Geometric embedding methods have shown to be useful for multi-hop reasoning on knowledge graphs by mapping entities and logical operations to geometric regions and geometric transformations, respectively. Geometric embeddings provide direct interpretability framework for queries. However, current methods have only leveraged the geometric construction of entities, failing to map logical operations to geometric transformations and, instead, using neural components to learn these operations. We introduce GeometrE, a geometric embedding method for multi-hop reasoning, which does not require learning the logical operations and enables full geometric interpretability. Additionally, unlike previous methods, we introduce a transitive loss function and show that it can preserve the logical rule $\forall a,b,c: r(a,b) \land r(b,c) \to r(a,c)$. Our experiments show that GeometrE outperforms current state-of-the-art methods on standard benchmark datasets.
Rule mining in knowledge graphs enables interpretable link prediction. However, deep learning-based rule mining methods face significant memory and time challenges for large-scale knowledge graphs, whereas traditional approaches, limited by rigid confidence metrics, incur high computational costs despite sampling techniques. To address these challenges, we propose MPRM, a novel rule mining method that models rule-based inference as a Markov chain and uses an efficient confidence metric derived from aggregated path probabilities, significantly lowering computational demands. Experiments on multiple datasets show that MPRM efficiently mines knowledge graphs with over a million facts, sampling less than 1% of facts on a single CPU in 22 seconds, while preserving interpretability and boosting inference accuracy by up to 11% over baselines.
Knowledge graphs (KGs) serve as fundamental structures for organizing interconnected data across diverse domains. However, most KGs remain incomplete, limiting their effectiveness in downstream applications. Knowledge graph completion (KGC) aims to address this issue by inferring missing links, but existing methods face critical challenges: deep graph neural networks (GNNs) suffer from over-smoothing, while embedding-based models fail to capture abstract relational features. This study aims to overcome these limitations by proposing a unified framework that integrates GNN distillation and abstract probabilistic interaction modeling (APIM). GNN distillation approach introduces an iterative message-feature filtering process to mitigate over-smoothing, preserving the discriminative power of node representations. APIM module complements this by learning structured, abstract interaction patterns through probabilistic signatures and transition matrices, allowing for a richer, more flexible representation of entity and relation interactions. We apply these methods to GNN-based models and the APIM to embedding-based KGC models, conducting extensive evaluations on the widely used WN18RR and FB15K-237 datasets. Our results demonstrate significant performance gains over baseline models, showcasing the effectiveness of the proposed techniques. The findings highlight the importance of both controlling information propagation and leveraging structured probabilistic modeling, offering new avenues for advancing knowledge graph completion. And our codes are available at https://anonymous.4open.science/r/APIM_and_GNN-Distillation-461C.
Many real-world scientific and industrial applications require the optimization of expensive black-box functions. Bayesian Optimization (BO) provides an effective framework for such problems. However, traditional BO methods are prone to get trapped in local optima and often lack interpretable insights. To address this issue, this paper designs Reasoning BO, a novel framework that leverages reasoning models to guide the sampling process in BO while incorporating multi-agent systems and knowledge graphs for online knowledge accumulation. By integrating the reasoning and contextual understanding capabilities of Large Language Models (LLMs), we can provide strong guidance to enhance the BO process. As the optimization progresses, Reasoning BO provides real-time sampling recommendations along with critical insights grounded in plausible scientific theories, aiding in the discovery of superior solutions within the search space. We systematically evaluate our approach across 10 diverse tasks encompassing synthetic mathematical functions and complex real-world applications. The framework demonstrates its capability to progressively refine sampling strategies through real-time insights and hypothesis evolution, effectively identifying higher-performing regions of the search space for focused exploration. This process highlights the powerful reasoning and context-learning abilities of LLMs in optimization scenarios. For example, in the Direct Arylation task, our method increased the yield to 60.7%, whereas traditional BO achieved only a 25.2% yield. Furthermore, our investigation reveals that smaller LLMs, when fine-tuned through reinforcement learning, can attain comparable performance to their larger counterparts. This enhanced reasoning capability paves the way for more efficient automated scientific experimentation while maintaining computational feasibility.
Temporal Knowledge Graphs (TKGs), which utilize quadruples in the form of (subject, predicate, object, timestamp) to describe temporal facts, have attracted extensive attention. N-tuple TKGs (N-TKGs) further extend traditional TKGs by utilizing n-tuples to incorporate auxiliary elements alongside core elements (i.e., subject, predicate, and object) of facts, so as to represent them in a more fine-grained manner. Reasoning over N-TKGs aims to predict potential future facts based on historical ones. However, existing N-TKG reasoning methods often lack explainability due to their black-box nature. Therefore, we introduce a new Reinforcement Learning-based method, named MT-Path, which leverages the temporal information to traverse historical n-tuples and construct a temporal reasoning path. Specifically, in order to integrate the information encapsulated within n-tuples, i.e., the entity-irrelevant information within the predicate, the information about core elements, and the complete information about the entire n-tuples, MT-Path utilizes a mixture policy-driven action selector, which bases on three low-level policies, namely, the predicate-focused policy, the core-element-focused policy and the whole-fact-focused policy. Further, MT-Path utilizes an auxiliary element-aware GCN to capture the rich semantic dependencies among facts, thereby enabling the agent to gain a deep understanding of each n-tuple. Experimental results demonstrate the effectiveness and the explainability of MT-Path.
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.
The exponential growth of scientific literature presents significant challenges for researchers navigating the complex knowledge landscape. We propose "Agentic Publications", a novel LLM-driven framework complementing traditional publishing by transforming papers into interactive knowledge systems. Our architecture integrates structured data with unstructured content through retrieval-augmented generation and multi-agent verification. The framework offers interfaces for both humans and machines, combining narrative explanations with machine-readable outputs while addressing ethical considerations through automated validation and transparent governance. Key features include continuous knowledge updates, automatic integration of new findings, and customizable detail levels. Our proof-of-concept demonstrates multilingual interaction, API accessibility, and structured knowledge representation through vector databases, knowledge graphs, and verification agents. This approach enhances scientific communication across disciplines, improving efficiency and collaboration while preserving traditional publishing pathways, particularly valuable for interdisciplinary fields where knowledge integration remains challenging.
Natural medicines, particularly Traditional Chinese Medicine (TCM), are gaining global recognition for their therapeutic potential in addressing human symptoms and diseases. TCM, with its systematic theories and extensive practical experience, provides abundant resources for healthcare. However, the effective application of TCM requires precise syndrome diagnosis, determination of treatment principles, and prescription formulation, which demand decades of clinical expertise. Despite advancements in TCM-based decision systems, machine learning, and deep learning research, limitations in data and single-objective constraints hinder their practical application. In recent years, large language models (LLMs) have demonstrated potential in complex tasks, but lack specialization in TCM and face significant challenges, such as too big model scale to deploy and issues with hallucination. To address these challenges, we introduce Tianyi with 7.6-billion-parameter LLM, a model scale proper and specifically designed for TCM, pre-trained and fine-tuned on diverse TCM corpora, including classical texts, expert treatises, clinical records, and knowledge graphs. Tianyi is designed to assimilate interconnected and systematic TCM knowledge through a progressive learning manner. Additionally, we establish TCMEval, a comprehensive evaluation benchmark, to assess LLMs in TCM examinations, clinical tasks, domain-specific question-answering, and real-world trials. The extensive evaluations demonstrate the significant potential of Tianyi as an AI assistant in TCM clinical practice and research, bridging the gap between TCM knowledge and practical application.
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.
When knowledge graphs (KGs) are automatically extracted from text, are they accurate enough for downstream analysis? Unfortunately, current annotated datasets can not be used to evaluate this question, since their KGs are highly disconnected, too small, or overly complex. To address this gap, we introduce AffilKG (https://doi.org/10.5281/zenodo.15427977), which is a collection of six datasets that are the first to pair complete book scans with large, labeled knowledge graphs. Each dataset features affiliation graphs, which are simple KGs that capture Member relationships between Person and Organization entities -- useful in studies of migration, community interactions, and other social phenomena. In addition, three datasets include expanded KGs with a wider variety of relation types. Our preliminary experiments demonstrate significant variability in model performance across datasets, underscoring AffilKG's ability to enable two critical advances: (1) benchmarking how extraction errors propagate to graph-level analyses (e.g., community structure), and (2) validating KG extraction methods for real-world social science research.
Foundation models have demonstrated remarkable capabilities across various domains, but developing analogous models for knowledge graphs presents unique challenges due to their dynamic nature and the need for cross-domain reasoning. To address these issues, we introduce \textbf{\textsc{GraphOracle}}, a relation-centric foundation model that unifies reasoning across knowledge graphs by converting them into Relation-Dependency Graphs (RDG), explicitly encoding compositional patterns with fewer edges than prior methods. A query-dependent attention mechanism is further developed to learn inductive representations for both relations and entities. Pre-training on diverse knowledge graphs, followed by minutes-level fine-tuning, enables effective generalization to unseen entities, relations, and entire graphs. Through comprehensive experiments on 31 diverse benchmarks spanning transductive, inductive, and cross-domain settings, we demonstrate consistent state-of-the-art performance with minimal adaptation, improving the prediction performance by up to 35\% compared to the strongest baselines.
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.
Interaction sparsity is a long-standing challenge in recommendation systems. Sparsity manifests in environments with disproportional cardinality of groupings of entities, such as users and products in an online marketplace. It is also found for newly introduced entities, described as the cold-start problem. Recent efforts to mitigate this issue either enrich the connectivity data by incorporating social networks or external knowledge graphs, or fine-tune LLMs into interaction augmenters or next-item recommenders. However, these techniques tend to be resource demanding, requiring high computational power. They also have several limitations, including data availability, low quality, or synthetic noise issues. In this work, we propose LLM-based Intent Knowledge Graph Recommender (IKGR), a novel framework that leverages retrieval-augmented generation and an encoding approach to construct and densify a knowledge graph. IKGR leverages latent user-item affinities from an interaction knowledge graph and further densifies it through mutual intent connectivity. This addresses sparsity issues and allows the model to make intent-grounded recommendations with an interpretable embedding translation layer. Through extensive experiments on real-world datasets, we demonstrate that IKGR overcomes knowledge gaps and achieves substantial gains over state-of-the-art baselines on both publicly available and our internal recommendation datasets.
This paper addresses fine-tuning Large Language Models (LLMs) for function calling tasks when real user interaction data is unavailable. In digital content creation tools, where users express their needs through natural language queries that must be mapped to API calls, the lack of real-world task-specific data and privacy constraints for training on it necessitate synthetic data generation. Existing approaches to synthetic data generation fall short in diversity and complexity, failing to replicate real-world data distributions and leading to suboptimal performance after LLM fine-tuning. We present a novel router-based architecture that leverages domain resources like content metadata and structured knowledge graphs, along with text-to-text and vision-to-text language models to generate high-quality synthetic training data. Our architecture's flexible routing mechanism enables synthetic data generation that matches observed real-world distributions, addressing a fundamental limitation of traditional approaches. Evaluation on a comprehensive set of real user queries demonstrates significant improvements in both function classification accuracy and API parameter selection. Models fine-tuned with our synthetic data consistently outperform traditional approaches, establishing new benchmarks for function calling tasks.
Massive Open Online Courses (MOOCs) lack direct interaction between learners and instructors, making it challenging for learners to understand new knowledge concepts. Recently, learners have increasingly used Large Language Models (LLMs) to support them in acquiring new knowledge. However, LLMs are prone to hallucinations which limits their reliability. Retrieval-Augmented Generation (RAG) addresses this issue by retrieving relevant documents before generating a response. However, the application of RAG across different MOOCs is limited by unstructured learning material. Furthermore, current RAG systems do not actively guide learners toward their learning needs. To address these challenges, we propose a Graph RAG pipeline that leverages Educational Knowledge Graphs (EduKGs) and Personal Knowledge Graphs (PKGs) to guide learners to understand knowledge concepts in the MOOC platform CourseMapper. Specifically, we implement (1) a PKG-based Question Generation method to recommend personalized questions for learners in context, and (2) an EduKG-based Question Answering method that leverages the relationships between knowledge concepts in the EduKG to answer learner selected questions. To evaluate both methods, we conducted a study with 3 expert instructors on 3 different MOOCs in the MOOC platform CourseMapper. The results of the evaluation show the potential of Graph RAG to empower learners to understand new knowledge concepts in a personalized learning experience.
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 .
Democratic societies need accessible, reliable information. Videos and Podcasts have established themselves as the medium of choice for civic dissemination, but also as carriers of misinformation. The emerging Science Communication Knowledge Infrastructure (SciCom KI) curating non-textual media is still fragmented and not adequately equipped to scale against the content flood. Our work sets out to support the SciCom KI with a central, collaborative platform, the SciCom Wiki, to facilitate FAIR (findable, accessible, interoperable, reusable) media representation and the fact-checking of their content, particularly for videos and podcasts. Building an open-source service system centered around Wikibase, we survey requirements from 53 stakeholders, refine these in 11 interviews, and evaluate our prototype based on these requirements with another 14 participants. To address the most requested feature, fact-checking, we developed a neurosymbolic computational fact-checking approach, converting heterogenous media into knowledge graphs. This increases machine-readability and allows comparing statements against equally represented ground-truth. Our computational fact-checking tool was iteratively evaluated through 10 expert interviews, a public user survey with 43 participants verified the necessity and usability of our tool. Overall, our findings identified several needs to systematically support the SciCom KI. The SciCom Wiki, as a FAIR digital library complementing our neurosymbolic computational fact-checking framework, was found suitable to address the raised requirements. Further, we identified that the SciCom KI is severely underdeveloped regarding FAIR knowledge and related systems facilitating its collaborative creation and curation. Our system can provide a central knowledge node, yet a collaborative effort is required to scale against the imminent (mis-)information flood.
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.