arXiv subjects

Jiaoyan Chen

Publications and source records attributed to Jiaoyan Chen.

At least 19 recordsLinked to original sources

arXiv2026

MDB-Link: Hierarchical Schema Linking for Multi-Database Text-to-SQL

Traditional Text-to-SQL research and benchmarks assume a known target database, overlooking settings in which a query must be routed within a large, heterogeneous database collection. We therefore study schema linking in a multi-database setting, where the system must first locate the target database and then construct a compact, SQL-relevant schema for generation. We propose MDB-Link, a hierarchical schema-linking framework that retrieves question-relevant columns from a global index, aggregates retrieval evidence to shortlist databases, and uses a budget-aware large language model (LLM) for database reranking, table selection, and column grounding. With Qwen2.5-14B, MDB-Link outperforms LinkAlign on MMQA, Spider2-Snow, and BIRD-dev in database localization and column selection while producing schema subsets close in size to the gold schemas. Exact match improves from 16.88 to 51.41 on MMQA, 2.50 to 9.17 on Spider2-Snow, and 12.52 to 38.01 on BIRD-dev. MDB-Link also runs faster than LinkAlign and AutoLink, demonstrating the effectiveness of hierarchical schema reduction for downstream SQL generation.

cs.CL↗

arXiv2026

NeurOWL: An LLM-Based Neural-symbolic Framework for Incomplete OWL Ontology Reasoning

OWL ontologies provide a formal knowledge representation framework that enables semantic reasoning, and have been widely adopted across domains such as healthcare and bioinformatics. In practice, however, real-world ontologies are often incomplete, which pose challenges for reasoning. In this work, we focus on a fundamental subsumption reasoning problem: given an incomplete ontology and a candidate (non-entailed) subsumption, determine whether the subsumption is semantically plausible and, if so, providing a logically sound explanation containing potential missing axioms. This task unifies subsumption verification with ontology abduction, and generalizes the latter by removing the need for a predefined candidate set of missing axioms. To address this subsumption reasoning problem, we propose NeurOWL, an end-to-end neuro-symbolic framework that jointly performs verification and abduction, leveraging both formally defined semantics and textual semantics through Large Language Models and ontology embeddings. We evaluate NeurOWL on real-world ontologies across multiple domains, demonstrating strong and robust performance across different domains.

cs.AI↗

arXiv2026

AgentMap: Joint Equivalence and Subsumption Discovery for Ontology Matching

Ontology matching (OM) has traditionally been formulated as either equivalence discovery or subsumption matching. The existing OM systems identify only one type of semantic correspondence and cannot simultaneously discover equivalence and subsumption mappings. In this paper, we introduce Hybrid Ontology Matching (HOM), a new OM task that unifies equivalence and subsumption discovery, and accordingly propose a Large Language Model (LLM)-based multi-agent OM framework AgentMap that is implemented by a series of interdependent semantic decisions. Given a concept in the source ontology, AgentMap integrates semantic retrieval, hierarchical search, and collaborative multi-agent LLM reasoning to progressively explore the target ontology, identifying either the equivalent concept, if one exists, or the most fine-grained subsumer. We further extend four OM datasets for a HOM benchmark and evaluate AgentMap under hybrid, equivalence-only, and subsumption-only settings. Experimental results show that AgentMap achieves promising performance on the hybrid setting, and at the same time outperforms equivalence matching and subsumption matching baselines on the equivalence-only and subsumption-only settings, respectively.

cs.AI↗

arXiv2026

Beyond Factual Accuracy: Evaluating Global Reasoning Integrity in RAG Systems with LogicScore

Current evaluation methods for Retrieval Augmented Generation (RAG) suffer from \textit{factual myopia}: they relentlessly emphasize factual accuracy yet neglect global logical integrity in long-form answer generation. This drives models to force unnatural connections, producing factually grounded yet logically incoherent responses with unaddressed gaps, ambiguous links, or redundant premises. To mitigate this, we present \textsc{LogicScore}, shifting from local, fact-by-fact assessment to rigorous global reasoning scrutiny. Grounded in Horn Rules, our approach integrates a backward verification mechanism to systematically evaluate three key reasoning dimensions: \textit{Completeness} (logically sound deduction), \textit{Essentiality} (non-redundancy), and \textit{Determinateness} (consistent answer entailment). Extensive experiments across three multi-hop QA datasets (HotpotQA, MusiQue, and 2WikiMultiHopQA) and over 20 LLMs (including GPT-5, Gemini-3-Pro, LLaMA3, and task-specific tuned models) reveal a critical capability gap: leading models often achieve high factual accuracy (e.g., 92.85\% precision for Gemini-3 Pro) but struggle with global reasoning quality (e.g., 35.11\% Essentiality for Gemini-3 Pro). Our work establishes a robust standard for logical evaluation, highlighting the need to prioritize reasoning coherence alongside factual grounding in LLM development.

cs.CL↗

arXiv2026

CAGE: Cognitive Attribution Graphs for Faithful Inline Citation Generation in Long-Form Question Answering

Long-form question answering increasingly relies on retrieved evidence to make LLM outputs verifiable, with inline citations tracing claims to source documents. However, existing systems often attach citations that are topically related but insufficient to support their claims. We identify attribution ambiguity as a structural challenge: end-to-end generation must implicitly resolve combinatorial claim--document assignments, obscuring evidential boundaries and increasing the risk of evidence-boundary overrun, where claims exceed cited support. To address this challenge, we propose CAGE (Cognitive Attribution Graphs for Citation Generation), a two-stage framework that introduces an explicit cognitive attribution map before answer generation. CAGE first trains a plug-and-play Cognitive Map Induction Model to construct answer-centered support subgraphs, aligning each semantic answer unit with supporting documents through explicit relations. A Structured Citation Reasoning Model then realizes these units as sentence-level claims with map-aligned citations. Experiments on ASQA, ELI5, and ExpertQA show that CAGE achieves state-of-the-art performance, demonstrating the effectiveness of attribution-space contraction and map-guided citation generation.

cs.CL↗

arXiv2026

OmniPhys: Knowledge-Graph-Driven Benchmarking and Collective Optimization for Physical Commonsense in Text-to-Image Generation

While text-to-image models exhibit remarkable visual fidelity, they frequently violate fundamental physical commonsense. Existing benchmarks often rely on coarse-grained descriptions, failing to diagnose the mastery of specific physical principles. Moreover, the high stochasticity of generative processes causes current prompt optimization methods to suffer from gradient hallucinations, where optimizers are misled by transient visual artifacts rather than systemic flaws. To address these challenges, we introduce OmniPhys, a rigorous benchmark of 1,551 samples grounded in a Physical Knowledge Graph. By aligning PhET simulations with standard curricula, OmniPhys operationalizes a knowledge-to-scenario pipeline that performs diagnostic stress tests via a dual-path verification protocol. We further propose OmniPrompt, an iterative framework that treats physical alignment as a discrete optimization problem. For each query, OmniPrompt aggregates K stochastic images into a per-query feedback buffer. Across training, it further merges feedback from batches of B queries before each meta-policy update, filtering seed and query-local noise. Evaluations across 12 representative text-to-image models reveal universal physical bottlenecks. Results demonstrate that OmniPrompt significantly enhances physical consistency across diverse backbones, proving the transferability and efficacy of our evolved meta-policies. The code and data are available at https://github.com/zjukg/OmniPhys

cs.CV↗

arXiv2026

Can LLMs Write Reliable Rubrics? A Meta-Evaluation for Experiment Reproduction

Rubric-based evaluation is a promising approach for assessing open-ended outputs from LLM-based research agents, particularly in paper reproduction, where direct paper-to-repository comparison is prone to hallucination. However, constructing paper-specific rubrics requires substantial expert effort, limiting the scalability of benchmarks such as PaperBench. In this work, we present, to our knowledge, the first systematic meta-evaluation of LLM-generated rubrics for paper reproduction. We reformulate rubrics into a checklist-style format and evaluate four generation settings across two backbone models. We meta-evaluate generated rubrics intrinsically by semantic similarity and extrinsically by score alignment with ground-truth rubrics. Our results show that the augmented settings substantially improves downstream evaluation alignment, with the strongest setting approaching the human baseline, while intrinsic gains are more modest. Further analyses reveal that LLM-generated rubrics are often overly fine-grained, biased toward high scores, and less adaptive to paper domains, highlighting both the affordances and limitations.

cs.CL↗

arXiv2026

Single and Multi Truth Data Fusion using Large Language Models

Data fusion, also known as truth discovery, is a data integration problem that aims to determine the correct value or set of values for each attribute of an object when presented with potentially conflicting values from multiple sources. Data fusion tasks belong to two main categories: single-truth scenarios, where each attribute has only one correct value, and multi-truth scenarios, where multiple values can be valid simultaneously. This paper investigates the use of Large Language Models (LLMs) in data fusion tasks for tabular data. Various prompting strategies, encompassing both single-truth and multi-truth scenarios, are investigated empirically. Domain-dependent, domain-independent, zero-shot and one-shot prompts are evaluated on three different benchmark datasets. Experimental results demonstrate that LLM-based approaches outperform traditional unsupervised truth discovery methods, such as DART and LTM, across all datasets. The codebase of this study has been made publicly available on GitHub.

cs.DB↗

arXiv2026

KG2Code: Bridging Knowledge Graphs and Large Language Models via Executable Code for Question Answering

Recent research has explored the integration of knowledge graphs (KGs) with large language models (LLMs) to enhance their performance on downstream knowledge-intensive tasks, particularly knowledge graph question answering (KGQA). Existing approaches primarily combine LLMs with KGs through retrieval-augmented generation (RAG)-based, agent-based, and SPARQL-based methods. Although these methods have achieved notable success, they still suffer from several limitations, including structural information loss, unfaithful reasoning, and limited flexibility and generalization. To address these challenges, this paper proposes KG2Code, a novel approach that transforms knowledge graphs into a code-based representation, preserving structural semantics while naturally aligning with the code-aware pretraining of modern LLMs. Based on KG2Code, KG2Code-QA is further introduced as a KGQA framework that formulates KGQA as a code generation task. This formulation enables the generation of verifiable reasoning traces and executable code, thereby substantially mitigating the impact of hallucinations. In addition, an automated pipeline is developed to construct a large-scale, high-quality code corpus for effectively training open-source LLMs on KG2Code-QA. After training, LLMs are able to perform KGQA in zero-shot scenarios. Extensive experiments demonstrate that the proposed approach significantly outperforms existing KG-enhanced LLM methods for KGQA, while exhibiting strong generalization to unseen KGs. The code and data are available at Github.

cs.AI↗

arXiv2026

ReaLM: Residual Quantization Bridging Knowledge Graph Embeddings and Large Language Models

Large Language Models (LLMs) have recently emerged as a powerful paradigm for Knowledge Graph Completion (KGC), offering strong reasoning and generalization capabilities beyond traditional embedding-based approaches. However, existing LLM-based methods often struggle to fully exploit structured semantic representations, as the continuous embedding space of pretrained KG models is fundamentally misaligned with the discrete token space of LLMs. This discrepancy hinders effective semantic transfer and limits their performance. To address this challenge, we propose ReaLM, a novel and effective framework that bridges the gap between KG embeddings and LLM tokenization through the mechanism of residual vector quantization. ReaLM discretizes pretrained KG embeddings into compact code sequences and integrates them as learnable tokens within the LLM vocabulary, enabling seamless fusion of symbolic and contextual knowledge. Furthermore, we incorporate ontology-guided class constraints to enforce semantic consistency, refining entity predictions based on class-level compatibility. Extensive experiments on two widely used benchmark datasets demonstrate that ReaLM achieves state-of-the-art performance, confirming its effectiveness in aligning structured knowledge with large-scale language models.

cs.CL↗

arXiv2026

Conceptual Schema Inference for Tabular Datasets using Large Language Models

Large collections of tabular data from data lakes, web tables and open data portals often originate from heterogeneous sources, leading to representational inconsistencies. Understanding and organizing such repositories therefore remains a major challenge. While prior work has primarily focused on dataset discovery and exploration, this paper addresses the complementary problem of conceptual schema inference: automatically deriving a conceptual schema that captures entity types, attributes and inter-type relationships directly from raw tables. We propose two large language model (LLM)-based approaches that use only column headers and cell values: GeSI uses generative LLMs to infer hierarchical types and their attributes from table- and column-level semantics, and to integrate them into a global schema that also captures relationships across types; EmSI employs LLM-based table embeddings to group tables by column-level semantics, infer attributes within each group, and construct hierarchical structures from shared attribute patterns. Finally, we report an experimental analysis demonstrating the effectiveness of our approaches in terms of the conciseness and structural quality of the inferred schema components, their scalability to large repositories, and a case study illustrating end-to-end schema inference.

cs.DB↗

arXiv2026

Conceptual Schema Inference for Tabular Datasets using Large Language Models

cs.DB↗

arXiv2026

HiRAS: A Hierarchical Multi-Agent Framework for Paper-to-Code Generation and Execution

Recent advances in large language models have highlighted their potential to automate computational research, particularly reproducing experimental results. However, existing approaches still use fixed sequential agent pipelines with weak global coordination, which limits their robustness and overall performance. In this work, we propose Hierarchical Research Agent System (HiRAS), a hierarchical multi-agent framework for end-to-end experiment reproduction that employs supervisory manager agents to coordinate specialised agents across fine-grained stages. We also identify limitations in the reference-free evaluation of the Paper2Code benchmark and introduce Paper2Code-Extra (P2C-Ex), a refined protocol that incorporates repository-level information and better aligns with the original reference-based metric. We conduct extensive evaluation, validating the effectiveness and robustness of our proposed methods, and observing improvements, including >10\% relative performance gain beyond the previous state-of-the-art using open-source backbone models and significantly reduced hallucination in evaluation. Our work is available on GitHub: https://github.com/KOU-199024/HiRAS.

cs.CL↗

arXiv2026

Hierarchical Retrieval with Out-Of-Vocabulary Queries: A Case Study on SNOMED CT

SNOMED CT is a biomedical ontology with a hierarchical representation, modelling terminological concepts at a large scale. Knowledge retrieval in SNOMED CT is critical for its application but often proves challenging due to linguistic ambiguity, synonymy, polysemy, and so on. This problem is exacerbated when the queries are out-of-vocabulary (OOV), i.e., lacking any equivalent matches in the ontology. In this work, we focus on the problem of hierarchical concept retrieval from SNOMED CT with OOV queries, and propose an approach driven by utilising language model-based ontology embeddings, which represent hierarchical concepts in a hyperbolic space for enabling efficient subsumption inference between a textual query and an arbitrary concept. For evaluation, we construct three datasets where OOV queries are annotated against SNOMED CT concepts, testing the retrieval of the most specific subsumers and their less relevant ancestors. We find that our method outperforms the baselines, including SBERT, SapBERT, and two lexical matching methods. While evaluated against SNOMED CT, the approach is generalisable and can be extended to other ontologies. We release all the experiment codes and datasets at https://github.com/jonathondilworth/HR-OOV-SNOMED-CT.

cs.CL↗

arXiv2026

RegD: Hierarchical Embeddings via Dissimilarity between Arbitrary Euclidean Regions

Hierarchical data is common in many domains like life sciences and e-commerce, and its embeddings often play a critical role. While hyperbolic embeddings offer a theoretically grounded approach to representing hierarchies in low-dimensional spaces, current methods often rely on specific geometric constructs as embedding candidates. This reliance limits their generalizability and makes it difficult to integrate with techniques that model semantic relationships beyond pure hierarchies, such as ontology embeddings. In this paper, we present RegD, a flexible Euclidean framework that supports the use of arbitrary geometric regions -- such as boxes and balls -- as embedding representations. Although RegD operates entirely in Euclidean space, we formally prove that it achieves hyperbolic-like expressiveness by incorporating a depth-based dissimilarity between regions, enabling it to emulate key properties of hyperbolic geometry, including exponential growth. Our empirical evaluation on diverse real-world datasets shows consistent performance gains over state-of-the-art methods and demonstrates RegD's potential for broader applications such as the ontology embedding task that goes beyond hierarchy.

cs.LG↗

arXiv2026

Exploring Knowledge Conflicts for Faithful LLM Reasoning: Benchmark and Method

Large language models (LLMs) have achieved remarkable success across a wide range of applications especially when augmented by external knowledge through retrieval-augmented generation (RAG). Despite their widespread adoption, recent studies have shown that LLMs often struggle to perform faithful reasoning when conflicting knowledge is retrieved. However, existing work primarily focuses on conflicts between external knowledge and the parametric knowledge of LLMs, leaving conflicts across external knowledge largely unexplored. Meanwhile, modern RAG systems increasingly emphasize the integration of unstructured text and (semi-)structured data like knowledge graphs (KGs) to improve knowledge completeness and reasoning faithfulness. To address this gap, we introduce ConflictQA, a novel benchmark that systematically instantiates conflicts between textual evidence and KG evidence. Extensive evaluations across representative LLMs reveal that, facing such cross-source conflicts, LLMs often fail to identify reliable evidence for correct reasoning. Instead, LLMs become more sensitive to prompting choices and tend to rely exclusively on either KG or textual evidence, resulting in incorrect responses. Based on these findings, we further propose XoT, a two-stage explanation-based thinking framework tailored for reasoning over heterogeneous conflicting evidence, and verify its effectiveness with extensive experiments.

cs.CL↗

arXiv2026

GenOM: Ontology Matching with Description Generation and Large Language Model

Ontology matching (OM) plays an essential role in enabling semantic interoperability and integration across heterogeneous knowledge sources, particularly in the biomedical domain which contains numerous complex concepts related to diseases and pharmaceuticals. This paper introduces GenOM, a large language model (LLM)-based ontology alignment framework, which enriches the semantic representations of ontology concepts via generating textual definitions, retrieves alignment candidates with an embedding model, and incorporates exact matching-based tools to improve precision. Extensive experiments conducted on the OAEI Bio-ML track demonstrate that GenOM can often achieve competitive performance, surpassing many baselines including traditional OM systems and recent LLM-based methods. Further ablation studies confirm the effectiveness of semantic enrichment and few-shot prompting, highlighting the framework's robustness and adaptability.

cs.AI↗

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↗