehong-Wang/TANS.

Graph-based retrieval-augmented generation (GraphRAG) systems construct knowledge graphs over document collections to support multi-hop reasoning. While prior work shows that GraphRAG responses may leak retrieved subgraphs, the feasibility of query-efficient reconstruction of the hidden graph structure remains unexplored under realistic query budgets. We study a budget-constrained black-box setting where an adversary adaptively queries the system to steal its latent entity-relation graph. We propose AGEA (Agentic Graph Extraction Attack), a framework that leverages a novelty-guided exploration-exploitation strategy, external graph memory modules, and a two-stage graph extraction pipeline combining lightweight discovery with LLM-based filtering. We evaluate AGEA on medical, agriculture, and literary datasets across Microsoft-GraphRAG and LightRAG systems. Under identical query budgets, AGEA significantly outperforms prior attack baselines, recovering up to 90% of entities and relationships while maintaining high precision. These results demonstrate that modern GraphRAG systems are highly vulnerable to structured, agentic extraction attacks, even under strict query limits. The code is available at https://github.com/shuashua0608/AGEA.

Large language models (LLMs), such as ChatGPT and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data are associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data are paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graph scenarios (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-rich graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we mention the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

Graphs can be used to represent and reason about systems and a variety of metrics have been devised to quantify their global characteristics. However, little is currently known about how to construct a graph or improve an existing one given a target objective. In this work, we formulate the construction of a graph as a decision-making process in which a central agent creates topologies by trial and error and receives rewards proportional to the value of the target objective. By means of this conceptual framework, we propose an algorithm based on reinforcement learning and graph neural networks to learn graph construction and improvement strategies. Our core case study focuses on robustness to failures and attacks, a property relevant for the infrastructure and communication networks that power modern society. Experiments on synthetic and real-world graphs show that this approach can outperform existing methods while being cheaper to evaluate. It also allows generalization to out-of-sample graphs, as well as to larger out-of-distribution graphs in some cases. The approach is applicable to the optimization of other global structural properties of graphs.

Graph is powerful for representing various types of real-world data. The topology (edges' presence) and edges' features of a graph decides the message passing mechanism among vertices within the graph. While most existing approaches only manually define a single-value edge to describe the connectivity or strength of association between a pair of vertices, task-specific and crucial relationship cues may be disregarded by such manually defined topology and single-value edge features. In this paper, we propose the first general graph representation learning framework (called GRATIS) which can generate a strong graph representation with a task-specific topology and task-specific multi-dimensional edge features from any arbitrary input. To learn each edge's presence and multi-dimensional feature, our framework takes both of the corresponding vertices pair and their global contextual information into consideration, enabling the generated graph representation to have a globally optimal message passing mechanism for different down-stream tasks. The principled investigation results achieved for various graph analysis tasks on 11 graph and non-graph datasets show that our GRATIS can not only largely enhance pre-defined graphs but also learns a strong graph representation for non-graph data, with clear performance improvements on all tasks. In particular, the learned topology and multi-dimensional edge features provide complementary task-related cues for graph analysis tasks. Our framework is effective, robust and flexible, and is a plug-and-play module that can be combined with different backbones and Graph Neural Networks (GNNs) to generate a task-specific graph representation from various graph and non-graph data. Our code is made publicly available at https://github.com/SSYSteve/Learning-Graph-Representation-with-Task-specific-Topology-and-Multi-dimensional-Edge-Features.

Graph-based Retrieval-Augmented Generation (GraphRAG) organizes external knowledge as a hierarchical graph, enabling efficient retrieval and aggregation of scattered evidence across multiple documents. However, many existing benchmarks for GraphRAG rely on short, curated passages as external knowledge, failing to adequately evaluate systems in realistic settings involving long contexts and large-scale heterogeneous documents. To bridge this gap, we introduce WildGraphBench, a benchmark designed to assess GraphRAG performance in the wild. We leverage Wikipedia's unique structure, where cohesive narratives are grounded in long and heterogeneous external reference documents, to construct a benchmark reflecting real-word scenarios. Specifically, we sample articles across 12 top-level topics, using their external references as the retrieval corpus and citation-linked statements as ground truth, resulting in 1,100 questions spanning three levels of complexity: single-fact QA, multi-fact QA, and section-level summarization. Experiments across multiple baselines reveal that current GraphRAG pipelines help on multi-fact aggregation when evidence comes from a moderate number of sources, but this aggregation paradigm may overemphasize high-level statements at the expense of fine-grained details, leading to weaker performance on summarization tasks. Project page:https://github.com/BstWPY/WildGraphBench.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

This work aims to tackle the challenging heterogeneous graph encoding problem in the text-to-SQL task. Previous methods are typically node-centric and merely utilize different weight matrices to parameterize edge types, which 1) ignore the rich semantics embedded in the topological structure of edges, and 2) fail to distinguish local and non-local relations for each node. To this end, we propose a Line Graph Enhanced Text-to-SQL (LGESQL) model to mine the underlying relational features without constructing meta-paths. By virtue of the line graph, messages propagate more efficiently through not only connections between nodes, but also the topology of directed edges. Furthermore, both local and non-local relations are integrated distinctively during the graph iteration. We also design an auxiliary task called graph pruning to improve the discriminative capability of the encoder. Our framework achieves state-of-the-art results (62.8% with Glove, 72.0% with Electra) on the cross-domain text-to-SQL benchmark Spider at the time of writing.

Text-Attributed Graphs (TAGs) augment graph structures with natural language descriptions, facilitating detailed depictions of data and their interconnections across various real-world settings. However, existing TAG datasets predominantly feature textual information only at the nodes, with edges typically represented by mere binary or categorical attributes. This lack of rich textual edge annotations significantly limits the exploration of contextual relationships between entities, hindering deeper insights into graph-structured data. To address this gap, we introduce Textual-Edge Graphs Datasets and Benchmark (TEG-DB), a comprehensive and diverse collection of benchmark textual-edge datasets featuring rich textual descriptions on nodes and edges. The TEG-DB datasets are large-scale and encompass a wide range of domains, from citation networks to social networks. In addition, we conduct extensive benchmark experiments on TEG-DB to assess the extent to which current techniques, including pre-trained language models, graph neural networks, and their combinations, can utilize textual node and edge information. Our goal is to elicit advancements in textual-edge graph research, specifically in developing methodologies that exploit rich textual node and edge descriptions to enhance graph analysis and provide deeper insights into complex real-world networks. The entire TEG-DB project is publicly accessible as an open-source repository on Github, accessible at https://github.com/Zhuofeng-Li/TEG-Benchmark.

Associating unstructured data with structured information is crucial for real-world tasks that require relevance search. However, existing graph learning benchmarks often overlook the rich semantic information associate with each node. To bridge such gap, we introduce the Multimodal Graph Benchmark (MM-GRAPH), the first comprehensive multi-modal graph benchmark that incorporates both textual and visual information. MM-GRAPH surpasses previous efforts, which have primarily focused on text-attributed graphs with various connectivity patterns. MM-GRAPH consists of five graph learning datasets of various scales that are appropriate for different learning tasks. Their multimodal node features, enabling a more comprehensive evaluation of graph learning algorithms in real-world scenarios. To facilitate research on multimodal graph learning, we further provide an extensive study on the performance of various graph neural networks in the presence of features from various modalities. MM-GRAPH aims to foster research on multimodal graph learning and drive the development of more advanced and robust graph learning algorithms. By providing a diverse set of datasets and benchmarks, MM-GRAPH enables researchers to evaluate and compare their models in realistic settings, ultimately leading to improved performance on real-world applications that rely on multimodal graph data.

Real-world networks, with their evolving relations, are best captured as temporal graphs. However, existing software libraries are largely designed for static graphs where the dynamic nature of temporal graphs is ignored. Bridging this gap, we introduce TGX, a Python package specially designed for analysis of temporal networks that encompasses an automated pipeline for data loading, data processing, and analysis of evolving graphs. TGX provides access to eleven built-in datasets and eight external Temporal Graph Benchmark (TGB) datasets as well as any novel datasets in the .csv format. Beyond data loading, TGX facilitates data processing functionalities such as discretization of temporal graphs and node subsampling to accelerate working with larger datasets. For comprehensive investigation, TGX offers network analysis by providing a diverse set of measures, including average node degree and the evolving number of nodes and edges per timestamp. Additionally, the package consolidates meaningful visualization plots indicating the evolution of temporal patterns, such as Temporal Edge Appearance (TEA) and Temporal Edge Trafficc (TET) plots. The TGX package is a robust tool for examining the features of temporal graphs and can be used in various areas like studying social networks, citation networks, and tracking user interactions. We plan to continuously support and update TGX based on community feedback. TGX is publicly available on: https://github.com/ComplexData-MILA/TGX.

Text-Attributed Graphs (TAGs) enhance graph structures with natural language descriptions, enabling detailed representation of data and their relationships across a broad spectrum of real-world scenarios. Despite the potential for deeper insights, existing TAG representation learning primarily relies on supervised methods, necessitating extensive labeled data and limiting applicability across diverse contexts. This paper introduces a new self-supervised learning framework, Text-And-Graph Multi-View Alignment (TAGA), which overcomes these constraints by integrating TAGs' structural and semantic dimensions. TAGA constructs two complementary views: Text-of-Graph view, which organizes node texts into structured documents based on graph topology, and the Graph-of-Text view, which converts textual nodes and connections into graph data. By aligning representations from both views, TAGA captures joint textual and structural information. In addition, a novel structure-preserving random walk algorithm is proposed for efficient training on large-sized TAGs. Our framework demonstrates strong performance in zero-shot and few-shot scenarios across eight real-world datasets.

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

We introduce a self-supervised approach for learning node and graph level representations by contrasting structural views of graphs. We show that unlike visual representation learning, increasing the number of views to more than two or contrasting multi-scale encodings do not improve performance, and the best performance is achieved by contrasting encodings from first-order neighbors and a graph diffusion. We achieve new state-of-the-art results in self-supervised learning on 8 out of 8 node and graph classification benchmarks under the linear evaluation protocol. For example, on Cora (node) and Reddit-Binary (graph) classification benchmarks, we achieve 86.8% and 84.5% accuracy, which are 5.5% and 2.4% relative improvements over previous state-of-the-art. When compared to supervised baselines, our approach outperforms them in 4 out of 8 benchmarks. Source code is released at: https://github.com/kavehhassani/mvgrl

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.

Legal documents including judgments and court orders require highly sophisticated legal knowledge for understanding. To disclose expert knowledge for non-experts, we explore the problem of visualizing legal texts with easy-to-understand diagrams and propose a novel dataset of LegalViz with 23 languages and 7,010 cases of legal document and visualization pairs, using the DOT graph description language of Graphviz. LegalViz provides a simple diagram from a complicated legal corpus identifying legal entities, transactions, legal sources, and statements at a glance, that are essential in each judgment. In addition, we provide new evaluation metrics for the legal diagram visualization by considering graph structures, textual similarities, and legal contents. We conducted empirical studies on few-shot and finetuning large language models for generating legal diagrams and evaluated them with these metrics, including legal content-based evaluation within 23 languages. Models trained with LegalViz outperform existing models including GPTs, confirming the effectiveness of our dataset.

Real-world tasks consist of multiple inter-dependent subtasks (e.g., a dirty pan needs to be washed before it can be used for cooking). In this work, we aim to model the causal dependencies between such subtasks from instructional videos describing the task. This is a challenging problem since complete information about the world is often inaccessible from videos, which demands robust learning mechanisms to understand the causal structure of events. We present Multimodal Subtask Graph Generation (MSG2), an approach that constructs a Subtask Graph defining the dependency between a task's subtasks relevant to a task from noisy web videos. Graphs generated by our multimodal approach are closer to human-annotated graphs compared to prior approaches. MSG2 further performs the downstream task of next subtask prediction 85% and 30% more accurately than recent video transformer models in the ProceL and CrossTask datasets, respectively.

Large Language Models (LLMs) have achieved impressive performance in text understanding and have become an essential tool for building smart assistants. Originally focusing on text, they have been enhanced with multimodal capabilities in recent works that successfully built visual instruction following assistants. As far as the graph modality goes, however, no such assistants have yet been developed. Graph structures are complex in that they represent relation between different features and are permutation invariant. Moreover, representing them in purely textual form does not always lead to good LLM performance even for finetuned models. As a result, there is a need to develop a new method to integrate graphs in LLMs for general graph understanding. This work explores the integration of the graph modality in LLM for general graph instruction following tasks. It aims at producing a deep learning model that enhances an underlying LLM with graph embeddings and trains it to understand them and to produce, given an instruction, an answer grounded in the graph representation. The approach performs significantly better than a graph to text approach and remains consistent even for larger graphs.

For a graph G with n vertices and m edges, Lin et al. Lin define the atom--bond sum-connectivity (ABS) matrix of G such that the (i,j)^{th} entry is \[ 1 - \frac{2{d_i + d_j}} \] if vertex v_i is adjacent to the vertex v_j, and 0 otherwise. In this article, we determine the characteristic polynomial of the ABS matrix for certain specific classes of graphs. Furthermore, we compute the ABS eigenvalues and the ABS energy for these classes.

For a broad range of research, governmental and commercial applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As social media data sets are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present a single-machine real-time system for large-scale graph processing that allows analysts to interactively explore graph structures. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates user similarities while being robust to noise and queryable in real-time. We achieve single machine real-time performance by compressing the neighbourhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e. communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetise their data, helping them to continue to provide free services that are valued by billions of people globally.

Weighted graphs are ubiquitous throughout biology, chemistry, and the social sciences, motivating the development of generative models for abstract weighted graph data using deep neural networks. However, most current deep generative models are either designed for unweighted graphs and are not easily extended to weighted topologies or incorporate edge weights without consideration of a joint distribution with topology. Furthermore, learning a distribution over weighted graphs must account for complex nonlocal dependencies between both the edges of the graph and corresponding weights of each edge. We develop an autoregressive model BiGG-E, a nontrivial extension of the BiGG model, that learns a joint distribution over weighted graphs while still exploiting sparsity to generate a weighted graph with n nodes and m edges in O((n + m)log n) time. Simulation studies and experiments on a variety of benchmark datasets demonstrate that BiGG-E best captures distributions over weighted graphs while remaining scalable and computationally efficient.

The growing importance of understanding and addressing algorithmic bias in artificial intelligence (AI) has led to a surge in research on AI fairness, which often assumes that the underlying data is independent and identically distributed (IID). However, real-world data frequently exists in non-IID graph structures that capture connections among individual units. To effectively mitigate bias in AI systems, it is essential to bridge the gap between traditional fairness literature, designed for IID data, and the prevalence of non-IID graph data. This survey reviews recent advancements in fairness amidst non-IID graph data, including the newly introduced fair graph generation and the commonly studied fair graph classification. In addition, available datasets and evaluation metrics for future research are identified, the limitations of existing work are highlighted, and promising future directions are proposed.

This work studies self-supervised graph learning for text-attributed graphs (TAGs) where nodes are represented by textual attributes. Unlike traditional graph contrastive methods that perturb the numerical feature space and alter the graph's topological structure, we aim to improve view generation through language supervision. This is driven by the prevalence of textual attributes in real applications, which complement graph structures with rich semantic information. However, this presents challenges because of two major reasons. First, text attributes often vary in length and quality, making it difficulty to perturb raw text descriptions without altering their original semantic meanings. Second, although text attributes complement graph structures, they are not inherently well-aligned. To bridge the gap, we introduce GAugLLM, a novel framework for augmenting TAGs. It leverages advanced large language models like Mistral to enhance self-supervised graph learning. Specifically, we introduce a mixture-of-prompt-expert technique to generate augmented node features. This approach adaptively maps multiple prompt experts, each of which modifies raw text attributes using prompt engineering, into numerical feature space. Additionally, we devise a collaborative edge modifier to leverage structural and textual commonalities, enhancing edge augmentation by examining or building connections between nodes. Empirical results across five benchmark datasets spanning various domains underscore our framework's ability to enhance the performance of leading contrastive methods as a plug-in tool. Notably, we observe that the augmented features and graph structure can also enhance the performance of standard generative methods, as well as popular graph neural networks. The open-sourced implementation of our GAugLLM is available at Github.

Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are essential, making prior methods potentially unsuitable in such contexts. Moreover, while trivial adaptations are available, empirical investigations reveal their limited efficacy as they do not properly model the interplay among graph components. To address this, we propose a joint score-based model of nodes and edges for graph generation that considers all graph components. Our approach offers two key novelties: (i) node and edge attributes are combined in an attention module that generates samples based on the two ingredients; and (ii) node, edge and adjacency information are mutually dependent during the graph diffusion process. We evaluate our method on challenging benchmarks involving real-world and synthetic datasets in which edge features are crucial. Additionally, we introduce a new synthetic dataset that incorporates edge values. Furthermore, we propose a novel application that greatly benefits from the method due to its nature: the generation of traffic scenes represented as graphs. Our method outperforms other graph generation methods, demonstrating a significant advantage in edge-related measures.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

This paper studies the problem of embedding very large information networks into low-dimensional vector spaces, which is useful in many tasks such as visualization, node classification, and link prediction. Most existing graph embedding methods do not scale for real world information networks which usually contain millions of nodes. In this paper, we propose a novel network embedding method called the "LINE," which is suitable for arbitrary types of information networks: undirected, directed, and/or weighted. The method optimizes a carefully designed objective function that preserves both the local and global network structures. An edge-sampling algorithm is proposed that addresses the limitation of the classical stochastic gradient descent and improves both the effectiveness and the efficiency of the inference. Empirical experiments prove the effectiveness of the LINE on a variety of real-world information networks, including language networks, social networks, and citation networks. The algorithm is very efficient, which is able to learn the embedding of a network with millions of vertices and billions of edges in a few hours on a typical single machine. The source code of the LINE is available online.

The growing interest in machine learning problems over graphs with additional node information such as texts, images, or labels has popularized methods that require the costly operation of processing the entire graph. Yet, little effort has been made to the development of fast local methods (i.e. without accessing the entire graph) that extract useful information from such data. To that end, we propose a study of local graph clustering using noisy node labels as a proxy for additional node information. In this setting, nodes receive initial binary labels based on cluster affiliation: 1 if they belong to the target cluster and 0 otherwise. Subsequently, a fraction of these labels is flipped. We investigate the benefits of incorporating noisy labels for local graph clustering. By constructing a weighted graph with such labels, we study the performance of graph diffusion-based local clustering method on both the original and the weighted graphs. From a theoretical perspective, we consider recovering an unknown target cluster with a single seed node in a random graph with independent noisy node labels. We provide sufficient conditions on the label noise under which, with high probability, using diffusion in the weighted graph yields a more accurate recovery of the target cluster. This approach proves more effective than using the given labels alone or using diffusion in the label-free original graph. Empirically, we show that reliable node labels can be obtained with just a few samples from an attributed graph. Moreover, utilizing these labels via diffusion in the weighted graph leads to significantly better local clustering performance across several real-world datasets, improving F1 scores by up to 13%.

Graph Convolutional Networks (GCNs) have shown strong performance in learning text representations for various tasks such as text classification, due to its expressive power in modeling graph structure data (e.g., a literature citation network). Most existing GCNs are limited to deal with documents included in a pre-defined graph, i.e., it cannot be generalized to out-of-graph documents. To address this issue, we propose to transform the document graph into a word graph, to decouple data samples (i.e., documents in training and test sets) and a GCN model by using a document-independent graph. Such word-level GCN could therefore naturally inference out-of-graph documents in an inductive way. The proposed Word-level Graph (WGraph) can not only implicitly learning word presentation with commonly-used word co-occurrences in corpora, but also incorporate extra global semantic dependency derived from inter-document relationships (e.g., literature citations). An inductive Word-grounded Graph Convolutional Network (WGCN) is proposed to learn word and document representations based on WGraph in a supervised manner. Experiments on text classification with and without citation networks evidence that the proposed WGCN model outperforms existing methods in terms of effectiveness and efficiency.

Understanding the origins of militarized conflict is a complex, yet important undertaking. Existing research seeks to build this understanding by considering bi-lateral relationships between entity pairs (dyadic causes) and multi-lateral relationships among multiple entities (systemic causes). The aim of this work is to compare these two causes in terms of how they correlate with conflict between two entities. We do this by devising a set of textual and graph-based features which represent each of the causes. The features are extracted from Wikipedia and modeled as a large graph. Nodes in this graph represent entities connected by labeled edges representing ally or enemy-relationships. This allows casting the problem as an edge classification task, which we term dyad classification. We propose and evaluate classifiers to determine if a particular pair of entities are allies or enemies. Our results suggest that our systemic features might be slightly better correlates of conflict. Further, we find that Wikipedia articles of allies are semantically more similar than enemies.

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

As economics scales, a key bottleneck is representing what papers claim in a comparable, aggregable form. We introduce evidence-annotated claim graphs that map each paper into a directed network of standardized economic concepts (nodes) and stated relationships (edges), with each edge labeled by evidentiary basis, including whether it is supported by causal inference designs or by non-causal evidence. Using a structured multi-stage AI workflow, we construct claim graphs for 44,852 economics papers from 1980-2023. The share of causal edges rises from 7.7% in 1990 to 31.7% in 2020. Measures of causal narrative structure and causal novelty are positively associated with top-five publication and long-run citations, whereas non-causal counterparts are weakly related or negative.

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

Graph self-supervised learning (SSL) is now a go-to method for pre-training graph foundation models (GFMs). There is a wide variety of knowledge patterns embedded in the graph data, such as node properties and clusters, which are crucial to learning generalized representations for GFMs. However, existing surveys of GFMs have several shortcomings: they lack comprehensiveness regarding the most recent progress, have unclear categorization of self-supervised methods, and take a limited architecture-based perspective that is restricted to only certain types of graph models. As the ultimate goal of GFMs is to learn generalized graph knowledge, we provide a comprehensive survey of self-supervised GFMs from a novel knowledge-based perspective. We propose a knowledge-based taxonomy, which categorizes self-supervised graph models by the specific graph knowledge utilized. Our taxonomy consists of microscopic (nodes, links, etc.), mesoscopic (context, clusters, etc.), and macroscopic knowledge (global structure, manifolds, etc.). It covers a total of 9 knowledge categories and more than 25 pretext tasks for pre-training GFMs, as well as various downstream task generalization strategies. Such a knowledge-based taxonomy allows us to re-examine graph models based on new architectures more clearly, such as graph language models, as well as provide more in-depth insights for constructing GFMs.

This paper aims to generate materials for 3D meshes from text descriptions. Unlike existing methods that synthesize texture maps, we propose to generate segment-wise procedural material graphs as the appearance representation, which supports high-quality rendering and provides substantial flexibility in editing. Instead of relying on extensive paired data, i.e., 3D meshes with material graphs and corresponding text descriptions, to train a material graph generative model, we propose to leverage the pre-trained 2D diffusion model as a bridge to connect the text and material graphs. Specifically, our approach decomposes a shape into a set of segments and designs a segment-controlled diffusion model to synthesize 2D images that are aligned with mesh parts. Based on generated images, we initialize parameters of material graphs and fine-tune them through the differentiable rendering module to produce materials in accordance with the textual description. Extensive experiments demonstrate the superior performance of our framework in photorealism, resolution, and editability over existing methods. Project page: https://zhanghe3z.github.io/MaPa/

Despite the prevalence of recent success in learning from static graphs, learning from time-evolving graphs remains an open challenge. In this work, we design new, more stringent evaluation procedures for link prediction specific to dynamic graphs, which reflect real-world considerations, to better compare the strengths and weaknesses of methods. First, we create two visualization techniques to understand the reoccurring patterns of edges over time and show that many edges reoccur at later time steps. Based on this observation, we propose a pure memorization baseline called EdgeBank. EdgeBank achieves surprisingly strong performance across multiple settings because easy negative edges are often used in the current evaluation setting. To evaluate against more difficult negative edges, we introduce two more challenging negative sampling strategies that improve robustness and better match real-world applications. Lastly, we introduce six new dynamic graph datasets from a diverse set of domains missing from current benchmarks, providing new challenges and opportunities for future research. Our code repository is accessible at https://github.com/fpour/DGB.git.

Retrieving external knowledge and prompting large language models with relevant information is an effective paradigm to enhance the performance of question-answering tasks. Previous research typically handles paragraphs from external documents in isolation, resulting in a lack of context and ambiguous references, particularly in multi-document and complex tasks. To overcome these challenges, we propose a new retrieval framework IIER, that leverages Inter-chunk Interactions to Enhance Retrieval. This framework captures the internal connections between document chunks by considering three types of interactions: structural, keyword, and semantic. We then construct a unified Chunk-Interaction Graph to represent all external documents comprehensively. Additionally, we design a graph-based evidence chain retriever that utilizes previous paths and chunk interactions to guide the retrieval process. It identifies multiple seed nodes based on the target question and iteratively searches for relevant chunks to gather supporting evidence. This retrieval process refines the context and reasoning chain, aiding the large language model in reasoning and answer generation. Extensive experiments demonstrate that IIER outperforms strong baselines across four datasets, highlighting its effectiveness in improving retrieval and reasoning capabilities.

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose One for All (OFA), the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

Biomedical knowledge graphs (KGs) are widely used in the life sciences, yet many are derived from unstructured documents and therefore lack schema-level constrains, whereas graphs assembled from structured resources are difficult to harmonize into a unified representation. We present OptimusKG, a multimodal biomedical labeled property graph (LPG) built from structured and semi-structured resources to preserve factual, type-specific metadata across molecular, anatomical, clinical, and environmental domains. OptimusKG contains 190,531 nodes across 10 entity types, 21,813,816 edges across 26 relation types, and 67,249,863 property instances encoding 110,276,843 values across 150 distinct property keys, derived from 18 ontologies and controlled vocabularies. The graph enforces a top-level schema for nodes and edges and retains granular, type-specific properties, cross-references, and provenance across molecular, anatomical, clinical, and environmental domains. We assessed the validity of OptimusKG by evaluating whether graph relationships are supported by evidence from the scientific literature using a multimodal agent, PaperQA3. PaperQA3 identified supporting evidence for 70.0% of sampled edges, whereas 83.4% of sampled false edges received no supporting evidence. Edges without literature support were concentrated in associations derived from experimental and functional genomics resources, suggesting that OptimusKG captures biomedical knowledge that may precede synthesis in the scientific literature. OptimusKG is distributed as Apache Parquet files, providing a standardized resource for graph-based machine learning, knowledge-grounded retrieval with large language models, and biomedical discovery use cases such as hypothesis generation.

Graph generative models become increasingly effective for data distribution approximation and data augmentation. While they have aroused public concerns about their malicious misuses or misinformation broadcasts, just as what Deepfake visual and auditory media has been delivering to society. Hence it is essential to regulate the prevalence of generated graphs. To tackle this problem, we pioneer the formulation of the generated graph detection problem to distinguish generated graphs from real ones. We propose the first framework to systematically investigate a set of sophisticated models and their performance in four classification scenarios. Each scenario switches between seen and unseen datasets/generators during testing to get closer to real-world settings and progressively challenge the classifiers. Extensive experiments evidence that all the models are qualified for generated graph detection, with specific models having advantages in specific scenarios. Resulting from the validated generality and oblivion of the classifiers to unseen datasets/generators, we draw a safe conclusion that our solution can sustain for a decent while to curb generated graph misuses.

A Harris Graph is a tough, Eulerian, non-Hamiltonian graph. Several approaches to creating new Harris graphs from existing ones are explored, including creating families of Harris graphs and combining Harris graphs. Pictures of all Harris Graphs through order 9 and the number of Harris graphs through order 12 are included. We also prove a result about barnacle-free Harris graphs.

Graph transformers have emerged as a promising architecture for a variety of graph learning and representation tasks. Despite their successes, though, it remains challenging to scale graph transformers to large graphs while maintaining accuracy competitive with message-passing networks. In this paper, we introduce Exphormer, a framework for building powerful and scalable graph transformers. Exphormer consists of a sparse attention mechanism based on two mechanisms: virtual global nodes and expander graphs, whose mathematical characteristics, such as spectral expansion, pseduorandomness, and sparsity, yield graph transformers with complexity only linear in the size of the graph, while allowing us to prove desirable theoretical properties of the resulting transformer models. We show that incorporating Exphormer into the recently-proposed GraphGPS framework produces models with competitive empirical results on a wide variety of graph datasets, including state-of-the-art results on three datasets. We also show that Exphormer can scale to datasets on larger graphs than shown in previous graph transformer architectures. Code can be found at https://github.com/hamed1375/Exphormer.

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