arXiv AI

HCOE: Hyperbolic Clinical Ontology Embeddings from Biomedical Language Models

The paper introduces Hyperbolic Clinical Ontology Embeddings (HCOE), a method that transforms frozen BioBERT embeddings into a Poincaré ball to capture medical code hierarchies. HCOE employs ontology-guided contrastive learning and coarse‑to‑fine ontology‑path aggregation, leveraging ICD, CCS, and ATC hierarchies. Experiments on MIMIC‑IV demonstrate superior performance in clinical relation prediction, hierarchy transfer, and various predictive tasks such as mortality, readmission, medication recommendation, and rare drug prediction.

arXiv AI

Sep 15

Discovering Hierarchy-Grounded Domains with Adaptive Granularity for Clinical Domain Generalization

The paper introduces UdonCare, a hierarchy‑pruning method that iteratively partitions patients into latent domains using medical ontologies, aiming to improve domain generalization in clinical prediction tasks. It addresses challenges of missing domain labels and lack of clinical insight by discovering hierarchy‑grounded patient domains. Experiments on MIMIC‑III, MIMIC‑IV, and eICU datasets show UdonCare outperforms eight baseline methods across four prediction tasks with significant domain gaps.

By Pengfei Hu, Xiaoxue Han, Fei Wang, Yue Ning

efficiency

arXiv Machine Learning

Sep 15

Knowledge-Enriched Structured EHR Features for 30-Day Hospital Readmission Prediction on MIMIC-IV

arXiv:2609.15713v1 Announce Type: new Abstract: Recent approaches to 30-day hospital readmission prediction rely on pre-trained language models applied to discharge summaries. Although these methods...

By Mohamad Najafi, Hongyun Fu, Mathias Brochhausen, Jian Wu, Yaohang Li

llms rag safety

arXiv Computation and Language

Sep 10

OntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization

arXiv:2609.10055v1 Announce Type: cross Abstract: Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical dat...

By Jie Song, Zhichuan Xu, Ziyu Lu, Meng Xiao, Cheng Bi, Yuxin Zhang, Xin Zheng, Xiaoran Li, Qiongfang Cao, Hao Yang, Bairong Shen

llms rag benchmarks

Hugging Face Trending Papers

Sep 9

OntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization

Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical va...

llms rag benchmarks

arXiv Machine Learning

1d ago

HADRec: A Hierarchy-Aware Drug Recommendation Framework by Fusing Molecular Knowledge and Electronic Health Record

HADRec is a Hierarchy-Aware Drug Recommendation framework that fuses molecular knowledge and electronic health records to improve medication recommendation. It uses LLaMA-7B to encode clinical notes, ChemBERTa to encode drug SMILES strings, and a cross‑attention mechanism for multimodal fusion, while a hierarchical predictor and consistency constraint loss enforce adherence to the ATC classification system. Experiments on MIMIC‑III and MIMIC‑IV show state‑of‑the‑art performance, strong generalization, and well‑calibrated predictions, with counterfactual evaluation indicating clinically aligned reasoning.

By Junke Wang, Hongshun Ling, Li Zhang, Jinjing Wu, Tong Shao, Fang Wang, Yuan Gao

llms rag multimodal benchmarks safety

arXiv AI

Sep 17

Hyperbolic Graph Representation Learning for Differential Diagnosis on Biomedical Knowledge Graphs

The paper investigates hyperbolic graph representation learning applied to biomedical knowledge graphs for Mendelian-disease differential diagnosis. It shows that hyperbolic embeddings outperform Euclidean baselines on isolated ontology subgraphs while requiring fewer dimensions. In a link-prediction task, hyperbolic models rank candidate diseases for patients, indicating they can leverage hierarchical structure in heterogeneous patient-level graphs.

By Pietro Miotto, Lucia Mellini, Tommaso Marzi, Cesare Alippi, Elena Casiraghi, Alberto Paccanaro, Giorgio Valentini, Mauricio Soto-Gomez

rag

arXiv AI

Jul 22

OntoBook: Ontology-Grounded Synthetic Textbooks for Medical Encoder Pretraining

arXiv:2607. 18927v1 Announce Type: new Abstract: We present OntoBook, a method that converts medical ontology structure into pretraining signal for encoder language models.

By Rian Touchent (ALMAnaCH), \'Eric de la Clergerie (ALMAnaCH)

llms benchmarks safety

arXiv AI

Jun 16

Hierarchical Modeling of ICD Codes in EHR Foundation Models

arXiv:2606. 15447v1 Announce Type: new Abstract: Electronic health record foundation models typically treat ICD diagnosis codes as flat tokens, overlooking the clinically meaningful hierarchical structure that captures disease families, subcategories, and fine-grained diagnostic detail.

By Megha Thukral, Dong Gyun Kang, Rudra Pratap Singh, Shruthi Kashinath Hiremath, Katrin H\"ansel, Thomas Pl\"otz

llms rag safety

arXiv Machine Learning

Aug 6

Neighborhood-Aware Dual Biomedical Entity Linking

arXiv:2608. 04144v1 Announce Type: cross Abstract: Biomedical entity linking grounds mentions in clinical and scientific text to entities in a curated knowledge base (KB) with ontological structure, which supports downstream applications such as literature-scale information extraction and patient-record normalization.

By Yicheng Tao, Jie Liu

rag benchmarks

arXiv AI

Sep 10

OntologyBench: Can Dense Retrieval Satisfy Structured Biomedical Constraints?

arXiv:2609.08174v1 Announce Type: new Abstract: We introduce OntologyBench, a tiered biomedical retrieval benchmark comprising 471,854 training and 125,744 evaluation query-document relevance pairs a...

By Xiao Yu Cindy Zhang, Wyeth Wasserman, Jian Zhu

llms rag fine-tuning benchmarks

arXiv AI

Jun 30

NEURON: A Neuro-symbolic System for Grounded Clinical Explainability

arXiv:2605. 01189v2 Announce Type: replace Abstract: Clinical AI adoption is hindered by the black-box/grey-box nature of high-performing models, which lack the ontological grounding and narrative transparency required for professional-level explainability.

By Anuradha Chandrasekaran, Dimitrios Zikos, Mutlu Mete, Alan Pang, Brady D. Lund, Kewei Sha

llms rag safety

arXiv Machine Learning

Aug 4

xMICD: Explainable Representation of Multiple ICD Codes

arXiv:2608. 00935v1 Announce Type: new Abstract: Electronic Health Records (EHRs) are widely used for clinical risk prediction using machine learning.

By Pat Vatiwutipong, Kumkup Keeratisiwakul, Albert Phuoc Kien Van Truong, Nutcha Yodrabum, Wasin Pansiritanachot, Marvin N. Wright, Thanapon Noraset

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