Machine Learning Applications for Therapeutic Tasks with Genomics Data
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Abstract (arXiv)
Thanks to the increasing availability of genomics and other biomedical data, many machine learning approaches have been proposed for a wide range of therapeutic discovery and development tasks. In this survey, we review the literature on machine learning applications for genomics through the lens of therapeutic development. We investigate the interplay among genomics, compounds, proteins, electronic health records (EHR), cellular images, and clinical texts. We identify twenty-two machine learning in genomics applications across the entire therapeutics pipeline, from discovering novel targets, personalized medicine, developing gene-editing tools all the way to clinical trials and post-market studies. We also pinpoint seven important challenges in this field with opportunities for expansion and impact. This survey overviews recent research at the intersection of machine learning, genomics, and therapeutic development.
Key facts. Cited by 3 papers in the map (data through 7 Oct 2026). Builds on 35 of its 241 references that are in the map. First posted on arXiv 3 May 2021.
Builds on
35 of 241 references.
References · 35
- 2017Attention Is All You Needcited by 59,932
- 2018BERT: Pre-training of Deep Bidirectional Transformers for Language Understandingcited by 40,204
- 2016Semi-Supervised Classification with Graph Convolutional Networkscited by 11,282
- 2017Model-Agnostic Meta-Learning for Fast Adaptation of Deep Networkscited by 4,861
- 2013Auto-Encoding Variational Bayescited by 3,980
- 2017Prototypical Networks for Few-shot Learningcited by 3,001
- 2019Invariant Risk Minimizationcited by 1,832
- 2020Reformer: The Efficient Transformercited by 1,658
- 2014On the Properties of Neural Machine Translation: Encoder-Decoder Approachescited by 1,303
- 2019Strategies for Pre-training Graph Neural Networkscited by 964
- 2019GNNExplainer: Generating Explanations for Graph Neural Networkscited by 735
- 2018Junction Tree Variational Autoencoder for Molecular Graph Generationcited by 647
23 more
- 2018Deep Visual Domain Adaptation: A Surveycited by 634
- 2016Recurrent Neural Networks for Multivariate Time Series with Missing Valuescited by 548
- 2019ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmissioncited by 487
- 2019Federated Machine Learning: Concept and Applicationscited by 409
- 2020Does the Whole Exceed its Parts? The Effect of AI Explanations on Complementary Team Performancecited by 396
- 2019Unsupervised Label Noise Modeling and Loss Correctioncited by 327
- 2020Fairness in Machine Learningcited by 194
- 2018Graph Convolution over Pruned Dependency Trees Improves Relation Extractioncited by 146
- 2020Handling Missing Data with Graph Representation Learningcited by 132
- 2020MolTrans: Molecular Interaction Transformer for Drug Target Interaction Predictioncited by 63
- 2020SkipGNN: Predicting Molecular Interactions with Skip-Graph Networkscited by 44
- 2018Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunitiescited by 43
- 2020COMPOSE: Cross-Modal Pseudo-Siamese Network for Patient Trial Matchingcited by 37
- 2019CORE: Automatic Molecule Optimization Using Copy & Refine Strategycited by 27
- 2020Utilising Graph Machine Learning within Drug Discovery and Developmentcited by 26
- 2019LoRAS: An oversampling approach for imbalanced datasetscited by 15
- 2018Learning Eligibility in Cancer Clinical Trials using Deep Neural Networkscited by 14
- 2016Diet Networks: Thin Parameters for Fat Genomicscited by 12
- 2019CONAN: Complementary Pattern Augmentation for Rare Disease Detectioncited by 9
- 2018Machine learning and genomics: precision medicine vs. patient privacycited by 4
- 2016Drug response prediction by inferring pathway-response associations with Kernelized Bayesian Matrix Factorizationcited by 3
- 2018Drug response prediction by ensemble learning and drug-induced gene expression signaturescited by 2
- 2020An Interpretable End-to-end Fine-tuning Approach for Long Clinical Textcited by 1
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Citing papers per year: 2022: 3.
3 papers.