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Dec 26

Unveiling LLMs: The Evolution of Latent Representations in a Dynamic Knowledge Graph

Large Language Models (LLMs) demonstrate an impressive capacity to recall a vast range of factual knowledge. However, understanding their underlying reasoning and internal mechanisms in exploiting this knowledge remains a key research area. This work unveils the factual information an LLM represents internally for sentence-level claim verification. We propose an end-to-end framework to decode factual knowledge embedded in token representations from a vector space to a set of ground predicates, showing its layer-wise evolution using a dynamic knowledge graph. Our framework employs activation patching, a vector-level technique that alters a token representation during inference, to extract encoded knowledge. Accordingly, we neither rely on training nor external models. Using factual and common-sense claims from two claim verification datasets, we showcase interpretability analyses at local and global levels. The local analysis highlights entity centrality in LLM reasoning, from claim-related information and multi-hop reasoning to representation errors causing erroneous evaluation. On the other hand, the global reveals trends in the underlying evolution, such as word-based knowledge evolving into claim-related facts. By interpreting semantics from LLM latent representations and enabling graph-related analyses, this work enhances the understanding of the factual knowledge resolution process.

  • 5 authors
·
Apr 4, 2024

SymAgent: A Neural-Symbolic Self-Learning Agent Framework for Complex Reasoning over Knowledge Graphs

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.

  • 6 authors
·
Feb 5

Graph2Eval: Automatic Multimodal Task Generation for Agents via Knowledge Graphs

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.

LLM-Powered Decentralized Generative Agents with Adaptive Hierarchical Knowledge Graph for Cooperative Planning

Developing intelligent agents for long-term cooperation in dynamic open-world scenarios is a major challenge in multi-agent systems. Traditional Multi-agent Reinforcement Learning (MARL) frameworks like centralized training decentralized execution (CTDE) struggle with scalability and flexibility. They require centralized long-term planning, which is difficult without custom reward functions, and face challenges in processing multi-modal data. CTDE approaches also assume fixed cooperation strategies, making them impractical in dynamic environments where agents need to adapt and plan independently. To address decentralized multi-agent cooperation, we propose Decentralized Adaptive Knowledge Graph Memory and Structured Communication System (DAMCS) in a novel Multi-agent Crafter environment. Our generative agents, powered by Large Language Models (LLMs), are more scalable than traditional MARL agents by leveraging external knowledge and language for long-term planning and reasoning. Instead of fully sharing information from all past experiences, DAMCS introduces a multi-modal memory system organized as a hierarchical knowledge graph and a structured communication protocol to optimize agent cooperation. This allows agents to reason from past interactions and share relevant information efficiently. Experiments on novel multi-agent open-world tasks show that DAMCS outperforms both MARL and LLM baselines in task efficiency and collaboration. Compared to single-agent scenarios, the two-agent scenario achieves the same goal with 63% fewer steps, and the six-agent scenario with 74% fewer steps, highlighting the importance of adaptive memory and structured communication in achieving long-term goals. We publicly release our project at: https://happyeureka.github.io/damcs.

  • 5 authors
·
Feb 8

MIRAGE: Scaling Test-Time Inference with Parallel Graph-Retrieval-Augmented Reasoning Chains

Large reasoning models (LRMs) have shown significant progress in test-time scaling through chain-of-thought prompting. Current approaches like search-o1 integrate retrieval augmented generation (RAG) into multi-step reasoning processes but rely on a single, linear reasoning chain while incorporating unstructured textual information in a flat, context-agnostic manner. As a result, these approaches can lead to error accumulation throughout the reasoning chain, which significantly limits its effectiveness in medical question-answering (QA) tasks where both accuracy and traceability are critical requirements. To address these challenges, we propose MIRAGE (Multi-chain Inference with Retrieval-Augmented Graph Exploration), a novel test-time scalable reasoning framework that performs dynamic multi-chain inference over structured medical knowledge graphs. Specifically, MIRAGE 1) decomposes complex queries into entity-grounded sub-questions, 2) executes parallel inference chains, 3) retrieves evidence adaptively via neighbor expansion and multi-hop traversal, and 4) integrates answers using cross-chain verification to resolve contradictions. Experiments on three medical QA benchmarks (GenMedGPT-5k, CMCQA, and ExplainCPE) show that MIRAGE consistently outperforms GPT-4o, Tree-of-Thought variants, and other retrieval-augmented baselines in both automatic and human evaluations. Additionally, MIRAGE improves interpretability by generating explicit reasoning chains that trace each factual claim to concrete chains within the knowledge graph, making it well-suited for complex medical reasoning scenarios. The code will be available for further research.

  • 7 authors
·
Aug 25

Spatial-Temporal Knowledge Distillation for Takeaway Recommendation

The takeaway recommendation system aims to recommend users' future takeaway purchases based on their historical purchase behaviors, thereby improving user satisfaction and boosting merchant sales. Existing methods focus on incorporating auxiliary information or leveraging knowledge graphs to alleviate the sparsity issue of user purchase sequences. However, two main challenges limit the performance of these approaches: (1) capturing dynamic user preferences on complex geospatial information and (2) efficiently integrating spatial-temporal knowledge from both graphs and sequence data with low computational costs. In this paper, we propose a novel spatial-temporal knowledge distillation model for takeaway recommendation (STKDRec) based on the two-stage training process. Specifically, during the first pre-training stage, a spatial-temporal knowledge graph (STKG) encoder is trained to extract high-order spatial-temporal dependencies and collaborative associations from the STKG. During the second spatial-temporal knowledge distillation (STKD) stage, a spatial-temporal Transformer (ST-Transformer) is employed to comprehensively model dynamic user preferences on various types of fine-grained geospatial information from a sequential perspective. Furthermore, the STKD strategy is introduced to transfer graph-based spatial-temporal knowledge to the ST-Transformer, facilitating the adaptive fusion of rich knowledge derived from both the STKG and sequence data while reducing computational overhead. Extensive experiments on three real-world datasets show that STKDRec significantly outperforms the state-of-the-art baselines.

  • 6 authors
·
Dec 21, 2024

3D Dynamic Scene Graphs: Actionable Spatial Perception with Places, Objects, and Humans

We present a unified representation for actionable spatial perception: 3D Dynamic Scene Graphs. Scene graphs are directed graphs where nodes represent entities in the scene (e.g. objects, walls, rooms), and edges represent relations (e.g. inclusion, adjacency) among nodes. Dynamic scene graphs (DSGs) extend this notion to represent dynamic scenes with moving agents (e.g. humans, robots), and to include actionable information that supports planning and decision-making (e.g. spatio-temporal relations, topology at different levels of abstraction). Our second contribution is to provide the first fully automatic Spatial PerceptIon eNgine(SPIN) to build a DSG from visual-inertial data. We integrate state-of-the-art techniques for object and human detection and pose estimation, and we describe how to robustly infer object, robot, and human nodes in crowded scenes. To the best of our knowledge, this is the first paper that reconciles visual-inertial SLAM and dense human mesh tracking. Moreover, we provide algorithms to obtain hierarchical representations of indoor environments (e.g. places, structures, rooms) and their relations. Our third contribution is to demonstrate the proposed spatial perception engine in a photo-realistic Unity-based simulator, where we assess its robustness and expressiveness. Finally, we discuss the implications of our proposal on modern robotics applications. 3D Dynamic Scene Graphs can have a profound impact on planning and decision-making, human-robot interaction, long-term autonomy, and scene prediction. A video abstract is available at https://youtu.be/SWbofjhyPzI

  • 5 authors
·
Feb 14, 2020 1

EvolveGCN: Evolving Graph Convolutional Networks for Dynamic Graphs

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at https://github.com/IBM/EvolveGCN.

  • 9 authors
·
Feb 26, 2019

EmbodiedVSR: Dynamic Scene Graph-Guided Chain-of-Thought Reasoning for Visual Spatial Tasks

While multimodal large language models (MLLMs) have made groundbreaking progress in embodied intelligence, they still face significant challenges in spatial reasoning for complex long-horizon tasks. To address this gap, we propose EmbodiedVSR (Embodied Visual Spatial Reasoning), a novel framework that integrates dynamic scene graph-guided Chain-of-Thought (CoT) reasoning to enhance spatial understanding for embodied agents. By explicitly constructing structured knowledge representations through dynamic scene graphs, our method enables zero-shot spatial reasoning without task-specific fine-tuning. This approach not only disentangles intricate spatial relationships but also aligns reasoning steps with actionable environmental dynamics. To rigorously evaluate performance, we introduce the eSpatial-Benchmark, a comprehensive dataset including real-world embodied scenarios with fine-grained spatial annotations and adaptive task difficulty levels. Experiments demonstrate that our framework significantly outperforms existing MLLM-based methods in accuracy and reasoning coherence, particularly in long-horizon tasks requiring iterative environment interaction. The results reveal the untapped potential of MLLMs for embodied intelligence when equipped with structured, explainable reasoning mechanisms, paving the way for more reliable deployment in real-world spatial applications. The codes and datasets will be released soon.

  • 16 authors
·
Mar 14

Think-on-Graph 3.0: Efficient and Adaptive LLM Reasoning on Heterogeneous Graphs via Multi-Agent Dual-Evolving Context Retrieval

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.

Zep: A Temporal Knowledge Graph Architecture for Agent Memory

We introduce Zep, a novel memory layer service for AI agents that outperforms the current state-of-the-art system, MemGPT, in the Deep Memory Retrieval (DMR) benchmark. Additionally, Zep excels in more comprehensive and challenging evaluations than DMR that better reflect real-world enterprise use cases. While existing retrieval-augmented generation (RAG) frameworks for large language model (LLM)-based agents are limited to static document retrieval, enterprise applications demand dynamic knowledge integration from diverse sources including ongoing conversations and business data. Zep addresses this fundamental limitation through its core component Graphiti -- a temporally-aware knowledge graph engine that dynamically synthesizes both unstructured conversational data and structured business data while maintaining historical relationships. In the DMR benchmark, which the MemGPT team established as their primary evaluation metric, Zep demonstrates superior performance (94.8% vs 93.4%). Beyond DMR, Zep's capabilities are further validated through the more challenging LongMemEval benchmark, which better reflects enterprise use cases through complex temporal reasoning tasks. In this evaluation, Zep achieves substantial results with accuracy improvements of up to 18.5% while simultaneously reducing response latency by 90% compared to baseline implementations. These results are particularly pronounced in enterprise-critical tasks such as cross-session information synthesis and long-term context maintenance, demonstrating Zep's effectiveness for deployment in real-world applications.

  • 5 authors
·
Jan 20

GraphMASAL: A Graph-based Multi-Agent System for Adaptive Learning

The advent of Intelligent Tutoring Systems (ITSs) has marked a paradigm shift in education, enabling highly personalized learning pathways. However, true personalization requires adapting to learners' complex knowledge states (multi-source) and diverse goals (multi-sink); existing ITSs often lack the necessary structural-reasoning capability and knowledge dynamism to generate genuinely effective learning paths, and they lack scientifically rigorous validation paradigms. In this paper we propose GraphMASAL (A Graph-based Multi-Agent System for Adaptive Learning), which integrates (i) a dynamic knowledge graph for persistent, stateful learner modeling; (ii) a LangGraph-orchestrated trio of agents (Diagnostician, Planner, Tutor); (iii) a knowledge-graph-grounded two-stage neural IR component (dual-encoder dense retrieval with cross-encoder listwise re-ranking and calibrated score fusion); and (iv) a multi-source multi-sink (MSMS) planning engine with a cognitively grounded cost and an approximation guarantee via greedy set cover. Under blinded automated evaluations with matched inputs and inference settings across diverse student profiles, GraphMASAL consistently outperforms LLM prompting and structured ablations in planning--achieving stronger structural/sequence alignment of learning paths, higher coverage of weak concepts, and lower learning cost--while also surpassing prompt-based baselines in cognitive diagnosis. Agreement with expert/LLM-proxy ratings further supports the validity of our evaluation protocol. These findings indicate that grounding LLM agents in a dynamic knowledge graph, coupled with optimization under educational constraints, yields reliable, interpretable, and pedagogically plausible learning plans, advancing personalized and goal-oriented education.

  • 3 authors
·
Nov 14

RoboMemory: A Brain-inspired Multi-memory Agentic Framework for Lifelong Learning in Physical Embodied Systems

We present RoboMemory, a brain-inspired multi-memory framework for lifelong learning in physical embodied systems, addressing critical challenges in real-world environments: continuous learning, multi-module memory latency, task correlation capture, and infinite-loop mitigation in closed-loop planning. Grounded in cognitive neuroscience, it integrates four core modules: the Information Preprocessor (thalamus-like), the Lifelong Embodied Memory System (hippocampus-like), the Closed-Loop Planning Module (prefrontal lobe-like), and the Low-Level Executer (cerebellum-like) to enable long-term planning and cumulative learning. The Lifelong Embodied Memory System, central to the framework, alleviates inference speed issues in complex memory frameworks via parallelized updates/retrieval across Spatial, Temporal, Episodic, and Semantic submodules. It incorporates a dynamic Knowledge Graph (KG) and consistent architectural design to enhance memory consistency and scalability. Evaluations on EmbodiedBench show RoboMemory outperforms the open-source baseline (Qwen2.5-VL-72B-Ins) by 25% in average success rate and surpasses the closed-source State-of-the-Art (SOTA) (Claude3.5-Sonnet) by 5%, establishing new SOTA. Ablation studies validate key components (critic, spatial memory, long-term memory), while real-world deployment confirms its lifelong learning capability with significantly improved success rates across repeated tasks. RoboMemory alleviates high latency challenges with scalability, serving as a foundational reference for integrating multi-modal memory systems in physical robots.

PRefLexOR: Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning and Agentic Thinking

PRefLexOR (Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning) combines preference optimization with concepts from Reinforcement Learning to enable models to self-teach through iterative reasoning improvements. We propose a recursive learning approach that engages the model in multi-step reasoning, revisiting, and refining intermediate steps before producing a final output in training and inference phases. Through multiple training stages, the model first learns to align its reasoning with accurate decision paths by optimizing the log odds between preferred and non-preferred responses. During this process, PRefLexOR builds a dynamic knowledge graph by generating questions from random text chunks and retrieval-augmentation to contextualize relevant details from the entire training corpus. In the second stage, preference optimization enhances model performance by using rejection sampling to fine-tune reasoning quality by continually producing in-situ training data while masking the reasoning steps. Recursive optimization within a thinking token framework introduces iterative feedback loops, where the model refines reasoning, achieving deeper coherence, consistency, and adaptability. Implemented in small language models with only 3 billion parameters, we should that even tiny models can iteratively teach themselves to reason with greater depth and reflectivity. Our implementation is straightforward and can be incorporated into any existing pretrained LLM. We focus our examples on applications in biological materials science and demonstrate the method in a variety of case studies that range from in-domain to cross-domain applications. Using reasoning strategies that include thinking and reflection modalities we build a multi-agent recursive self-improving inference approach to successively improve responses via repeated sampling in inference time.

  • 1 authors
·
Oct 16, 2024

MemoTime: Memory-Augmented Temporal Knowledge Graph Enhanced Large Language Model Reasoning

Large Language Models (LLMs) have achieved impressive reasoning abilities, but struggle with temporal understanding, especially when questions involve multiple entities, compound operators, and evolving event sequences. Temporal Knowledge Graphs (TKGs), which capture vast amounts of temporal facts in a structured format, offer a reliable source for temporal reasoning. However, existing TKG-based LLM reasoning methods still struggle with four major challenges: maintaining temporal faithfulness in multi-hop reasoning, achieving multi-entity temporal synchronization, adapting retrieval to diverse temporal operators, and reusing prior reasoning experience for stability and efficiency. To address these issues, we propose MemoTime, a memory-augmented temporal knowledge graph framework that enhances LLM reasoning through structured grounding, recursive reasoning, and continual experience learning. MemoTime decomposes complex temporal questions into a hierarchical Tree of Time, enabling operator-aware reasoning that enforces monotonic timestamps and co-constrains multiple entities under unified temporal bounds. A dynamic evidence retrieval layer adaptively selects operator-specific retrieval strategies, while a self-evolving experience memory stores verified reasoning traces, toolkit decisions, and sub-question embeddings for cross-type reuse. Comprehensive experiments on multiple temporal QA benchmarks show that MemoTime achieves overall state-of-the-art results, outperforming the strong baseline by up to 24.0%. Furthermore, MemoTime enables smaller models (e.g., Qwen3-4B) to achieve reasoning performance comparable to that of GPT-4-Turbo.

  • 7 authors
·
Oct 15

Paths-over-Graph: Knowledge Graph Empowered Large Language Model Reasoning

Large Language Models (LLMs) have achieved impressive results in various tasks but struggle with hallucination problems and lack of relevant knowledge, especially in deep complex reasoning and knowledge-intensive tasks. Knowledge Graphs (KGs), which capture vast amounts of facts in a structured format, offer a reliable source of knowledge for reasoning. However, existing KG-based LLM reasoning methods face challenges like handling multi-hop reasoning, multi-entity questions, and effectively utilizing graph structures. To address these issues, we propose Paths-over-Graph (PoG), a novel method that enhances LLM reasoning by integrating knowledge reasoning paths from KGs, improving the interpretability and faithfulness of LLM outputs. PoG tackles multi-hop and multi-entity questions through a three-phase dynamic multi-hop path exploration, which combines the inherent knowledge of LLMs with factual knowledge from KGs. In order to improve the efficiency, PoG prunes irrelevant information from the graph exploration first and introduces efficient three-step pruning techniques that incorporate graph structures, LLM prompting, and a pre-trained language model (e.g., SBERT) to effectively narrow down the explored candidate paths. This ensures all reasoning paths contain highly relevant information captured from KGs, making the reasoning faithful and interpretable in problem-solving. PoG innovatively utilizes graph structure to prune the irrelevant noise and represents the first method to implement multi-entity deep path detection on KGs for LLM reasoning tasks. Comprehensive experiments on five benchmark KGQA datasets demonstrate PoG outperforms the state-of-the-art method ToG across GPT-3.5-Turbo and GPT-4, achieving an average accuracy improvement of 18.9%. Notably, PoG with GPT-3.5-Turbo surpasses ToG with GPT-4 by up to 23.9%.

  • 6 authors
·
Oct 18, 2024

UniOQA: A Unified Framework for Knowledge Graph Question Answering with Large Language Models

OwnThink stands as the most extensive Chinese open-domain knowledge graph introduced in recent times. Despite prior attempts in question answering over OwnThink (OQA), existing studies have faced limitations in model representation capabilities, posing challenges in further enhancing overall accuracy in question answering. In this paper, we introduce UniOQA, a unified framework that integrates two complementary parallel workflows. Unlike conventional approaches, UniOQA harnesses large language models (LLMs) for precise question answering and incorporates a direct-answer-prediction process as a cost-effective complement. Initially, to bolster representation capacity, we fine-tune an LLM to translate questions into the Cypher query language (CQL), tackling issues associated with restricted semantic understanding and hallucinations. Subsequently, we introduce the Entity and Relation Replacement algorithm to ensure the executability of the generated CQL. Concurrently, to augment overall accuracy in question answering, we further adapt the Retrieval-Augmented Generation (RAG) process to the knowledge graph. Ultimately, we optimize answer accuracy through a dynamic decision algorithm. Experimental findings illustrate that UniOQA notably advances SpCQL Logical Accuracy to 21.2% and Execution Accuracy to 54.9%, achieving the new state-of-the-art results on this benchmark. Through ablation experiments, we delve into the superior representation capacity of UniOQA and quantify its performance breakthrough.

  • 5 authors
·
Jun 4, 2024

What's In Your Field? Mapping Scientific Research with Knowledge Graphs and Large Language Models

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

  • 4 authors
·
Mar 12

Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

  • 6 authors
·
May 3

RareBench: Can LLMs Serve as Rare Diseases Specialists?

Generalist Large Language Models (LLMs), such as GPT-4, have shown considerable promise in various domains, including medical diagnosis. Rare diseases, affecting approximately 300 million people worldwide, often have unsatisfactory clinical diagnosis rates primarily due to a lack of experienced physicians and the complexity of differentiating among many rare diseases. In this context, recent news such as "ChatGPT correctly diagnosed a 4-year-old's rare disease after 17 doctors failed" underscore LLMs' potential, yet underexplored, role in clinically diagnosing rare diseases. To bridge this research gap, we introduce RareBench, a pioneering benchmark designed to systematically evaluate the capabilities of LLMs on 4 critical dimensions within the realm of rare diseases. Meanwhile, we have compiled the largest open-source dataset on rare disease patients, establishing a benchmark for future studies in this domain. To facilitate differential diagnosis of rare diseases, we develop a dynamic few-shot prompt methodology, leveraging a comprehensive rare disease knowledge graph synthesized from multiple knowledge bases, significantly enhancing LLMs' diagnostic performance. Moreover, we present an exhaustive comparative study of GPT-4's diagnostic capabilities against those of specialist physicians. Our experimental findings underscore the promising potential of integrating LLMs into the clinical diagnostic process for rare diseases. This paves the way for exciting possibilities in future advancements in this field.

  • 6 authors
·
Feb 9, 2024

HM-RAG: Hierarchical Multi-Agent Multimodal Retrieval Augmented Generation

While Retrieval-Augmented Generation (RAG) augments Large Language Models (LLMs) with external knowledge, conventional single-agent RAG remains fundamentally limited in resolving complex queries demanding coordinated reasoning across heterogeneous data ecosystems. We present HM-RAG, a novel Hierarchical Multi-agent Multimodal RAG framework that pioneers collaborative intelligence for dynamic knowledge synthesis across structured, unstructured, and graph-based data. The framework is composed of three-tiered architecture with specialized agents: a Decomposition Agent that dissects complex queries into contextually coherent sub-tasks via semantic-aware query rewriting and schema-guided context augmentation; Multi-source Retrieval Agents that carry out parallel, modality-specific retrieval using plug-and-play modules designed for vector, graph, and web-based databases; and a Decision Agent that uses consistency voting to integrate multi-source answers and resolve discrepancies in retrieval results through Expert Model Refinement. This architecture attains comprehensive query understanding by combining textual, graph-relational, and web-derived evidence, resulting in a remarkable 12.95% improvement in answer accuracy and a 3.56% boost in question classification accuracy over baseline RAG systems on the ScienceQA and CrisisMMD benchmarks. Notably, HM-RAG establishes state-of-the-art results in zero-shot settings on both datasets. Its modular architecture ensures seamless integration of new data modalities while maintaining strict data governance, marking a significant advancement in addressing the critical challenges of multimodal reasoning and knowledge synthesis in RAG systems. Code is available at https://github.com/ocean-luna/HMRAG.

  • 7 authors
·
Apr 13

BioGraphFusion: Graph Knowledge Embedding for Biological Completion and Reasoning

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

  • 6 authors
·
Jul 19

HuixiangDou2: A Robustly Optimized GraphRAG Approach

Large Language Models (LLMs) perform well on familiar queries but struggle with specialized or emerging topics. Graph-based Retrieval-Augmented Generation (GraphRAG) addresses this by structuring domain knowledge as a graph for dynamic retrieval. However, existing pipelines involve complex engineering workflows, making it difficult to isolate the impact of individual components. Evaluating retrieval effectiveness is also challenging due to dataset overlap with LLM pretraining data. In this work, we introduce HuixiangDou2, a robustly optimized GraphRAG framework. Specifically, we leverage the effectiveness of dual-level retrieval and optimize its performance in a 32k context for maximum precision, and compare logic-based retrieval and dual-level retrieval to enhance overall functionality. Our implementation includes comparative experiments on a test set, where Qwen2.5-7B-Instruct initially underperformed. With our approach, the score improved significantly from 60 to 74.5, as illustrated in the Figure. Experiments on domain-specific datasets reveal that dual-level retrieval enhances fuzzy matching, while logic-form retrieval improves structured reasoning. Furthermore, we propose a multi-stage verification mechanism to improve retrieval robustness without increasing computational cost. Empirical results show significant accuracy gains over baselines, highlighting the importance of adaptive retrieval. To support research and adoption, we release HuixiangDou2 as an open-source resource https://github.com/tpoisonooo/huixiangdou2.

  • 5 authors
·
Mar 9

Agentic Deep Graph Reasoning Yields Self-Organizing Knowledge Networks

We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.

  • 1 authors
·
Feb 18

PointDistiller: Structured Knowledge Distillation Towards Efficient and Compact 3D Detection

The remarkable breakthroughs in point cloud representation learning have boosted their usage in real-world applications such as self-driving cars and virtual reality. However, these applications usually have an urgent requirement for not only accurate but also efficient 3D object detection. Recently, knowledge distillation has been proposed as an effective model compression technique, which transfers the knowledge from an over-parameterized teacher to a lightweight student and achieves consistent effectiveness in 2D vision. However, due to point clouds' sparsity and irregularity, directly applying previous image-based knowledge distillation methods to point cloud detectors usually leads to unsatisfactory performance. To fill the gap, this paper proposes PointDistiller, a structured knowledge distillation framework for point clouds-based 3D detection. Concretely, PointDistiller includes local distillation which extracts and distills the local geometric structure of point clouds with dynamic graph convolution and reweighted learning strategy, which highlights student learning on the crucial points or voxels to improve knowledge distillation efficiency. Extensive experiments on both voxels-based and raw points-based detectors have demonstrated the effectiveness of our method over seven previous knowledge distillation methods. For instance, our 4X compressed PointPillars student achieves 2.8 and 3.4 mAP improvements on BEV and 3D object detection, outperforming its teacher by 0.9 and 1.8 mAP, respectively. Codes have been released at https://github.com/RunpeiDong/PointDistiller.

  • 4 authors
·
May 23, 2022

MedKGent: A Large Language Model Agent Framework for Constructing Temporally Evolving Medical Knowledge Graph

The rapid expansion of medical literature presents growing challenges for structuring and integrating domain knowledge at scale. Knowledge Graphs (KGs) offer a promising solution by enabling efficient retrieval, automated reasoning, and knowledge discovery. However, current KG construction methods often rely on supervised pipelines with limited generalizability or naively aggregate outputs from Large Language Models (LLMs), treating biomedical corpora as static and ignoring the temporal dynamics and contextual uncertainty of evolving knowledge. To address these limitations, we introduce MedKGent, a LLM agent framework for constructing temporally evolving medical KGs. Leveraging over 10 million PubMed abstracts published between 1975 and 2023, we simulate the emergence of biomedical knowledge via a fine-grained daily time series. MedKGent incrementally builds the KG in a day-by-day manner using two specialized agents powered by the Qwen2.5-32B-Instruct model. The Extractor Agent identifies knowledge triples and assigns confidence scores via sampling-based estimation, which are used to filter low-confidence extractions and inform downstream processing. The Constructor Agent incrementally integrates the retained triples into a temporally evolving graph, guided by confidence scores and timestamps to reinforce recurring knowledge and resolve conflicts. The resulting KG contains 156,275 entities and 2,971,384 relational triples. Quality assessments by two SOTA LLMs and three domain experts demonstrate an accuracy approaching 90%, with strong inter-rater agreement. To evaluate downstream utility, we conduct RAG across seven medical question answering benchmarks using five leading LLMs, consistently observing significant improvements over non-augmented baselines. Case studies further demonstrate the KG's value in literature-based drug repurposing via confidence-aware causal inference.

  • 13 authors
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Aug 17