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Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities

30 June 2018

Papers citing "Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities"

44 / 44 papers shown

Title
NeuBM: Mitigating Model Bias in Graph Neural Networks through Neutral Input Calibration Jiawei Gu Ziyue Qiao Xiao Luo 220 0 0 21 May 2025
Longitudinal Ensemble Integration for sequential classification with multimodal data Aviad Susman Repack Krishnamurthy Richard Yan Chak Li Mohammad Al Olaimat S. Bozdag Bino Varghese Nasim Sheikh-Bahei Gaurav Pandey 24 0 0 08 Nov 2024
SHAP-CAT: A interpretable multi-modal framework enhancing WSI classification via virtual staining and shapley-value-based multimodal fusion Jun Wang Yu Mao Nan Guan Chun Jason Xue 67 1 0 02 Oct 2024
RGDA-DDI: Residual graph attention network and dual-attention based framework for drug-drug interaction prediction Changjian Zhou Xin Zhang Jiafeng Li Jia Song Wensheng Xiang 50 0 0 27 Aug 2024
Trustworthy Enhanced Multi-view Multi-modal Alzheimer's Disease Prediction with Brain-wide Imaging Transcriptomics Data Shan Cong Zhoujie Fan Hongwei Liu Yinghan Zhang Xin Wang Haoran Luo Xiaohui Yao 172 2 0 21 Jun 2024
FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction Zhaohan Meng Zaiqiao Meng I. Ounis 93 4 0 03 Jun 2024
Domain adaptation in small-scale and heterogeneous biological datasets Seyedmehdi Orouji Martin C. Liu T. Korem Megan A. K. Peters 82 9 0 29 May 2024
HiGraphDTI: Hierarchical Graph Representation Learning for Drug-Target Interaction Prediction Bin Liu Siqi Wu Jin Wang Xin Deng Ao Zhou 26 1 0 16 Apr 2024
Empowering Biomedical Discovery with AI Agents Shanghua Gao Ada Fang Yepeng Huang Valentina Giunchiglia Ayush Noori Jonathan Richard Schwarz Yasha Ektefaie Jovana Kondic Marinka Zitnik LLMAG AI4CE 108 98 0 03 Apr 2024
Deep Learning in Computational Biology: Advancements, Challenges, and Future Outlook Suresh Kumar Dhanyashri Guruparan Pavithren Aaron Philemon Telajan Kavinesh Mahadevan Dinesh Davagandhi Ong Xin Yue AI4CE 44 6 0 02 Oct 2023
Human-Producible Adversarial Examples David Khachaturov Yue Gao Ilia Shumailov Robert D. Mullins Ross J. Anderson Kassem Fawaz AAML WIGM 66 1 0 30 Sep 2023
Survival Prediction from Imbalance colorectal cancer dataset using hybrid sampling methods and tree-based classifiers Sadegh Soleimani Mahsa Bahrami M. Vali 58 2 0 04 Sep 2023
A Survey on Explainability of Graph Neural Networks Jaykumar Kakkad Jaspal Jannu Kartik Sharma Charu C. Aggarwal Sourav Medya 62 28 0 02 Jun 2023
Analysing Biomedical Knowledge Graphs using Prime Adjacency Matrices K. Bougiatiotis George Giannakopoulos 55 1 0 17 May 2023
Generating Post-hoc Explanations for Skip-gram-based Node Embeddings by Identifying Important Nodes with Bridgeness Hogun Park Jennifer Neville 62 5 0 24 Apr 2023
Studying Limits of Explainability by Integrated Gradients for Gene Expression Models Myriam Bontonou Anais Haget Maria Boulougouri J. Arbona Benjamin Audit Pierre Borgnat 27 2 0 19 Mar 2023
Multi-modal Multi-kernel Graph Learning for Autism Prediction and Biomarker Discovery Junbin Mao Jin Liu Han Lin Hulin Kuang Shirui Pan Yi-Lun Pan Shan Xie Fei Liu Yi Pan 73 2 0 03 Mar 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability Zhiqiang Zhong A. Barkova Davide Mottin 85 8 0 16 Feb 2023
DDeMON: Ontology-based function prediction by Deep Learning from Dynamic Multiplex Networks Jan Kralj Blaž Škrlj Živa Ramšak Nada Lavrac K. Gruden 26 1 0 08 Feb 2023
Explainable Multilayer Graph Neural Network for Cancer Gene Prediction Michail Chatzianastasis Michalis Vazirgiannis Zijun Zhang 17 17 0 20 Jan 2023
CustOmics: A versatile deep-learning based strategy for multi-omics integration Hakim Benkirane Yoann Pradat Stefan Michiels P. Cournède SyDa 41 4 0 12 Sep 2022
Multimodal learning with graphs Yasha Ektefaie George Dasoulas Ayush Noori Maha Farhat Marinka Zitnik 143 92 0 07 Sep 2022
Interpretable bilinear attention network with domain adaptation improves drug-target prediction Peizhen Bai Filip Miljković Bino John Haiping Lu OOD 47 162 0 03 Aug 2022
Graph-in-Graph (GiG): Learning interpretable latent graphs in non-Euclidean domain for biological and healthcare applications Kamilia Mullakaeva Luca Cosmo Anees Kazi Seyed-Ahmad Ahmadi Nassir Navab Michael M. Bronstein 83 8 0 01 Apr 2022
Multimodal Learning on Graphs for Disease Relation Extraction Yucong Lin Keming Lu Sheng Yu Tianxi Cai Marinka Zitnik 60 31 0 16 Mar 2022
Are Your Sensitive Attributes Private? Novel Model Inversion Attribute Inference Attacks on Classification Models Shagufta Mehnaz S. V. Dibbo Ehsanul Kabir Ninghui Li E. Bertino MIACV 97 64 0 23 Jan 2022
Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health Ryan T. Scott E. Antonsen Lauren M Sanders Jaden J. A. Hastings Seung-min Park ... Baltimore. Biochemistry Jason H. Yang Re-Emerging Pathogens Harvard University 48 7 0 22 Dec 2021
Application of Machine Learning in understanding plant virus pathogenesis: Trends and perspectives on emergence, diagnosis, host-virus interplay and management Dibyendu Ghosh Srija Chakraborty H. Kodamana S. Chakraborty 29 19 0 03 Dec 2021
ContIG: Self-supervised Multimodal Contrastive Learning for Medical Imaging with Genetics Aiham Taleb Matthias Kirchler Remo Monti C. Lippert SSL MedIm 75 58 0 26 Nov 2021
Machine Learning Applications for Therapeutic Tasks with Genomics Data Kexin Huang Cao Xiao Lucas Glass C. Critchlow G. Gibson Jimeng Sun LM&MA VLM SyDa 47 27 0 03 May 2021
A Study into patient similarity through representation learning from medical records Hoda Memarzadeh Nasser Ghadiri Matthias Samwald Maryam Lotfi Shahreza 65 7 0 29 Apr 2021
Neural Multi-Hop Reasoning With Logical Rules on Biomedical Knowledge Graphs Yushan Liu Marcel Hildebrandt Mitchell Joblin Martin Ringsquandl Rime Raissouni Volker Tresp 91 45 0 18 Mar 2021
Segmentation and genome annotation algorithms Maxwell W. Libbrecht Rachel C W Chan Michael M. Hoffman 31 21 0 03 Jan 2021
Black-box Model Inversion Attribute Inference Attacks on Classification Models Shagufta Mehnaz Ninghui Li E. Bertino MIACV 81 13 0 07 Dec 2020
Dr-COVID: Graph Neural Networks for SARS-CoV-2 Drug Repurposing Siddhant Doshi S. Chepuri 21 6 0 03 Dec 2020
Using ontology embeddings for structural inductive bias in gene expression data analysis Maja Trebacz Z. Shams M. Jamnik P. Scherer Nikola Simidjievski Helena Andrés-Terré Pietro Lio 30 5 0 22 Nov 2020
Multi-typed Objects Multi-view Multi-instance Multi-label Learning Yuanlin Yang Guoxian Yu Jun Wang C. Domeniconi Xiangliang Zhang 16 1 0 06 Oct 2020
Characterizing Communities of Hashtag Usage on Twitter During the 2020 COVID-19 Pandemic by Multi-view Clustering Iain J. Cruickshank Kathleen M. Carley 51 41 0 03 Aug 2020
SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks Kexin Huang C. Xiao Lucas Glass Marinka Zitnik Jimeng Sun GNN 67 124 0 30 Apr 2020
Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19 D. Gysi Ì. Valle Marinka Zitnik Asher Ameli Xiao Gan ... D. Ghiassian R. Baron Helia Sanchez J. Loscalzo Albert-László Barabási 66 442 0 15 Apr 2020
Differentiable Graph Module (DGM) for Graph Convolutional Networks Anees Kazi Luca Cosmo Seyed-Ahmad Ahmadi Nassir Navab M. Bronstein GNN MedIm 91 133 0 11 Feb 2020
Leveraging binding-site structure for drug discovery with point-cloud methods Vincent Mallet Carlos Oliver N. Moitessier J. Waldispühl 43 7 0 28 May 2019
Probabilistic Forecasting of Sensory Data with Generative Adversarial Networks - ForGAN Alireza Koochali P. Schichtel Sheraz Ahmed Andreas Dengel AI4TS 74 73 0 29 Mar 2019
Stacked Penalized Logistic Regression for Selecting Views in Multi-View Learning Lingbing Guo M. Fokkema E. Cao M. Rooij 51 21 0 06 Nov 2018