arXiv subjects

Jiaoyan Chen

Publications and source records attributed to Jiaoyan Chen.

At least 37 records · Page 2Linked to original sources

arXiv2026

Embedding Ontologies via Incorporating Extensional and Intensional Knowledge

Ontologies contain rich knowledge within domain, which can be divided into two categories, namely extensional knowledge and intensional knowledge. Extensional knowledge provides information about the concrete instances that belong to specific concepts in the ontology, while intensional knowledge details inherent properties, characteristics, and semantic associations among concepts. However, existing ontology embedding approaches fail to take both extensional knowledge and intensional knowledge into fine consideration simultaneously. In this paper, we propose a novel ontology embedding approach named EIKE (Extensional and Intensional Knowledge Embedding) by representing ontologies in two spaces, called extensional space and intensional space. EIKE presents a unified framework for embedding instances, concepts and their relations in an ontology, applying a geometry-based method to model extensional knowledge and a pretrained language model to model intensional knowledge, which can capture both structure information and textual information. Experimental results show that EIKE significantly outperforms state-of-the-art methods in three datasets for both triple classification and link prediction, indicating that EIKE provides a more comprehensive and representative perspective of the domain.

cs.AI↗

arXiv2026

Aggregation Queries over Unstructured Text: Benchmark and Agentic Method

Aggregation query over free text is a long-standing yet underexplored problem. Unlike ordinary question answering, aggregate queries require exhaustive evidence collection and systems are required to "find all," not merely "find one." Existing paradigms such as Text-to-SQL and Retrieval-Augmented Generation fail to achieve this completeness. In this work, we formalize entity-level aggregation querying over text in a corpus-bounded setting with strict completeness requirement. To enable principled evaluation, we introduce AGGBench, a benchmark designed to evaluate completeness-oriented aggregation under realistic large-scale corpus. To accompany the benchmark, we propose DFA (Disambiguation--Filtering--Aggregation), a modular agentic baseline that decomposes aggregation querying into interpretable stages and exposes key failure modes related to ambiguity, filtering, and aggregation. Empirical results show that DFA consistently improves aggregation evidence coverage over strong RAG and agentic baselines. The data and code are available in \href{https://anonymous.4open.science/r/DFA-A4C1}.

cs.AI↗

arXiv2026

Large Language Model for OWL Proofs

The ability of Large Language Models (LLMs) to perform reasoning tasks such as deduction has been widely investigated in recent years. Yet, their capacity to generate proofs-faithful, human-readable explanations of why conclusions follow-remains largely under explored. In this work, we study proof generation in the context of OWL ontologies, which are widely adopted for representing and reasoning over complex knowledge, by developing an automated dataset construction and evaluation framework. Our evaluation encompassing three sequential tasks for complete proving: Extraction, Simplification, and Explanation, as well as an additional task of assessing Logic Completeness of the premise. Through extensive experiments on widely used reasoning LLMs, we achieve important findings including: (1) Some models achieve overall strong results but remain limited on complex cases; (2) Logical complexity, rather than representation format (formal logic language versus natural language), is the dominant factor shaping LLM performance; and (3) Noise and incompleteness in input data substantially diminish LLMs' performance. Together, these results underscore both the promise of LLMs for explanation with rigorous logics and the gap of supporting resilient reasoning under complex or imperfect conditions. Code and data are available at https://github.com/HuiYang1997/LLMOwlR.

cs.AI↗

arXiv2026

What Breaks Knowledge Graph based RAG? Benchmarking and Empirical Insights into Reasoning under Incomplete Knowledge

Knowledge Graph-based Retrieval-Augmented Generation (KG-RAG) is an increasingly explored approach for combining the reasoning capabilities of large language models with the structured evidence of knowledge graphs. However, current evaluation practices fall short: existing benchmarks often include questions that can be directly answered using existing triples in KG, making it unclear whether models perform reasoning or simply retrieve answers directly. Moreover, inconsistent evaluation metrics and lenient answer matching criteria further obscure meaningful comparisons. In this work, we introduce a general method for constructing benchmarks and present BRINK (Benchmark for Reasoning under Incomplete Knowledge) to systematically assess KG-RAG methods under knowledge incompleteness. Our empirical results show that current KG-RAG methods have limited reasoning ability under missing knowledge, often rely on internal memorization, and exhibit varying degrees of generalization depending on their design.

cs.AI↗

arXiv2025

GR-Agent: Adaptive Graph Reasoning Agent under Incomplete Knowledge

Large language models (LLMs) achieve strong results on knowledge graph question answering (KGQA), but most benchmarks assume complete knowledge graphs (KGs) where direct supporting triples exist. This reduces evaluation to shallow retrieval and overlooks the reality of incomplete KGs, where many facts are missing and answers must be inferred from existing facts. We bridge this gap by proposing a methodology for constructing benchmarks under KG incompleteness, which removes direct supporting triples while ensuring that alternative reasoning paths required to infer the answer remain. Experiments on benchmarks constructed using our methodology show that existing methods suffer consistent performance degradation under incompleteness, highlighting their limited reasoning ability. To overcome this limitation, we present the Adaptive Graph Reasoning Agent (GR-Agent). It first constructs an interactive environment from the KG, and then formalizes KGQA as agent environment interaction within this environment. GR-Agent operates over an action space comprising graph reasoning tools and maintains a memory of potential supporting reasoning evidence, including relevant relations and reasoning paths. Extensive experiments demonstrate that GR-Agent outperforms non-training baselines and performs comparably to training-based methods under both complete and incomplete settings.

cs.AI↗

arXiv2025

CoTKR: Chain-of-Thought Enhanced Knowledge Rewriting for Complex Knowledge Graph Question Answering

Recent studies have explored the use of Large Language Models (LLMs) with Retrieval Augmented Generation (RAG) for Knowledge Graph Question Answering (KGQA). They typically require rewriting retrieved subgraphs into natural language formats comprehensible to LLMs. However, when tackling complex questions, the knowledge rewritten by existing methods may include irrelevant information, omit crucial details, or fail to align with the question's semantics. To address them, we propose a novel rewriting method CoTKR, Chain-of-Thought Enhanced Knowledge Rewriting, for generating reasoning traces and corresponding knowledge in an interleaved manner, thereby mitigating the limitations of single-step knowledge rewriting. Additionally, to bridge the preference gap between the knowledge rewriter and the question answering (QA) model, we propose a training strategy PAQAF, Preference Alignment from Question Answering Feedback, for leveraging feedback from the QA model to further optimize the knowledge rewriter. We conduct experiments using various LLMs across several KGQA benchmarks. Experimental results demonstrate that, compared with previous knowledge rewriting methods, CoTKR generates the most beneficial knowledge representation for QA models, which significantly improves the performance of LLMs in KGQA.

cs.CL↗

arXiv2025

On the Influence of Shape, Texture and Color for Learning Semantic Segmentation

Recent research has investigated the shape and texture biases of pre-trained deep neural networks (DNNs) in image classification. Those works test how much a trained DNN relies on specific image cues like texture. The present study shifts the focus to understanding the cue influence during training, analyzing what DNNs can learn from shape, texture, and color cues in absence of the others; investigating their individual and combined influence on the learning success. We analyze these cue influences at multiple levels by decomposing datasets into cue-specific versions. Addressing semantic segmentation, we learn the given task from these reduced cue datasets, creating cue experts. Early fusion of cues is performed by constructing appropriate datasets. This is complemented by a late fusion of experts which allows us to study cue influence location-dependent on pixel level. Experiments on Cityscapes, PASCAL Context, and a synthetic CARLA dataset show that while no single cue dominates, the shape + color expert predominantly improves the prediction of small objects and border pixels. The cue performance order is consistent for the tested convolutional and transformer architecture, indicating similar cue extraction capabilities, although pre-trained transformers are said to be more biased towards shape than convolutional neural networks.

cs.CV↗

arXiv2025

Ontology-Enhanced Knowledge Graph Completion using Large Language Models

Large Language Models (LLMs) have been extensively adopted in Knowledge Graph Completion (KGC), showcasing significant research advancements. However, as black-box models driven by deep neural architectures, current LLM-based KGC methods rely on implicit knowledge representation with parallel propagation of erroneous knowledge, thereby hindering their ability to produce conclusive and decisive reasoning outcomes. We aim to integrate neural-perceptual structural information with ontological knowledge, leveraging the powerful capabilities of LLMs to achieve a deeper understanding of the intrinsic logic of the knowledge. We propose an ontology enhanced KGC method using LLMs -- OL-KGC. It first leverages neural perceptual mechanisms to effectively embed structural information into the textual space, and then uses an automated extraction algorithm to retrieve ontological knowledge from the knowledge graphs (KGs) that needs to be completed, which is further transformed into a textual format comprehensible to LLMs for providing logic guidance. We conducted extensive experiments on three widely-used benchmarks -- FB15K-237, UMLS and WN18RR. The experimental results demonstrate that OL-KGC significantly outperforms existing mainstream KGC methods across multiple evaluation metrics, achieving state-of-the-art performance.

cs.CL↗

arXiv2025

Certainty in Uncertainty: Reasoning over Uncertain Knowledge Graphs with Statistical Guarantees

Uncertain knowledge graph embedding (UnKGE) methods learn vector representations that capture both structural and uncertainty information to predict scores of unseen triples. However, existing methods produce only point estimates, without quantifying predictive uncertainty-limiting their reliability in high-stakes applications where understanding confidence in predictions is crucial. To address this limitation, we propose \textsc{UnKGCP}, a framework that generates prediction intervals guaranteed to contain the true score with a user-specified level of confidence. The length of the intervals reflects the model's predictive uncertainty. \textsc{UnKGCP} builds on the conformal prediction framework but introduces a novel nonconformity measure tailored to UnKGE methods and an efficient procedure for interval construction. We provide theoretical guarantees for the intervals and empirically verify these guarantees. Extensive experiments on standard benchmarks across diverse UnKGE methods further demonstrate that the intervals are sharp and effectively capture predictive uncertainty.

stat.ML↗

arXiv2025

Atomic Fact Decomposition Helps Attributed Question Answering

Attributed Question Answering (AQA) aims to provide both a trustworthy answer and a reliable attribution report for a given question. Retrieval is a widely adopted approach, including two general paradigms: Retrieval-Then-Read (RTR) and post-hoc retrieval. Recently, Large Language Models (LLMs) have shown remarkable proficiency, prompting growing interest in AQA among researchers. However, RTR-based AQA often suffers from irrelevant knowledge and rapidly changing information, even when LLMs are adopted, while post-hoc retrieval-based AQA struggles with comprehending long-form answers with complex logic, and precisely identifying the content needing revision and preserving the original intent. To tackle these problems, this paper proposes an Atomic fact decomposition-based Retrieval and Editing (ARE) framework, which decomposes the generated long-form answers into molecular clauses and atomic facts by the instruction-tuned LLMs. Notably, the instruction-tuned LLMs are fine-tuned using a well-constructed dataset, generated from large scale Knowledge Graphs (KGs). This process involves extracting one-hop neighbors from a given set of entities and transforming the result into coherent long-form text. Subsequently, ARE leverages a search engine to retrieve evidences related to atomic facts, inputting these evidences into an LLM-based verifier to determine whether the facts require expansion for re-retrieval or editing. Furthermore, the edited facts are backtracked into the original answer, with evidence aggregated based on the relationship between molecular clauses and atomic facts. Extensive evaluations demonstrate the superior performance of our proposed method over the state-of-the-arts on several datasets, with an additionally proposed new metric $Attr_{p}$ for evaluating the precision of evidence attribution.

cs.CL↗

arXiv2025

Evaluating Knowledge Graph Based Retrieval Augmented Generation Methods under Knowledge Incompleteness

Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) is a technique that enhances Large Language Model (LLM) inference in tasks like Question Answering (QA) by retrieving relevant information from knowledge graphs (KGs). However, real-world KGs are often incomplete, meaning that essential information for answering questions may be missing. Existing benchmarks do not adequately capture the impact of KG incompleteness on KG-RAG performance. In this paper, we systematically evaluate KG-RAG methods under incomplete KGs by removing triples using different methods and analyzing the resulting effects. We demonstrate that KG-RAG methods are sensitive to KG incompleteness, highlighting the need for more robust approaches in realistic settings.

cs.AI↗

arXiv2025

MINTQA: A Multi-Hop Question Answering Benchmark for Evaluating LLMs on New and Tail Knowledge

Large language models (LLMs) have demonstrated impressive capabilities in various reasoning tasks but face significant challenges with complex, knowledge-intensive multi-hop queries, particularly those involving new or long-tail knowledge. Existing benchmarks often fail to fully address these challenges. To bridge this gap, we introduce MINTQA (Multi-hop Question Answering on New and Tail Knowledge), a comprehensive benchmark to evaluate LLMs' capabilities in multi-hop reasoning across four critical dimensions: question handling strategy, sub-question generation, retrieval-augmented generation, and iterative or dynamic decomposition and retrieval. MINTQA comprises 10,479 question-answer pairs for evaluating new knowledge and 17,887 pairs for assessing long-tail knowledge, with each question equipped with corresponding sub-questions and answers. Our systematic evaluation of 22 state-of-the-art LLMs on MINTQA reveals significant limitations in their ability to handle complex knowledge base queries, particularly in handling new or unpopular knowledge. Our findings highlight critical challenges and offer insights for advancing multi-hop reasoning capabilities. The MINTQA benchmark is available at https://github.com/probe2/multi-hop/.

cs.CL↗

arXiv2025

Prompting Large Language Models with Partial Knowledge for Answering Questions with Unseen Entities

Retrieval-Augmented Generation (RAG) shows impressive performance by supplementing and substituting parametric knowledge in Large Language Models (LLMs). Retrieved knowledge can be divided into three types: explicit answer evidence, implicit answer clue, and insufficient answer context which can be further categorized into totally irrelevant and partially relevant information. Effectively utilizing partially relevant knowledge remains a key challenge for RAG systems, especially in incomplete knowledge base retrieval. Contrary to the conventional view, we propose a new perspective: LLMs can be awakened via partially relevant knowledge already embedded in LLMs. To comprehensively investigate this phenomenon, the triplets located in the gold reasoning path and their variants are used to construct partially relevant knowledge by removing the path that contains the answer. We provide theoretical analysis of the awakening effect in LLMs and support our hypothesis with experiments on two Knowledge Graphs (KGs) Question Answering (QA) datasets. Furthermore, we present a new task, Unseen Entity KGQA, simulating real-world challenges where entity linking fails due to KG incompleteness. Our awakening-based approach demonstrates greater efficacy in practical applications, outperforms traditional methods that rely on embedding-based similarity which are prone to returning noisy information.

cs.CL↗

arXiv2025

Language Models as Ontology Encoders

OWL (Web Ontology Language) ontologies which are able to formally represent complex knowledge and support semantic reasoning have been widely adopted across various domains such as healthcare and bioinformatics. Recently, ontology embeddings have gained wide attention due to its potential to infer plausible new knowledge and approximate complex reasoning. However, existing methods face notable limitations: geometric model-based embeddings typically overlook valuable textual information, resulting in suboptimal performance, while the approaches that incorporate text, which are often based on language models, fail to preserve the logical structure. In this work, we propose a new ontology embedding method OnT, which tunes a Pretrained Language Model (PLM) via geometric modeling in a hyperbolic space for effectively incorporating textual labels and simultaneously preserving class hierarchies and other logical relationships of Description Logic EL. Extensive experiments on four real-world ontologies show that OnT consistently outperforms the baselines including the state-of-the-art across both tasks of prediction and inference of axioms. OnT also demonstrates strong potential in real-world applications, indicated by its robust transfer learning abilities and effectiveness in real cases of constructing a new ontology from SNOMED CT. Data and code are available at https://github.com/HuiYang1997/OnT.

cs.AI↗

arXiv2025

Supposedly Equivalent Facts That Aren't? Entity Frequency in Pre-training Induces Asymmetry in LLMs

Understanding and mitigating hallucinations in Large Language Models (LLMs) is crucial for ensuring reliable content generation. While previous research has primarily focused on "when" LLMs hallucinate, our work explains "why" and directly links model behaviour to the pre-training data that forms their prior knowledge. Specifically, we demonstrate that an asymmetry exists in the recognition of logically equivalent facts, which can be attributed to frequency discrepancies of entities appearing as subjects versus objects. Given that most pre-training datasets are inaccessible, we leverage the fully open-source OLMo series by indexing its Dolma dataset to estimate entity frequencies. Using relational facts (represented as triples) from Wikidata5M, we construct probing datasets to isolate this effect. Our experiments reveal that facts with a high-frequency subject and a low-frequency object are better recognised than their inverse, despite their logical equivalence. The pattern reverses in low-to-high frequency settings, and no statistically significant asymmetry emerges when both entities are high-frequency. These findings highlight the influential role of pre-training data in shaping model predictions and provide insights for inferring the characteristics of pre-training data in closed or partially closed LLMs.

cs.CL↗

arXiv2025

RAG Safety: Exploring Knowledge Poisoning Attacks to Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) enhances large language models (LLMs) by retrieving external data to mitigate hallucinations and outdated knowledge issues. Benefiting from the strong ability in facilitating diverse data sources and supporting faithful reasoning, knowledge graphs (KGs) have been increasingly adopted in RAG systems, giving rise to KG-based RAG (KG-RAG) methods. Though RAG systems are widely applied in various applications, recent studies have also revealed its vulnerabilities to data poisoning attacks, where malicious information injected into external knowledge sources can mislead the system into producing incorrect or harmful responses. However, these studies focus exclusively on RAG systems using unstructured textual data sources, leaving the security risks of KG-RAG largely unexplored, despite the fact that KGs present unique vulnerabilities due to their structured and editable nature. In this work, we conduct the first systematic investigation of the security issue of KG-RAG methods through data poisoning attacks. To this end, we introduce a practical, stealthy attack setting that aligns with real-world implementation. We propose an attack strategy that first identifies adversarial target answers and then inserts perturbation triples to complete misleading inference chains in the KG, increasing the likelihood that KG-RAG methods retrieve and rely on these perturbations during generation. Through extensive experiments on two benchmarks and four recent KG-RAG methods, our attack strategy demonstrates strong effectiveness in degrading KG-RAG performance, even with minimal KG perturbations. In-depth analyses are also conducted to understand the safety threats within the internal stages of KG-RAG systems and to explore the robustness of LLMs against adversarial knowledge.

cs.CR↗

arXiv2025

Can LLMs Evaluate Complex Attribution in QA? Automatic Benchmarking using Knowledge Graphs

Attributed Question Answering (AQA) has attracted wide attention, but there are still several limitations in evaluating the attributions, including lacking fine-grained attribution categories, relying on manual annotations, and failing to compare attributions with only subtle differences. To bridge these gaps, we introduce Complex Attributed Question Answering (CAQA), a large-scale benchmark containing comprehensive attribution categories, automatically generated using Knowledge Graphs (KGs), and complex attribution scenarios. We have conducted extensive experiments to verify the effectiveness of CAQA, including the benchmarking of 25 automatic evaluators, their comparison with human evaluators, the testing of LLM evaluators fine-tuned by CAQA and so on. These experiments also lead to a series of important findings that can benefit the future research of AQA. All the codes and data are publicly accessible at https://github.com/HuuuNan/CAQA-Benchmark.

cs.CL↗

arXiv2025

Graph-guided Cross-composition Feature Disentanglement for Compositional Zero-shot Learning

Disentanglement of visual features of primitives (i.e., attributes and objects) has shown exceptional results in Compositional Zero-shot Learning (CZSL). However, due to the feature divergence of an attribute (resp. object) when combined with different objects (resp. attributes), it is challenging to learn disentangled primitive features that are general across different compositions. To this end, we propose the solution of cross-composition feature disentanglement, which takes multiple primitive-sharing compositions as inputs and constrains the disentangled primitive features to be general across these compositions. More specifically, we leverage a compositional graph to define the overall primitive-sharing relationships between compositions, and build a task-specific architecture upon the recently successful large pre-trained vision-language model (VLM) CLIP, with dual cross-composition disentangling adapters (called L-Adapter and V-Adapter) inserted into CLIP's frozen text and image encoders, respectively. Evaluation on three popular CZSL benchmarks shows that our proposed solution significantly improves the performance of CZSL, and its components have been verified by solid ablation studies. Our code and data are available at:https://github.com/zhurunkai/DCDA.

cs.CV↗