医学 AI

SemiGNN-PPI: Self-Ensembling Multi-Graph Neural Network for Efficient and Generalizable Protein-Protein Interaction Prediction

Ziyuan Zhao, Peisheng Qian, Xulei Yang, Zeng Zeng, Cuntai Guan, Wai Leong Tam, Xiaoli Li

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

Comments Accepted by IJCAI 2023

KG-Hub -- Building and Exchanging Biological Knowledge Graphs

J Harry Caufield, Tim Putman, Kevin Schaper, Deepak R Unni, Harshad Hegde, Tiffany J Callahan, Luca Cappelletti, Sierra AT Moxon, Vida Ravanmehr, Seth Carbon, Lauren E Chan, Katherina Cortes, Kent A Shefchek, Glass Elsarboukh, James P Balhoff, Tommaso Fontana, Nicolas Matentzoglu, Richard M Bruskiewich, Anne E Thessen, Nomi L Harris, Monica C Munoz-Torres, Melissa A Haendel, Peter N Robinson, Marcin P Joachimiak, Christopher J Mungall, Justin T Reese

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

An overview of open source Deep Learning-based libraries for Neuroscience

Louis Fabrice Tshimanga, Manfredo Atzori, Federico Del Pup, Maurizio Corbetta

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

Fast uncertainty quantification of tracer distribution in the brain interstitial fluid with multilevel and quasi Monte Carlo

Matteo Croci, Vegard Vinje, Marie E. Rognes

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

Comments Multilevel Monte Carlo, quasi Monte Carlo, brain simulation, brain fluids, finite element method, biomedical computing, random fields, diffusion-convection

Journal ref International Journal for Numerical Methods in Biomedical Engineering, 37(1), e3412 (2020)

Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response

Xihaier Luo, Sean McCorkle, Gilchan Park, Vanessa Lopez-Marrero, Shinjae Yoo, Edward R. Dougherty, Xiaoning Qian, Francis J. Alexander, Byung-Jun Yoon

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

Comments 9 pages, 6 figures

GraphIX: Graph-based In silico XAI(explainable artificial intelligence) for drug repositioning from biopharmaceutical network

Atsuko Takagi, Mayumi Kamada, Eri Hamatani, Ryosuke Kojima, Yasushi Okuno

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

Comments add supplementary materials

lgpr: An interpretable nonparametric method for inferring covariate effects from longitudinal data

Juho Timonen, Henrik Mannerström, Aki Vehtari, Harri Lähdesmäki

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

Comments Contains main manuscript and supplementary material. Tables S1-S3 are in ancillary files

Journal ref Bioinformatics, 37(13), 2021, 1860-1867

Opening Access to Visual Exploration of Audiovisual Digital Biomarkers: an OpenDBM Analytics Tool

Carla Floricel, Jacob Epifano, Stephanie Caamano, Sarah Kark, Rich Christie, Aaron Masino, Andre D Paredes

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

Comments 6 pages, 2 figures, 2022 IEEE VIS Workshop - Visualization in BioMedical AI

Attention-based Interpretable Regression of Gene Expression in Histology

Mara Graziani, Niccolò Marini, Nicolas Deutschmann, Nikita Janakarajan, Henning Müller, María Rodríguez Martínez

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

Comments Github Repo: https://github.com/maragraziani/interpretableWSItoRNAseq

Adaptive area-preserving parameterization of open and closed anatomical surfaces

Gary P. T. Choi, Amita Giri, Lalan Kumar

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

Journal ref Computers in Biology and Medicine, 105715 (2022)

Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery

Stephen Bonner, Ian P Barrett, Cheng Ye, Rowan Swiers, Ola Engkvist, Charles Tapley Hoyt, William L Hamilton

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

Journal ref Artificial Intelligence in the Life Sciences (2022): 100036

DProQ: A Gated-Graph Transformer for Protein Complex Structure Assessment

Xiao Chen, Alex Morehead, Jian Liu, Jianlin Cheng

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

Comments 18 pages, 3 figures, 13 tables. Under review

Calculation of Sub-bands {1,2,5,6} for 64-Point Complex FFT and Its extension to N (=2^N) Point FFT

Bhaskar Sen

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

Comments The paper is withdrawn as the there is more than one author for this paper

Deep learning for drug repurposing: methods, databases, and applications

Xiaoqin Pan, Xuan Lin, Dongsheng Cao, Xiangxiang Zeng, Philip S. Yu, Lifang He, Ruth Nussinov, Feixiong Cheng

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

Comments Accepted by WIREs Computational Molecular Science

Assigning function to protein-protein interactions: a weakly supervised BioBERT based approach using PubMed abstracts

Aparna Elangovan, Melissa Davis, Karin Verspoor

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

Comments Please see the updated version of this paper https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04504-x

Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health

Ryan T. Scott, Erik L. Antonsen, Lauren M. Sanders, Jaden J. A. Hastings, Seung-min Park, Graham Mackintosh, Robert J. Reynolds, Adrienne L. Hoarfrost, Aenor Sawyer, Casey S. Greene, Benjamin S. Glicksberg, Corey A. Theriot, Daniel C. Berrios, Jack Miller, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Stuart Chalk, Guillermo M. Delgado-Aparicio, Melissa Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, John Kalantari, Kia Khezeli, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Hector Garcia Martin, Christopher E. Mason, Mona Matar, George I. Mias, Jerry G. Myers,, Charlotte Nelson, Jonathan Oribello, Patricia Parsons-Wingerter, R. K. Prabhu, Amina Ann Qutub, Jon Rask, Amanda Saravia-Butler, Suchi Saria, Nitin Kumar Singh, Frank Soboczenski, Michael Snyder, Karthik Soman, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes

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

Comments 31 pages, 4 figures

Multimodal Pre-Training Model for Sequence-based Prediction of Protein-Protein Interaction

Yang Xue, Zijing Liu, Xiaomin Fang, Fan Wang

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

Comments MLCB 2021 Spotlight

Deep Molecular Representation Learning via Fusing Physical and Chemical Information

Shuwen Yang, Ziyao Li, Guojie Song, Lingsheng Cai

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

Comments In NeurIPS-2021, 18 pages, 5 figures, appendix included

When are Deep Networks really better than Decision Forests at small sample sizes, and how?

Haoyin Xu, Kaleab A. Kinfu, Will LeVine, Sambit Panda, Jayanta Dey, Michael Ainsworth, Yu-Chung Peng, Madi Kusmanov, Florian Engert, Christopher M. White, Joshua T. Vogelstein, Carey E. Priebe

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

Predicting the Mechanical Properties of Biopolymer Gels Using Neural Networks Trained on Discrete Fiber Network Data

Yue Leng, Vahidullah Tac, Sarah Calve, Adrian Buganza Tepole

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

Comments 20 pages, 9 figures, for associated files please see https://bitbucket.org/buganzalab/nn_rve/src/master/

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development

Kexin Huang, Tianfan Fu, Wenhao Gao, Yue Zhao, Yusuf Roohani, Jure Leskovec, Connor W. Coley, Cao Xiao, Jimeng Sun, Marinka Zitnik

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

Comments Published at NeurIPS 2021 Datasets and Benchmarks

EPGAT: Gene Essentiality Prediction With Graph Attention Networks

João Schapke, Anderson Tavares, Mariana Recamonde-Mendoza

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

Comments Published in IEEE/ACM Transactions on Computational Biology and Bioinformatics

Graph Representation Learning on Tissue-Specific Multi-Omics

Amine Amor, Pietro Lio', Vikash Singh, Ramon Viñas Torné, Helena Andres Terre

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

Comments This paper was accepted at the 2021 ICML Workshop on Computational Biology

Statistical power for cluster analysis

E. S. Dalmaijer, C. L. Nord, D. E. Astle

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

Comments 53 pages, 13 figures, 5 tables; for code and data see: https://www.github.com/esdalmaijer/cluster_power

SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization

Yue Yu, Kexin Huang, Chao Zhang, Lucas M. Glass, Jimeng Sun, Cao Xiao

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

Comments Published in Bioinformatics 2021

Machine Learning Applications for Therapeutic Tasks with Genomics Data

Kexin Huang, Cao Xiao, Lucas M. Glass, Cathy W. Critchlow, Greg Gibson, Jimeng Sun

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

Formal Methods for the Informal Engineer: Workshop Recommendations

Gopal Sarma, James Koppel, Gregory Malecha, Patrick Schultz, Eric Drexler, Ramana Kumar, Cody Roux, Philip Zucker

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

Comments 6 pages

sJIVE: Supervised Joint and Individual Variation Explained

Elise F. Palzer, Christine Wendt, Russell Bowler, Craig P. Hersh, Sandra E. Safo, Eric F. Lock

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

Comments 23 pages, 8 tables, 3 figures

Utilising Graph Machine Learning within Drug Discovery and Development

Thomas Gaudelet, Ben Day, Arian R. Jamasb, Jyothish Soman, Cristian Regep, Gertrude Liu, Jeremy B. R. Hayter, Richard Vickers, Charles Roberts, Jian Tang, David Roblin, Tom L. Blundell, Michael M. Bronstein, Jake P. Taylor-King

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

Comments 19 pages, 7 figures, 2 tables

Feature reduction for machine learning on molecular features: The GeneScore

Alexander Denker, Anastasia Steshina, Theresa Grooss, Frank Ueckert, Sylvia Nürnberg

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

Comments 11 pages, 9 figures, 4 tables