医学 AI - arXivDaily 专题

2403.05602 2024-03-12 q-bio.BM cs.CL cs.LG 80%

Extracting Protein-Protein Interactions (PPIs) from Biomedical Literature using Attention-based Relational Context Information

Gilchan Park, Sean McCorkle, Carlos Soto, Ian Blaby, Shinjae Yoo

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments 10 pages, 3 figures, 7 tables, 2022 IEEE International Conference on Big Data (Big Data)

Journal ref In 2022 IEEE Big Data, pp. 2052-2061 (2022)

2311.07632 2024-02-20 cs.LG cs.AI q-bio.MN 80%

ResMGCN: Residual Message Graph Convolution Network for Fast Biomedical Interactions Discovering

Zecheng Yin

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments In progress

2312.12989 2023-12-21 cs.LG cs.CL q-bio.QM 80%

Benchmarking and Analyzing In-context Learning, Fine-tuning and Supervised Learning for Biomedical Knowledge Curation: a focused study on chemical entities of biological interest

Emily Groves, Minhong Wang, Yusuf Abdulle, Holger Kunz, Jason Hoelscher-Obermaier, Ronin Wu, Honghan Wu

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments 26 pages, 5 figures, 14 tables

2311.09261 2023-11-17 q-bio.QM cs.AI cs.CE cs.LG 80%

Emerging Drug Interaction Prediction Enabled by Flow-based Graph Neural Network with Biomedical Network

Yongqi Zhang, Quanming Yao, Ling Yue, Xian Wu, Ziheng Zhang, Zhenxi Lin, Yefeng Zheng

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments Accepted by Nature Computational Science

2310.03221 2023-10-10 cs.LG cs.AI q-bio.QM 80%

Know2BIO: A Comprehensive Dual-View Benchmark for Evolving Biomedical Knowledge Graphs

Yijia Xiao, Dylan Steinecke, Alexander Russell Pelletier, Yushi Bai, Peipei Ping, Wei Wang

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments 26 pages, 2 figures, 14 figures

2301.01885 2023-08-21 stat.ML cs.CR cs.LG q-bio.NC 80%

Enhancement attacks in biomedical machine learning

Matthew Rosenblatt, Javid Dadashkarimi, Dustin Scheinost

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments 12 pages, 3 figures

2205.03447 2023-07-25 cs.AI cs.LG q-bio.GN 80%

Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching

Yuan He, Jiaoyan Chen, Hang Dong, Ernesto Jiménez-Ruiz, Ali Hadian, Ian Horrocks

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments Accepted paper (Best Resource Paper Candidate) in the 21st International Semantic Web Conference (ISWC-2022); Bio-ML Dataset: https://doi.org/10.5281/zenodo.6510086

2301.12040 2023-07-06 q-bio.BM cs.LG 80%

ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts

Minghao Xu, Xinyu Yuan, Santiago Miret, Jian Tang

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments Accpeted by ICML 2023 (Oral), code and data released

2305.10467 2023-05-19 q-bio.QM cs.LG 80%

Analysing Biomedical Knowledge Graphs using Prime Adjacency Matrices

Konstantinos Bougiatiotis, Georgios Paliouras

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments To be presented in CBMS2023. arXiv admin note: text overlap with arXiv:2209.06575

2305.07468 2023-05-15 cs.IR cs.AI cs.CL cs.LG q-bio.QM 80%

BactInt: A domain driven transfer learning approach and a corpus for extracting inter-bacterial interactions from biomedical text

Krishanu Das Baksi, Vatsala Pokhrel, Kuntal Kumar Bhusan, Sharmila Mande

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

2303.13566 2023-03-27 cs.AI cs.LG q-bio.QM 80%

Enhancing Embedding Representations of Biomedical Data using Logic Knowledge

Michelangelo Diligenti, Francesco Giannini, Stefano Fioravanti, Caterina Graziani, Moreno Falaschi, Giuseppe Marra

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

2303.09322 2023-03-17 cs.LG cs.HC q-bio.QM 80%

Interpretability from a new lens: Integrating Stratification and Domain knowledge for Biomedical Applications

Anthony Onoja, Francesco Raimondi

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments 10 pages concept paper

2201.04437 2022-12-20 cs.LG cs.AI q-bio.QM 80%

Multi-task Joint Strategies of Self-supervised Representation Learning on Biomedical Networks for Drug Discovery

Xiaoqi Wang, Yingjie Cheng, Yaning Yang, Yue Yu, Fei Li, Shaoliang Peng

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments 44 pages, 11 figures

2208.10315 2022-08-24 cs.LG cs.AI q-bio.GN 80%

Semi-supervised classification using a supervised autoencoder for biomedical applications

Cyprien Gille, Frederic Guyard, Michel Barlaud

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments 9 pages

2111.10683 2021-11-23 eess.IV cs.CV cs.LG cs.NE physics.med-ph 80%

A Review on The Division of Magnetic Resonant Prostate Images with Deep Learning

Elcin Huseyn, Emin Mammadov, Mohammad Hoseini

专题命中生物医学文本：MRI(abstract)；diagnosis(abstract)；biomedical(abstract)；分类 cs.CV、cs.LG、eess.IV

2005.05954 2021-03-17 cs.IR cs.CL cs.DL cs.LG q-bio.QM 80%

COVID-19Base: A knowledgebase to explore biomedical entities related to COVID-19

Junaed Younus Khan, Md. Tawkat Islam Khondaker, Iram Tazim Hoque, Hamada Al-Absi, Mohammad Saifur Rahman, Tanvir Alam, M. Sohel Rahman

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments 10 pages, 3 figures

Journal ref JMIR Med Inform 2020;8(11):e21648

1911.00996 2019-11-05 q-bio.QM cs.LG stat.ML 80%

A Study of Data Pre-processing Techniques for Imbalanced Biomedical Data Classification

Shigang Liu, Jun Zhang, Yang Xiang, Wanlei Zhou, Dongxi Xiang

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments This paper is scheduled for inclusion in V16 N3 2020, International Journal of Bioinformatics Research and Applications (IJBRA)

Journal ref V16 N3, International Journal of Bioinformatics Research and Applications (IJBRA), 2020

1909.06146 2019-09-16 cs.CL cs.LG q-bio.QM 80%

PubMedQA: A Dataset for Biomedical Research Question Answering

Qiao Jin, Bhuwan Dhingra, Zhengping Liu, William W. Cohen, Xinghua Lu

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Comments EMNLP 2019

1901.07455 2019-01-23 eess.SP q-bio.QM 80%

A Discussion on the Algorithm Design of Electrical Impedance Tomography for Biomedical Applications

Mingyong Zhou, Hongyu Zhu

专题命中生物医学文本：biomedical(title,abstract)；分类 q-bio、eess.SP

Comments accepted for ICSI 2018(2018 International Conference on Sensing and Image), liuzhou, October 15, China

1608.05605 2016-08-22 cs.CL 80%

Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts

Stéphan Tulkens, Simon Šuster, Walter Daelemans

专题命中生物医学文本：biomedical(title,abstract)

Comments 6 pages, 1 figure, presented at the 15th Workshop on Biomedical Natural Language Processing, Berlin 2016

Journal ref Proceedings of the 15th Workshop on Biomedical Natural Language Processing, Berlin, Germany, 2016, pages 77-82. Association for Computational Linguistics

0909.0638 2009-12-01 cs.LG q-bio.QM 80%

Median topographic maps for biomedical data sets

Barbara Hammer, Alexander Hasenfuß, Fabrice Rossi

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG、q-bio

Journal ref Similarity-Based Clustering, Villmann, Th.; Biehl, M.; Hammer, B.; Verleysen, M. (Ed.) (2009) 92-117

2606.19396 2026-06-19 q-bio.QM 新提交 80%

BioHarness: Substrate-Aware Evidence Assembly for Biomedical Question Answering across Literature, Knowledge Bases, and Biological Atlases

BioHarness：面向生物医学问答的底物感知证据组装——跨文献、知识库和生物图谱

Meng Xiao, Chuan Qin, Jinmiao Chen, Yihang Cheng, Yuanchun Zhou, Hengshu Zhu

专题命中生物医学文本：biomedical(title,abstract)；分类 q-bio

AI总结提出BioHarness，通过级联控制机制在文献检索、知识库和生物图谱间选择性组装证据，提升生物医学问答准确率，在19,302个问答项上得分从65.9提升至71.0。

Comments 14 Pages, 11 Figures, Keywords: biomedical question answering; retrieval-augmented generation; large language models; evidence assembly; biomedical knowledge bases; biological atlases

2504.19565 2025-12-19 cs.CL cs.AI q-bio.QM 80%

Knowledge-Driven Agentic Scientific Corpus Distillation Framework for Biomedical Large Language Models Training

面向生物医学大语言模型训练的知识驱动代理科学语料库精简框架

Meng Xiao, Xunxin Cai, Qingqing Long, Chengrui Wang, Yuanchun Zhou, Hengshu Zhu

机构 * Computer Network Information Center, Chinese Academy of Sciences, Beijing, China（中国科学院计算机网络信息中心）； University of Chinese Academy of Sciences, Beijing, China（中国科学院大学）； Duke-NUS Medical School, National University of Singapore, Singapore（新加坡国立大学杜克-新加坡医学部）

专题命中生物医学文本：biomedical(title,abstract)；分类 q-bio

AI总结本文提出一种知识驱动的代理框架，用于生物医学大语言模型训练中的语料库精简，通过多代理协作提升问答任务性能。

Comments Biomedical Large Language Models, Agentic Corpus Distillation, Synthetic Question-Answer Generation, Agentic AI, Knowledge Hierarchy Guidance

2004.03181 2020-04-08 q-bio.QM cs.CL cs.IR 80%

Multilingual enrichment of disease biomedical ontologies

Léo Bouscarrat, Antoine Bonnefoy, Cécile Capponi, Carlos Ramisch

专题命中生物医学文本：biomedical(title,abstract)；分类 q-bio

Journal ref 2nd workshop on MultilingualBIO: Multilingual Biomedical Text Processing, May 2020, Marseille, France

1902.02784 2019-02-11 q-bio.PE nlin.CG 80%

A Survey of the Individual-Based Model applied in Biomedical and Epidemiology

E. G. Nepomuceno, D. F. Resende, M. J. Lacerda

专题命中生物医学文本：biomedical(title,abstract)；分类 q-bio

Journal ref Journal of Biomedical Research and Reviews, vol. 1, no. 1, pp. 11-24, 2018

2505.20321 2026-08-13 cs.CL cs.AI cs.LG 79%

BiomedSQL: Text-to-SQL for Scientific Reasoning on Biomedical Knowledge Bases

BiomedSQL: 文本到SQL用于生物医学知识库上的科学推理

Mathew J. Koretsky, Maya Willey, Owen Bianchi, Chelsea X. Alvarado, Tanay Nayak, Nicole Kuznetsov, Sungwon Kim, Mike A. Nalls, Daniel Khashabi, Faraz Faghri

机构 * Center for Alzheimer’s and Related Dementias, NIA, NIH（阿尔茨海默病及相关痴呆症研究中心，国家老龄化研究所，国立卫生研究院）； DataTecnica LLC（DataTecnica公司）； Johns Hopkins University（约翰霍普金斯大学）； Laboratory of Neurogenetics, NIA, NIH（神经遗传学实验室，国家老龄化研究所，国立卫生研究院）

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG

AI总结 BiomedSQL通过评估文本到SQL生成中的科学推理能力，针对生物医学知识库设计了首个基准测试，展示了不同模型在复杂查询任务中的性能差异。

Comments Published as a conference paper at COLM 2026

2608.06713 2026-08-10 cs.AI cs.LG 新提交 79%

MolBioKG: Grounding Out-of-Graph Molecules in Biomedical Knowledge Graphs via Multi-Resolution Structural Anchoring

MolBioKG：通过多分辨率结构锚定将图外分子锚定到生物医学知识图谱中

Yiming Zhang, Hikaru Shindo, Shuan Chen, Kaushalya Madhawa, Jun Jin Choong, Yuna Oikawa, Takashi Fujiwara, Keisuke Ozawa

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG

AI总结 MolBioKG是解决生物医学KG中图外分子冷启动问题的两层系统，通过多分辨率结构锚定实现分子与KG的关联，在多项任务中优于基线并提升关键指标。

Comments Preprint

2608.04144 2026-08-06 cs.IR cs.CL cs.LG 新提交 79%

Neighborhood-Aware Dual Biomedical Entity Linking

感知邻域的双生物医学实体链接

Yicheng Tao, Jie Liu

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG

AI总结针对生物医学实体链接的挑战，提出三阶段框架PILOT，在五个基准上取得最优性能且推理高效。

2604.23054 2026-08-06 cs.CL cs.AI cs.LG 版本更新 79%

DeepImagine: Clinical Trial Outcome Prediction via Stepwise Local Counterfactual Imaginations

DeepImagine: 通过连续反事实想象学习生物医学推理

Youze Zheng, Jianyou Wang, Yuhan Chen, Matthew Feng, Longtian Bao, Hanyuan Zhang, Maxim Khan, Aditya K. Sehgal, Christopher D. Rosin, Umber Dube, Ramamohan Paturi

机构 * Laboratory for Emerging Intelligence, University of California, San Diego（新兴智能实验室，加州大学圣地亚哥分校）； Department of Dermatology, University of California, San Diego（皮肤科系，加州大学圣地亚哥分校）； University of Chicago（芝加哥大学）； Elsevier（艾尔斯特出版社）

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG

AI总结本文提出DeepImagine框架，通过连续反事实想象训练语言模型进行生物医学推理，利用反事实对偶和强化学习提升临床试验预测性能，展示模型在生物医学领域的可解释性改进。

Comments Preprint

2607.01444 2026-07-03 cs.LG cs.AI cs.CL 新提交 79%

On the Utility and Factual Reliability of Pruned Mixture-of-Experts Models in the Biomedical Domain

关于剪枝后的混合专家模型在生物医学领域的实用性与事实可靠性

Atsuki Yamaguchi, Szymon Palucha, Léo Bijar, Aline Villavicencio, Nikolaos Aletras

机构 * University of Sheffield（谢菲尔德大学）； AstraZeneca（阿斯利康）； University of Exeter（埃克塞特大学）； Federal University of Rio Grande do Norte（北里奥格兰德联邦大学）

专题命中生物医学文本：biomedical(title,abstract)；分类 cs.LG

AI总结研究通过结构化专家剪枝降低混合专家模型部署成本，评估剪枝对生物医学领域实用性与事实可靠性的影响，发现适度剪枝保持领域内性能但极端剪枝增加幻觉风险。

Comments Under review

1. 生物医学文本 4499 篇

Extracting Protein-Protein Interactions (PPIs) from Biomedical Literature using Attention-based Relational Context Information

ResMGCN: Residual Message Graph Convolution Network for Fast Biomedical Interactions Discovering

Benchmarking and Analyzing In-context Learning, Fine-tuning and Supervised Learning for Biomedical Knowledge Curation: a focused study on chemical entities of biological interest

Emerging Drug Interaction Prediction Enabled by Flow-based Graph Neural Network with Biomedical Network

Know2BIO: A Comprehensive Dual-View Benchmark for Evolving Biomedical Knowledge Graphs

Enhancement attacks in biomedical machine learning

Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching

ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts

Analysing Biomedical Knowledge Graphs using Prime Adjacency Matrices

BactInt: A domain driven transfer learning approach and a corpus for extracting inter-bacterial interactions from biomedical text

Enhancing Embedding Representations of Biomedical Data using Logic Knowledge

Interpretability from a new lens: Integrating Stratification and Domain knowledge for Biomedical Applications

Multi-task Joint Strategies of Self-supervised Representation Learning on Biomedical Networks for Drug Discovery

Semi-supervised classification using a supervised autoencoder for biomedical applications

A Review on The Division of Magnetic Resonant Prostate Images with Deep Learning

COVID-19Base: A knowledgebase to explore biomedical entities related to COVID-19

A Study of Data Pre-processing Techniques for Imbalanced Biomedical Data Classification

PubMedQA: A Dataset for Biomedical Research Question Answering

A Discussion on the Algorithm Design of Electrical Impedance Tomography for Biomedical Applications

Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts

Median topographic maps for biomedical data sets

BioHarness: Substrate-Aware Evidence Assembly for Biomedical Question Answering across Literature, Knowledge Bases, and Biological Atlases

Knowledge-Driven Agentic Scientific Corpus Distillation Framework for Biomedical Large Language Models Training

Multilingual enrichment of disease biomedical ontologies

A Survey of the Individual-Based Model applied in Biomedical and Epidemiology

BiomedSQL: Text-to-SQL for Scientific Reasoning on Biomedical Knowledge Bases

MolBioKG: Grounding Out-of-Graph Molecules in Biomedical Knowledge Graphs via Multi-Resolution Structural Anchoring

Neighborhood-Aware Dual Biomedical Entity Linking

DeepImagine: Clinical Trial Outcome Prediction via Stepwise Local Counterfactual Imaginations

On the Utility and Factual Reliability of Pruned Mixture-of-Experts Models in the Biomedical Domain