OntoEL: Neuro-Symbolic Biomedical Entity Linking with Differentiable Fuzzy EL⊥ Reasoning
sigir26-071 · Full research paper · Chang Lu, Yizheng Zhao
Entity Linking and Alignment · 100%
Abstract
Current neural biomedical entity linking (BioEL) models treat ontologies as flat dictionaries, ignoring the rich terminological knowledge (TBox) that defines concept boundaries. Consequently, they struggle with contextual ambiguity, often retrieving logically inconsistent candidates based solely on surface similarity. We present OntoEL, a neuro-symbolic framework that shifts BioEL from surface-level matching to logic-grounded reasoning. OntoEL integrates differentiable fuzzy EL⊥ reasoning into the retrieval pipeline as a consistency-aware re-ranker, employing a hybrid strategy: structural TBox reasoning is delegated to classical polynomial-time reasoners, while the sigmoidal Reichenbach implication performs soft type-consistency evaluation, effectively resolving the "implication bias" gradient pathology in previous neuro-symbolic methods. By enforcing ontological axioms as differentiable soft constraints, OntoEL aligns neural representations with logical truth. Comprehensive experiments on three benchmarks (MedMentions, BC5CDR, and NCBI Disease) demonstrate state-of-the-art performance, surpassing strong baselines by up to 4.2% in Accuracy@1. On highly ambiguous mentions requiring ontological reasoning, our method corrects 71.2% of retrieval errors, proving the efficacy of incorporating logical semantics into neural retrieval.
Assigned reviewers
| # | Reviewer | Match | Why (closest evidence publications in the taxonomy) | |
|---|---|---|---|---|
| 1 | Yuzhong Qu | 64 | 100 Revisiting Embedding-Based Entity Alignment: A Robust and Adaptive Method (2023) Entity Linking and Alignment 100 Facilitating Entity Navigation Through Top-K Link Patterns (2015) Entity Linking and Alignment 100 Incorporating compactness to generate term-association view snippets for ontology search (2013) Entity Linking and Alignment |
|
| 2 | Fu Zhang 0001 | 51 | 100 Probing Relative Interaction and Dynamic Calibration in Multi-modal Entity Alignment (2025) Entity Linking and Alignment 100 SGMEA: Structure-Guided Multimodal Entity Alignment (2025) Entity Linking and Alignment 100 Breaking the Noise Barrier: LLM-Guided Semantic Filtering and Enhancement for Multi-Modal Entity Alignment (2025) Entity Linking and Alignment |
|
| 3 | Jingwei Cheng | 49 | 100 Probing Relative Interaction and Dynamic Calibration in Multi-modal Entity Alignment (2025) Entity Linking and Alignment 100 SGMEA: Structure-Guided Multimodal Entity Alignment (2025) Entity Linking and Alignment 100 Breaking the Noise Barrier: LLM-Guided Semantic Filtering and Enhancement for Multi-Modal Entity Alignment (2025) Entity Linking and Alignment |
Area chair
| Area chair | Match | |
|---|---|---|
| Chenyan Xiong | 31 |
Area-chair candidates (5)
| Chenyan Xiong assigned | 31 | 15 papers | |
| Xiaoxi Li 0005 | 29 | 15 papers | |
| Kam-Fai Wong | 28 | 6 papers | |
| Hongjin Qian | 28 | 12 papers | |
| Xiaoye Qu | 28 | 15 papers |
Candidates from the panel ranked by match score
| # | Reviewer | Match | Load | Why | |
|---|---|---|---|---|---|
| 1 | Yuzhong Qu assigned | 64 | 3 | 100 Revisiting Embedding-Based Entity Alignment: A Robust and Adaptive Method (2023) Entity Linking and Alignment 100 Facilitating Entity Navigation Through Top-K Link Patterns (2015) Entity Linking and Alignment |
|
| 2 | Fu Zhang 0001 assigned | 51 | 3 | 100 Probing Relative Interaction and Dynamic Calibration in Multi-modal Entity Alignment (2025) Entity Linking and Alignment 100 SGMEA: Structure-Guided Multimodal Entity Alignment (2025) Entity Linking and Alignment |
|
| 3 | Jingwei Cheng assigned | 49 | 3 | 100 Probing Relative Interaction and Dynamic Calibration in Multi-modal Entity Alignment (2025) Entity Linking and Alignment 100 SGMEA: Structure-Guided Multimodal Entity Alignment (2025) Entity Linking and Alignment |
|
| 4 | Wonduk Seo | 48 | 3 | 100 Question-to-Knowledge (Q2K): Multi-Agent Generation of Inspectable Facts for Product Mapping (2025) Entity Linking and Alignment 32 A New Query Expansion Approach for Enhancing Information Retrieval via Agent-Mediated Dialogic Inquiry (2026) Query Reformulation and Expansion |
|
| 5 | Xuhui Sui | 45 | 3 | 100 Introducing high correlation and high quality instances for few-shot entity linking (2025) Entity Linking and Alignment 100 ME3A: A Multimodal Entity Entailment framework for multimodal Entity Alignment (2025) Entity Linking and Alignment |
|
| 6 | Qinggang Zhang | 41 | 3 | 100 Entity Alignment with Noisy Annotations from Large Language Models (2024) Entity Linking and Alignment 65 LoSemB: Logic-Guided Semantic Bridging for Inductive Tool Retrieval (2026) Reasoning Evaluation and Benchmarks |
|
| 7 | Xiaolong Jin 0001 | 39 | 3 | 47 Stepwise Reasoning for Multi-Relation Question Answering over Knowledge Graph with Weak Supervision (2020) Knowledge Graph Question Answering 47 Hierarchical Query Graph Generation for Complex Question Answering over Knowledge Graph (2020) Knowledge Graph Question Answering |
|
| 8 | Wenyu Huang | 38 | 3 | 59 A Large-scale Offer Alignment Model for Partitioning Filtering and Matching Product Offers (2024) Entity Linking and Alignment 36 Prompting large language models with knowledge graphs for question answering involving long-tail facts (2025) KG-Augmented LLM Reasoning |
|
| 9 | Xiangyu Ke | 37 | 3 | 100 In-context Clustering-based Entity Resolution with Large Language Models: A Design Space Exploration (2025) Entity Linking and Alignment 100 Select Your Questions Wisely: For Entity Resolution With Crowd Errors (2017) Entity Linking and Alignment |
|
| 10 | Ben Liu 0002 | 37 | 3 | 41 Clarified Aggregation and Predictive Modeling (CAPM): High-Interpretability Framework for Inductive Link Prediction (2024) Knowledge Graph Embedding and Completion 41 Neighboring relation enhanced inductive knowledge graph link prediction via meta-learning (2023) Knowledge Graph Embedding and Completion |
|
| 11 | Yu Gu 0016 | 37 | 3 | 59 Reviving the Context: Camera Trap Species Classification as Link Prediction on Multimodal Knowledge Graphs (2024) Multimodal and Cross-Modal Retrieval › Others 41 Relevance Search over Schema-Rich Knowledge Graphs (2019) Knowledge Graph Embedding and Completion |
|
| 12 | Jiapu Wang | 37 | 3 | 47 Effective Instruction Parsing Plugin for Complex Logical Query Answering on Knowledge Graphs (2025) Knowledge Graph Question Answering 47 Progressive Prefix-Memory Tuning for Complex Logical Query Answering on Knowledge Graphs (2025) Knowledge Graph Question Answering |
|
| 13 | Armin Toroghi | 35 | 3 | 47 Bayesian Inference with Complex Knowledge Graph Evidence (2024) Knowledge Graph Question Answering 43 CommonWhy: A Dataset for Evaluating Entity-Based Causal Commonsense Reasoning in Large Language Models (2026) Knowledge Graph Question Answering |
|
| 14 | Xinying Qian | 34 | 3 | 41 Contrast then Memorize: Semantic Neighbor Retrieval-Enhanced Inductive Multimodal Knowledge Graph Completion (2024) Knowledge Graph Embedding and Completion 41 Few-shot temporal knowledge graph completion based on query-adaptive Mamba-enhanced temporal relation learning (2025) Knowledge Graph Embedding and Completion |
|
| 15 | Xingyu Tan 0001 | 34 | 3 | 39 PRoH: Dynamic Planning and Reasoning over Knowledge Hypergraphs for Retrieval-Augmented Generation (2026) Multimodal and Graph RAG 37 Paths-over-Graph: Knowledge Graph Empowered Large Language Model Reasoning (2025) KG-Augmented LLM Reasoning |
|
| 16 | Tianzhe Zhao | 33 | 3 | 41 Rethinking Continual Knowledge Graph Embedding: Benchmarks and Analysis (2025) Knowledge Graph Embedding and Completion 41 SAGE: Scale-Aware Gradual Evolution for Continual Knowledge Graph Embedding (2025) Knowledge Graph Embedding and Completion |
|
| 17 | Farzad Shami | 33 | 3 | 38 Benchmarking Large Language Models for Knowledge Graph Validation (2026) KG-Augmented LLM Reasoning 38 Fact Verification in Knowledge Graphs Using LLMs (2025) KG-Augmented LLM Reasoning |
|
| 19 | Jinheon Baek | 31 | 3 | 39 Learning to Extrapolate Knowledge: Transductive Few-shot Out-of-Graph Link Prediction (2020) Knowledge Graph Embedding and Completion 34 UniversalRAG: Retrieval-Augmented Generation over Corpora of Diverse Modalities and Granularities (2026) Multimodal and Graph RAG |
|
| 20 | Jing Liu 0022 | 30 | 3 | 68 A Hierarchical Entity-Based Approach to Structuralize User Generated Content in Social Media: A Case of Yahoo! Answers (2013) Domain-Specific and Structured Retrieval 34 REAR: A Relevance-Aware Retrieval-Augmented Framework for Open-Domain Question Answering (2024) Evidence Selection and Context Refinement |
|
| 21 | Jing Zhu 0005 | 30 | 3 | 37 Pitfalls in Link Prediction with Graph Neural Networks: Understanding the Impact of Target-link Inclusion & Better Practices (2024) Graph Learning for Text-Attributed and Heterogeneous Networks 37 On the Impact of Feature Heterophily on Link Prediction with Graph Neural Networks (2024) Graph Learning for Text-Attributed and Heterogeneous Networks |
|
| 22 | Zihao Yue | 30 | 3 | 31 POLYCHARTQA: Benchmarking Large Vision-Language Models with Multilingual Chart Question Answering (2026) Multimodal Evaluation and Benchmarks 31 Learning Descriptive Image Captioning via Semipermeable Maximum Likelihood Estimation (2023) Multimodal Evaluation and Benchmarks |
|
| 23 | Mariano Barone | 29 | 3 | 32 A Multilingual Multimodal Medical Examination Dataset for Visual Question Answering in Healthcare (2025) Retrieval-Augmented and Open-Domain QA 31 AMICO: A Semantic and Multimodal Framework for AI-Assisted Clinical Reporting (2025) Multimodal Evaluation and Benchmarks |
|
| 24 | Chen Zhao 0013 | 29 | 3 | 34 TaPERA: Enhancing Faithfulness and Interpretability in Long-Form Table QA by Content Planning and Execution-based Reasoning (2024) Multi-hop and Complex Reasoning QA 34 RobuT: A Systematic Study of Table QA Robustness Against Human-Annotated Adversarial Perturbations (2023) Multi-hop and Complex Reasoning QA |
|
| 25 | Weiwei Sun 0001 | 29 | 3 | 34 DukeNet: A Dual Knowledge Interaction Network for Knowledge-Grounded Conversation (2020) Conversational Search and Retrieval 34 Direct Retrieval-augmented Optimization: Synergizing Knowledge Selection and Language Models (2026) Evidence Selection and Context Refinement |
|
| 27 | Idan Szpektor | 29 | 3 | 33 On the Robustness of Dialogue History Representation in Conversational Question Answering: A Comprehensive Study and a New Prompt-based Method (2023) Conversational Search and Retrieval 33 SIGIR 2016 Workshop WebQA II: Web Question Answering Beyond Factoids (2016) Retrieval-Augmented and Open-Domain QA |
|
| 28 | Negar Arabzadeh | 29 | 3 | 65 LLM-as-a-Judge in Entity Retrieval: Assessing Explicit and Implicit Relevance (2025) Entity Linking and Alignment 30 Can QPP Choose the Right Query variant? Evaluating Query Variant Selection for RAG Pipelines (2026) Evidence Selection and Context Refinement |
|
| 30 | Xi Ye 0003 | 28 | 3 | 41 RNG-KBQA: Generation Augmented Iterative Ranking for Knowledge Base Question Answering (2022) Knowledge Graph Question Answering 34 Connecting Attributions and QA Model Behavior on Realistic Counterfactuals (2021) Multi-hop and Complex Reasoning QA |
|
| 31 | Kaixin Ma | 28 | 3 | 38 Knowledge-driven Data Construction for Zero-shot Evaluation in Commonsense Question Answering (2021) Retrieval-Augmented and Open-Domain QA 37 Open Domain Question Answering with A Unified Knowledge Interface (2022) Multimodal and Graph RAG |
|
| 32 | Haiyang Xu 0001 | 28 | 3 | 31 TinyChart: Efficient Chart Understanding with Program-of-Thoughts Learning and Visual Token Merging (2024) Multimodal Evaluation and Benchmarks 31 MIBench: Evaluating Multimodal Large Language Models over Multiple Images (2024) Multimodal Evaluation and Benchmarks |
|
| 34 | Navve Wasserman | 28 | 3 | 32 REAL-MM-RAG: A Real-World Multi-Modal Retrieval Benchmark (2025) Universal Multimodal Embedding and MLLM Retrieval 32 DocReRank: Single-Page Hard Negative Query Generation for Training Multi-Modal RAG Rerankers (2025) Universal Multimodal Embedding and MLLM Retrieval |