医学 AI

Identifying multi-omics interactions for lung cancer drug targets discovery using Kernel Machine Regression

Md. Imtyaz Ahmed, Md. Delwar Hossain, Md Mostafizer Rahman, Md. Ahsan Habib, Md. Mamunur Rashid, Md. Selim Reza, Md Ashad Alam

机构 * Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Dhaka, Bangladesh（信息与通信技术系，穆拉纳巴沙尼科学与技术大学） ； Department of Computer Science, Tulane University, New Orleans, LA, USA（计算机科学系，杜兰大学） ； Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 138632, Singapore（生物信息学研究所（BII），科技研究局（A*STAR）） ； Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA 70112, USA（杜兰大学生物医学信息学与基因组学中心，医学部） ； Ochsner Center for Outcomes Research, Ochsner Research, New Orleans, LA 70121, USA（Ochsner研究中心，Ochsner研究） 纠错

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

RAIDER: Rapid, anatomy-independent, deep learning-based PDFF and R2* estimation using magnitude-only signals

T. J. P. Bray, G. V. Minore, A. Bainbridge, L. Dwyer-Hemmings, S. A. Taylor, M. A. Hall-Craggs, H. Zhang

专题命中 生物医学文本 ：MRI(abstract)；biomedical(comments,journal_ref)

Comments Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA) https://melba-journal.org/é

Journal ref Machine.Learning.for.Biomedical.Imaging. 3 (2025)

Thin Bridges for Drug Text Alignment: Lightweight Contrastive Learning for Target Specific Drug Retrieval

Mallikarjuna Tupakula

机构 * Rochester Institute of Technology（罗切斯特技术研究所） 纠错

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

FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction

Zhaohan Meng, Zaiqiao Meng, Ke Yuan, Iadh Ounis

机构 * School of Computing Science（计算科学学院） ； School of Cancer Sciences（癌症科学学院） ； Cancer Research UK Scotland Institute（英国癌症研究苏格兰研究所） ； University of Glasgow（格拉斯哥大学） 纠错

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

Comments Findings of EMNLP 2025

Spatiotemporal graph neural process for reconstruction, extrapolation, and classification of cardiac trajectories

Jaume Banus, Augustin C. Ogier, Roger Hullin, Philippe Meyer, Ruud B. van Heeswijk, Jonas Richiardi

机构 * Department of Radiology, Lausanne University Hospital（放射科，洛桑大学医院） ； University of Lausanne（洛桑大学） ； Cardiovascular Department, Lausanne University Hospital（心血管科，洛桑大学医院） ； Department of Medicine, Geneva University Hospital（医学部，日内瓦大学医院） ； University of Geneva（日内瓦大学） ； CIBM Center for Biomedical Imaging（生物医学成像中心） 纠错

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

Alz-QNet: A Quantum Regression Network for Studying Alzheimer's Gene Interactions

Debanjan Konar, Neerav Sreekumar, Richard Jiang, Vaneet Aggarwal

机构 * University of the Moon（月球大学） ； Purdue University（普渡大学） ； Indian Institute of Technology Tirupati（印度理工学院特里普蒂） ； Lancaster University（兰卡斯特大学） 纠错

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

Journal ref Computers in Biology and Medicine, Volume 196, Part C, September 2025, 110837

Learning Causally Predictable Outcomes from Psychiatric Longitudinal Data

Eric V. Strobl

机构 * Departments of Biomedical Informatics \& Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States of America 纠错

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

Comments R code is available at github.com/ericstrobl/DEBIAS

Towards Interpretable Drug-Drug Interaction Prediction: A Graph-Based Approach with Molecular and Network-Level Explanations

Mengjie Chen, Ming Zhang, Cunquan Qu

机构 * Data Science Institute, School of Mathematics, Shandong University（数据科学研究院、数学学院、山东大学） ； Academy of Mathematics and Systems Science, Chinese Academy of Sciences（数学与系统科学研究院、中国科学院） ； Data Science Institute, Shandong University（数据科学研究院、山东大学） 纠错

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

BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects

Hongyang Li, Sanjoy Dey, Bum Chul Kwon, Michael Danziger, Michal Rosen-Tzvi, Jianying Hu, James Kozloski, Ching-Huei Tsou, Bharath Dandala, Pablo Meyer

机构 * IBM Research（IBM研究院） 纠错

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

Reconstructing Biological Pathways by Applying Selective Incremental Learning to (Very) Small Language Models

Pranta Saha, Joyce Reimer, Brook Byrns, Connor Burbridge, Neeraj Dhar, Jeffrey Chen, Steven Rayan, Gordon Broderick

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

Comments 9 pages, 6 figures, 3 tables + 28 pages of supplemental tables; submitted to 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB 2025) as submission no. 76

Molecular Machine Learning Using Euler Characteristic Transforms

Victor Toscano-Duran, Florian Rottach, Bastian Rieck

机构 * Department of Applied Mathematics I, University of Seville（塞维利亚大学应用数学系） ； Central Data Science, Boehringer Ingelheim GmbH（勃林格殷曼集团中央数据科学部） ； School of Medicine, University of Tübingen（图宾根大学医学院） 纠错

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

PINNet: a deep neural network with pathway prior knowledge for Alzheimer's disease

Yeojin Kim, Hyunju Lee

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

Graph Neural Networks in Modern AI-aided Drug Discovery

Odin Zhang, Haitao Lin, Xujun Zhang, Xiaorui Wang, Zhenxing Wu, Qing Ye, Weibo Zhao, Jike Wang, Kejun Ying, Yu Kang, Chang-yu Hsieh, Tingjun Hou

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

K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction

Tassallah Abdullahi, Ioanna Gemou, Nihal V. Nayak, Ghulam Murtaza, Stephen H. Bach, Carsten Eickhoff, Ritambhara Singh

机构 * Brown University（布朗大学） ； University of Tübingen（图宾根大学） 纠错

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

Journal ref Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining V.2 (KDD '25), August 3--7, 2025, Toronto, ON, Canada

Sparsity is All You Need: Rethinking Biological Pathway-Informed Approaches in Deep Learning

Isabella Caranzano, Corrado Pancotti, Cesare Rollo, Flavio Sartori, Pietro Liò, Piero Fariselli, Tiziana Sanavia

机构 * Computational Biomedicine Unit, Department of Medical Sciences, University of Torino（托斯尼亚大学医学科学系计算生物医学单元） ； Department of Computer Science and Technology, University of Cambridge（剑桥大学计算机科学与技术系） 纠错

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

Heterogeneous network drug-target interaction prediction model based on graph wavelet transform and multi-level contrastive learning

Wenfeng Dai, Yanhong Wang, Shuai Yan, Qingzhi Yu, Xiang Cheng

机构 * Jingdezhen Ceramics University（景德镇陶瓷大学） 纠错

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

A Graph Based Raman Spectral Processing Technique for Exosome Classification

Vuong M. Ngo, Edward Bolger, Stan Goodwin, John O'Sullivan, Dinh Viet Cuong, Mark Roantree

机构 * Insight Centre for Data Analytics（数据分析洞察中心） ； Dublin City University（都柏林城市大学） ； School of Computing（计算学院） ； School of Chemical Sciences（化学科学学院） ； Ho Chi Minh City Open University（胡志明市开放大学） 纠错

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

Comments The 23rd International Conference on Artificial Intelligence in Medicine (AIME 2025), LNAI, Springer, 11 pages

Knowledge-Driven Feature Selection and Engineering for Genotype Data with Large Language Models

Joseph Lee, Shu Yang, Jae Young Baik, Xiaoxi Liu, Zhen Tan, Dawei Li, Zixuan Wen, Bojian Hou, Duy Duong-Tran, Tianlong Chen, Li Shen

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

Comments accepted by AMIA-IS'25: AMIA Informatics Summit [Marco Ramoni Distinguished Paper Award for Translational Bioinformatics]

DataMap: A Portable Application for Visualizing High-Dimensional Data

Xijin Ge

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

Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction

Sepideh Maleki, Jan-Christian Huetter, Kangway V. Chuang, David Richmond, Gabriele Scalia, Tommaso Biancalani

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

On-Chip and Off-Chip TIA Amplifiers for Nanopore Signal Readout Design, Performance and Challenges: A Review

K. Ashoka Deepthi, Manoj Varma, Arup Polley

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

Comments 35 pages , 22 figures

Improving Diseases Predictions Utilizing External Bio-Banks

Hido Pinto, Eran Segal

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

Sequence Analysis Using the Bezier Curve

Taslim Murad, Sarwan Ali, Murray Patterson

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

Identifying Critical Phases for Disease Onset with Sparse Haematological Biomarkers

Andrea Zerio, Maya Bechler-Speicher, Tine Jess, Aleksejs Sazonovs

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

Consensus statement on the credibility assessment of ML predictors

Alessandra Aldieri, Thiranja Prasad Babarenda Gamage, Antonino Amedeo La Mattina, Yi Li, Axel Loewe, Francesco Pappalardo, Marco Viceconti Italy

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

Protein Large Language Models: A Comprehensive Survey

Yijia Xiao, Wanjia Zhao, Junkai Zhang, Yiqiao Jin, Han Zhang, Zhicheng Ren, Renliang Sun, Haixin Wang, Guancheng Wan, Pan Lu, Xiao Luo, Yu Zhang, James Zou, Yizhou Sun, Wei Wang

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

Comments 24 pages, 4 figures, 5 tables

Application-driven Validation of Posteriors in Inverse Problems

Tim J. Adler, Jan-Hinrich Nölke, Annika Reinke, Minu Dietlinde Tizabi, Sebastian Gruber, Dasha Trofimova, Lynton Ardizzone, Paul F. Jaeger, Florian Buettner, Ullrich Köthe, Lena Maier-Hein

专题命中 生物医学文本 ：medical image(comments,journal_ref)；分类 cs.CV、cs.LG、eess.IV

Comments Accepted at Medical Image Analysis. Shared first authors: Tim J. Adler and Jan-Hinrich Nölke. 24 pages, 9 figures, 1 table

Journal ref Medical Image Analysis, Volume 101, 2025, 103474, ISSN 1361-8415

Boosting drug-disease association prediction for drug repositioning via dual-feature extraction and cross-dual-domain decoding

Enqiang Zhu, Xiang Li, Chanjuan Liu, Nikhil R. Pal

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

Multi-modal Representation Learning Enables Accurate Protein Function Prediction in Low-Data Setting

Serbülent Ünsal, Sinem Özdemir, Bünyamin Kasap, M. Erşan Kalaycı, Kemal Turhan, Tunca Doğan, Aybar C. Acar

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

Graph Neural Networks for Quantifying Compatibility Mechanisms in Traditional Chinese Medicine

Jingqi Zeng, Xiaobin Jia

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

Comments 10 pages, 5 figures. Includes open-source dataset and code for reproducibility