Finding interesting phenomena is the core of scientific discovery, but it is a manual, ill-defined concept. We present an integrative pipeline for automating the discovery of interesting simple hypotheses (feature-target relations with effect direction and a potential underlying mechanism) in structured biomedical data. The pipeline combines machine learning, knowledge graphs, literature search and Large Language Models. We formalize "interestingness" as a combination of novelty, utility and plausibility. On 8 major diseases from the UK Biobank, our pipeline consistently recovers risk factors years before their appearance in the literature. 40--53% of our top candidates were validated as interesting, compared to 0--7% for a SHAP-based baseline. Overall, 28% of 109 candidates were interesting to medical experts. The pipeline addresses the challenge of operationalizing "interestingness" scalably and for any target. We release data and code: https://github.com/LinialLab/InterFeat
Recent advances in large language models (LLMs) have led to impressive progress in natural language generation, yet their tendency to produce hallucinated or unsubstantiated content remains a critical concern. To improve factual reliability, Retrieval-Augmented Generation (RAG) integrates external knowledge during inference. However, existing RAG systems face two major limitations: (1) unreliable adaptive control due to limited external knowledge supervision, and (2) hallucinations caused by inaccurate or irrelevant references. To address these issues, we propose Know3-RAG, a knowledge-aware RAG framework that leverages structured knowledge from knowledge graphs (KGs) to guide three core stages of the RAG process, including retrieval, generation, and filtering. Specifically, we introduce a knowledge-aware adaptive retrieval module that employs KG embedding to assess the confidence of the generated answer and determine retrieval necessity, a knowledge-enhanced reference generation strategy that enriches queries with KG-derived entities to improve generated reference relevance, and a knowledge-driven reference filtering mechanism that ensures semantic alignment and factual accuracy of references. Experiments on multiple open-domain QA benchmarks demonstrate that Know3-RAG consistently outperforms strong baselines, significantly reducing hallucinations and enhancing answer reliability.
Current Large Language Models (LLMs) can assist developing program code beside many other things, but can they support working with Knowledge Graphs (KGs) as well? Which LLM is offering the best capabilities in the field of Semantic Web and Knowledge Graph Engineering (KGE)? Is this possible to determine without checking many answers manually? The LLM-KG-Bench framework in Version 3.0 is designed to answer these questions. It consists of an extensible set of tasks for automated evaluation of LLM answers and covers different aspects of working with semantic technologies. In this paper the LLM-KG-Bench framework is presented in Version 3 along with a dataset of prompts, answers and evaluations generated with it and several state-of-the-art LLMs. Significant enhancements have been made to the framework since its initial release, including an updated task API that offers greater flexibility in handling evaluation tasks, revised tasks, and extended support for various open models through the vllm library, among other improvements. A comprehensive dataset has been generated using more than 30 contemporary open and proprietary LLMs, enabling the creation of exemplary model cards that demonstrate the models' capabilities in working with RDF and SPARQL, as well as comparing their performance on Turtle and JSON-LD RDF serialization tasks.
Recent studies on large language model (LLM) reasoning capabilities have demonstrated promising improvements in model performance by leveraging a lengthy thinking process and additional computational resources during inference, primarily in tasks involving mathematical reasoning (Muennighoff et al., 2025). However, it remains uncertain if longer reasoning chains inherently enhance factual accuracy, particularly beyond mathematical contexts. In this work, we thoroughly examine LLM reasoning within complex open-domain question-answering (QA) scenarios. We initially distill reasoning traces from advanced, large-scale reasoning models (QwQ-32B and DeepSeek-R1-671B), then fine-tune a variety of models ranging from smaller, instruction-tuned variants to larger architectures based on Qwen2.5. To enrich reasoning traces, we introduce factual information from knowledge graphs in the form of paths into our reasoning traces. Our experimental setup includes four baseline approaches and six different instruction-tuned models evaluated across a benchmark of six datasets, encompassing over 22.6K questions. Overall, we carry out 168 experimental runs and analyze approximately 1.7 million reasoning traces. Our findings indicate that, within a single run, smaller reasoning models achieve noticeable improvements in factual accuracy compared to their original instruction-tuned counterparts. Moreover, our analysis demonstrates that adding test-time compute and token budgets factual accuracy consistently improves by 2-8%, further confirming the effectiveness of test-time scaling for enhancing performance and consequently improving reasoning accuracy in open-domain QA tasks. We release all the experimental artifacts for further research.
Retrieval-Augmented Generation (RAG) has emerged as a powerful paradigm for enhancing the capabilities of large language models. However, existing RAG evaluation predominantly focuses on text retrieval and relies on opaque, end-to-end assessments of generated outputs. To address these limitations, we introduce mmRAG, a modular benchmark designed for evaluating multi-modal RAG systems. Our benchmark integrates queries from six diverse question-answering datasets spanning text, tables, and knowledge graphs, which we uniformly convert into retrievable documents. To enable direct, granular evaluation of individual RAG components -- such as the accuracy of retrieval and query routing -- beyond end-to-end generation quality, we follow standard information retrieval procedures to annotate document relevance and derive dataset relevance. We establish baseline performance by evaluating a wide range of RAG implementations on mmRAG.
The advent of large language models (LLMs) has allowed numerous applications, including the generation of queried responses, to be leveraged in chatbots and other conversational assistants. Being trained on a plethora of data, LLMs often undergo high levels of over-fitting, resulting in the generation of extra and incorrect data, thus causing hallucinations in output generation. One of the root causes of such problems is the lack of timely, factual, and personalized information fed to the LLM. In this paper, we propose an approach to address these problems by introducing retrieval augmented generation (RAG) using knowledge graphs (KGs) to assist the LLM in personalized response generation tailored to the users. KGs have the advantage of storing continuously updated factual information in a structured way. While our KGs can be used for a variety of frequently updated personal data, such as calendar, contact, and location data, we focus on calendar data in this paper. Our experimental results show that our approach works significantly better in understanding personal information and generating accurate responses compared to the baseline LLMs using personal data as text inputs, with a moderate reduction in response time.
In many real-world settings, machine learning models and interactive systems have access to both structured knowledge, e.g., knowledge graphs or tables, and unstructured content, e.g., natural language documents. However, most rely on either. Semi-Structured Knowledge Bases (SKBs) bridge this gap by linking unstructured content to nodes within structured data, thereby enabling new strategies for knowledge access and use. In this work, we present FocusedRetriever, a modular SKB-based framework for multi-hop question answering. It integrates components (VSS-based entity search, LLM-based generation of Cypher queries and pairwise re-ranking) in a way that enables it to outperform state-of-the-art methods across all three STaRK benchmark test sets, covering diverse domains and multiple performance metrics. The average first-hit rate exceeds that of the second-best method by 25.7%. FocusedRetriever leverages (1) the capacity of Large Language Models (LLMs) to extract relational facts and entity attributes from unstructured text, (2) node set joins to filter answer candidates based on these extracted triplets and constraints, (3) vector similarity search to retrieve and rank relevant unstructured content, and (4) the contextual capabilities of LLMs to finally rank the top-k answers. For generality, we only incorporate base LLMs in FocusedRetriever in our evaluation. However, our analysis of intermediate results highlights several opportunities for further upgrades including finetuning. The source code is publicly available at https://github.com/kramerlab/FocusedRetriever .
Benefiting from the effectiveness of graph neural networks (GNNs) and contrastive learning, GNN-based contrastive learning has become mainstream for knowledge-aware recommendation. However, most existing contrastive learning-based methods have difficulties in effectively capturing the underlying hierarchical structure within user-item bipartite graphs and knowledge graphs. Moreover, they commonly generate positive samples for contrastive learning by perturbing the graph structure, which may lead to a shift in user preference learning. To overcome these limitations, we propose hyperbolic contrastive learning with model-augmentation for knowledge-aware recommendation. To capture the intrinsic hierarchical graph structures, we first design a novel Lorentzian knowledge aggregation mechanism, which enables more effective representations of users and items. Then, we propose three model-level augmentation techniques to assist Hyperbolic contrastive learning. Different from the classical structure-level augmentation (e.g., edge dropping), the proposed model-augmentations can avoid preference shifts between the augmented positive pair. Finally, we conduct extensive experiments to demonstrate the superiority (maximum improvement of $11.03\%$) of proposed methods over existing baselines.
Outdated facts in temporal knowledge graphs (TKGs) result from exceeding the expiration date of facts, which negatively impact reasoning performance on TKGs. However, existing reasoning methods primarily focus on positive importance of historical facts, neglecting adverse effects of outdated facts. Besides, training on these outdated facts yields extra computational cost. To address these challenges, we propose an outdated fact filtering framework named HALO, which quantifies the temporal validity of historical facts by exploring the half-life theory to filter outdated facts in TKGs. HALO consists of three modules: the temporal fact attention module, the dynamic relation-aware encoder module, and the outdated fact filtering module. Firstly, the temporal fact attention module captures the evolution of historical facts over time to identify relevant facts. Secondly, the dynamic relation-aware encoder module is designed for efficiently predicting the half life of each fact. Finally, we construct a time decay function based on the half-life theory to quantify the temporal validity of facts and filter outdated facts. Experimental results show that HALO outperforms the state-of-the-art TKG reasoning methods on three public datasets, demonstrating its effectiveness in detecting and filtering outdated facts (Codes are available at https://github.com/yushuowiki/K-Half/tree/main ).
Knowledge Graphs (KGs), composed of triples in the form of (head, relation, tail) and consisting of entities and relations, play a key role in information retrieval systems such as question answering, entity search, and recommendation. In real-world KGs, although many entities exist, the relations exhibit a long-tail distribution, which can hinder information retrieval performance. Previous few-shot knowledge graph completion studies focused exclusively on the positive triple information that exists in the graph or, when negative triples were incorporated, used them merely as a signal to indicate incorrect triples. To overcome this limitation, we propose Relation-Based Conditional Diffusion with Attention Pooling (ReCDAP). First, negative triples are generated by randomly replacing the tail entity in the support set. By conditionally incorporating positive information in the KG and non-existent negative information into the diffusion process, the model separately estimates the latent distributions for positive and negative relations. Moreover, including an attention pooler enables the model to leverage the differences between positive and negative cases explicitly. Experiments on two widely used datasets demonstrate that our method outperforms existing approaches, achieving state-of-the-art performance. The code is available at https://github.com/hou27/ReCDAP-FKGC.
Large language models (LLMs) have achieved unprecedented performance by leveraging vast pretraining corpora, yet their performance remains suboptimal in knowledge-intensive domains such as medicine and scientific research, where high factual precision is required. While synthetic data provides a promising avenue for augmenting domain knowledge, existing methods frequently generate redundant samples that do not align with the model's true knowledge gaps. To overcome this limitation, we propose a novel Structural Entropy-guided Knowledge Navigator (SENATOR) framework that addresses the intrinsic knowledge deficiencies of LLMs. Our approach employs the Structure Entropy (SE) metric to quantify uncertainty along knowledge graph paths and leverages Monte Carlo Tree Search (MCTS) to selectively explore regions where the model lacks domain-specific knowledge. Guided by these insights, the framework generates targeted synthetic data for supervised fine-tuning, enabling continuous self-improvement. Experimental results on LLaMA-3 and Qwen2 across multiple domain-specific benchmarks show that SENATOR effectively detects and repairs knowledge deficiencies, achieving notable performance improvements. The code and data for our methods and experiments are available at https://github.com/weiyifan1023/senator.
Hierarchical Text Classification (HTC) involves assigning documents to labels organized within a taxonomy. Most previous research on HTC has focused on supervised methods. However, in real-world scenarios, employing supervised HTC can be challenging due to a lack of annotated data. Moreover, HTC often faces issues with large label spaces and long-tail distributions. In this work, we present Knowledge Graphs for zero-shot Hierarchical Text Classification (KG-HTC), which aims to address these challenges of HTC in applications by integrating knowledge graphs with Large Language Models (LLMs) to provide structured semantic context during classification. Our method retrieves relevant subgraphs from knowledge graphs related to the input text using a Retrieval-Augmented Generation (RAG) approach. Our KG-HTC can enhance LLMs to understand label semantics at various hierarchy levels. We evaluate KG-HTC on three open-source HTC datasets: WoS, DBpedia, and Amazon. Our experimental results show that KG-HTC significantly outperforms three baselines in the strict zero-shot setting, particularly achieving substantial improvements at deeper levels of the hierarchy. This evaluation demonstrates the effectiveness of incorporating structured knowledge into LLMs to address HTC's challenges in large label spaces and long-tailed label distributions. Our code is available at: https://github.com/QianboZang/KG-HTC.
Unstructured clinical data can serve as a unique and rich source of information that can meaningfully inform clinical practice. Extracting the most pertinent context from such data is critical for exploiting its true potential toward optimal and timely decision-making in patient care. While prior research has explored various methods for clinical text summarization, most prior studies either process all input tokens uniformly or rely on heuristic-based filters, which can overlook nuanced clinical cues and fail to prioritize information critical for decision-making. In this study, we propose Contextual, a novel framework that integrates a Context-Preserving Token Filtering method with a Domain-Specific Knowledge Graph (KG) for contextual augmentation. By preserving context-specific important tokens and enriching them with structured knowledge, ConTextual improves both linguistic coherence and clinical fidelity. Our extensive empirical evaluations on two public benchmark datasets demonstrate that ConTextual consistently outperforms other baselines. Our proposed approach highlights the complementary role of token-level filtering and structured retrieval in enhancing both linguistic and clinical integrity, as well as offering a scalable solution for improving precision in clinical text generation.
While Knowledge Graphs (KGs) have become increasingly popular across various scientific disciplines for their ability to model and interlink huge quantities of data, essentially all real-world KGs are known to be incomplete. As such, with the growth of KG use has been a concurrent development of machine learning tools designed to predict missing information in KGs, which is referred to as the Link Prediction Task. The majority of state-of-the-art link predictors to date have followed an embedding-based paradigm. In this paradigm, it is assumed that the information content of a KG is best represented by the (individual) vector representations of its nodes and edges, and that therefore node and edge embeddings are particularly well-suited to performing link prediction. This thesis proposes an alternative perspective on the field's approach to link prediction and KG data modelling. Specifically, this work re-analyses KGs and state-of-the-art link predictors from a graph-structure-first perspective that models the information content of a KG in terms of whole triples, rather than individual nodes and edges. Following a literature review and two core sets of experiments, this thesis concludes that a structure-first perspective on KGs and link prediction is both viable and useful for understanding KG learning and for enabling cross-KG transfer learning for the link prediction task. This observation is used to create and propose the Structural Alignment Hypothesis, which postulates that link prediction can be understood and modelled as a structural task. All code and data used for this thesis are open-sourced. This thesis was written bilingually, with the main document in English and an informal extended summary in Irish. An Irish-language translation dictionary of machine learning terms (the Focl\'oir Tr\'achtais) created for this work is open-sourced as well.
Can we build accurate world models out of large language models (LLMs)? How can world models benefit LLM agents? The gap between the prior knowledge of LLMs and the specified environment's dynamics usually bottlenecks LLMs' performance as world models. To bridge the gap, we propose a training-free "world alignment" that learns an environment's symbolic knowledge complementary to LLMs. The symbolic knowledge covers action rules, knowledge graphs, and scene graphs, which are extracted by LLMs from exploration trajectories and encoded into executable codes to regulate LLM agents' policies. We further propose an RL-free, model-based agent "WALL-E 2.0" through the model-predictive control (MPC) framework. Unlike classical MPC requiring costly optimization on the fly, we adopt an LLM agent as an efficient look-ahead optimizer of future steps' actions by interacting with the neurosymbolic world model. While the LLM agent's strong heuristics make it an efficient planner in MPC, the quality of its planned actions is also secured by the accurate predictions of the aligned world model. They together considerably improve learning efficiency in a new environment. On open-world challenges in Mars (Minecraft like) and ALFWorld (embodied indoor environments), WALL-E 2.0 significantly outperforms existing methods, e.g., surpassing baselines in Mars by 16.1%-51.6% of success rate and by at least 61.7% in score. In ALFWorld, it achieves a new record 98% success rate after only 4 iterations.
This paper presents a domain-specific implementation of Retrieval-Augmented Generation (RAG) tailored to the Fair Use Doctrine in U.S. copyright law. Motivated by the increasing prevalence of DMCA takedowns and the lack of accessible legal support for content creators, we propose a structured approach that combines semantic search with legal knowledge graphs and court citation networks to improve retrieval quality and reasoning reliability. Our prototype models legal precedents at the statutory factor level (e.g., purpose, nature, amount, market effect) and incorporates citation-weighted graph representations to prioritize doctrinally authoritative sources. We use Chain-of-Thought reasoning and interleaved retrieval steps to better emulate legal reasoning. Preliminary testing suggests this method improves doctrinal relevance in the retrieval process, laying groundwork for future evaluation and deployment of LLM-based legal assistance tools.
Automatic relationship extraction (RE) from biomedical literature is critical for managing the vast amount of scientific knowledge produced each year. In recent years, utilizing pre-trained language models (PLMs) has become the prevalent approach in RE. Several studies report improved performance when incorporating additional context information while fine-tuning PLMs for RE. However, variations in the PLMs applied, the databases used for augmentation, hyper-parameter optimization, and evaluation methods complicate direct comparisons between studies and raise questions about the generalizability of these findings. Our study addresses this research gap by evaluating PLMs enhanced with contextual information on five datasets spanning four relation scenarios within a consistent evaluation framework. We evaluate three baseline PLMs and first conduct extensive hyperparameter optimization. After selecting the top-performing model, we enhance it with additional data, including textual entity descriptions, relational information from knowledge graphs, and molecular structure encodings. Our findings illustrate the importance of i) the choice of the underlying language model and ii) a comprehensive hyperparameter optimization for achieving strong extraction performance. Although inclusion of context information yield only minor overall improvements, an ablation study reveals substantial benefits for smaller PLMs when such external data was included during fine-tuning.
Multi-Modal Entity Alignment (MMEA) aims to retrieve equivalent entities from different Multi-Modal Knowledge Graphs (MMKGs), a critical information retrieval task. Existing studies have explored various fusion paradigms and consistency constraints to improve the alignment of equivalent entities, while overlooking that the visual modality may not always contribute positively. Empirically, entities with low-similarity images usually generate unsatisfactory performance, highlighting the limitation of overly relying on visual features. We believe the model can be biased toward the visual modality, leading to a shortcut image-matching task. To address this, we propose a counterfactual debiasing framework for MMEA, termed CDMEA, which investigates visual modality bias from a causal perspective. Our approach aims to leverage both visual and graph modalities to enhance MMEA while suppressing the direct causal effect of the visual modality on model predictions. By estimating the Total Effect (TE) of both modalities and excluding the Natural Direct Effect (NDE) of the visual modality, we ensure that the model predicts based on the Total Indirect Effect (TIE), effectively utilizing both modalities and reducing visual modality bias. Extensive experiments on 9 benchmark datasets show that CDMEA outperforms 14 state-of-the-art methods, especially in low-similarity, high-noise, and low-resource data scenarios.
Training high-quality CLIP models typically requires enormous datasets, which limits the development of domain-specific models -- especially in areas that even the largest CLIP models do not cover well -- and drives up training costs. This poses challenges for scientific research that needs fine-grained control over the training procedure of CLIP models. In this work, we show that by employing smart web search strategies enhanced with knowledge graphs, a robust CLIP model can be trained from scratch with considerably less data. Specifically, we demonstrate that an expert foundation model for living organisms can be built using just 10M images. Moreover, we introduce EntityNet, a dataset comprising 33M images paired with 46M text descriptions, which enables the training of a generic CLIP model in significantly reduced time.
Knowledge Graphs have become increasingly popular due to their wide usage in various downstream applications, including information retrieval, chatbot development, language model construction, and many others. Link prediction (LP) is a crucial downstream task for knowledge graphs, as it helps to address the problem of the incompleteness of the knowledge graphs. However, previous research has shown that knowledge graphs, often created in a (semi) automatic manner, are not free from social biases. These biases can have harmful effects on downstream applications, especially by leading to unfair behavior toward minority groups. To understand this issue in detail, we develop a framework -- AuditLP -- deploying fairness metrics to identify biased outcomes in LP, specifically how occupations are classified as either male or female-dominated based on gender as a sensitive attribute. We have experimented with the sensitive attribute of age and observed that occupations are categorized as young-biased, old-biased, and age-neutral. We conduct our experiments on a large number of knowledge triples that belong to 21 different geographies extracted from the open-sourced knowledge graph, Wikidata. Our study shows that the variance in the biased outcomes across geographies neatly mirrors the socio-economic and cultural division of the world, resulting in a transparent partition of the Global North from the Global South.