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With an aim of developing a training course in machine / deep learning for life-science and chemistry researchers, this is a compilation of relevant materials.

  • Articles, reviews and tutorials
  • Books
  • Courses
  • Resources
  • References

Articles, reviews and tutorials

Year First author Title / Link Journal
2021 Jimenez-Luna Artificial intelligence in drug discovery: Recent advances and future perspectives Expert Opinion on Drug Discovery
2021 Bender Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 1: Ways to make an impact, and why we are not there yet Drug Discovery Today
2020 von Lilienfeld Retrospective on a decade of machine learning for chemical discovery Nature Communications
2020 Lopez Enhancing scientific discoveries in molecular biology with deep generative models Molecular Systems Biology
2020 Cao Ensemble deep learning in bioinformatics Nature Machine Intelligence
2020 Kopp Deep learning for genomics using Janggu Nature Communications
2020 Adam Machine learning approaches to drug response prediction: challenges and recent progress npj Precision Oncology
2020 Schreiber Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome Genome biology
2020 Schreiber Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples Genome biology
2020 Brown Artificial intelligence in chemistry and drug design Journal of Computer-Aided Molecular Design
2020 van der Schaar How artificial intelligence and machine learning can help healthcare systems respond to COVID-19 Group website
2020 Neves Deep Learning-driven research for drug discovery: Tackling Malaria PLOS Computational Biology
2020 Stokes A Deep Learning Approach to Antibiotic Discovery Cell
2020 Xu A comprehensive review of computational prediction of genome-wide features Briefings in Bioinformatics
2020 Walters Assessing the impact of generative AI on medicinal chemistry Nature Biotechnology
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2019 Schneider Rethinking drug design in the artificial intelligence era Nature Reviews Drug Discovery
2019 Dias Artificial intelligence in clinical and genomic diagnostics Genome Medicine
2019 Filipp Opportunities for artificial intelligence in advancing precision medicine arXiv
2019 Yang Machine-learning-guided directed evolution for protein engineering Nature methods
2019 Kopp Janggu - Deep learning for genomics bioRxiv
2019 Zhavoronkov Deep Aging Clocks: The Emergence of AI-Based Biomarkers of Aging and Longevity Trends in Pharmacological Sciences
2019 Mater Deep Learning in Chemistry J. Chem. Inf. Model.
2019 Eraslan Deep learning: new computational modelling techniques for genomics Nature Reviews Genetics
2019 Avsec The Kipoi repository accelerates community exchange and reuse of predictive models for genomics
2019 Xu Machine learning and complex biological data
2019 Vamathevan Applications of machine learning in drug discovery and development
2019 Preuer Interpretable Deep Learning in Drug Discovery
2019 Polykovskiy Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models
2019 Schneider Mind and machine in drug design
2019 Elton Deep learning for molecular generation and optimization-a review of the state of the art
2019 Topol High-performance medicine: the convergence of human and artificial intelligence
2019 Gromski How to explore chemical space using algorithms and automation
2019 Li Deep learning in bioinformatics: introduction, application, and perspective in big data era
2019 Zachary Machine-Learning-Assisted Directed Protein Evolution with Combinatorial Libraries
2019 Haghighatlari Advances of Machine Learning in Molecular Modeling and Simulation
2019 PLOS Collection in Machine Learning in Health and Biomedicine
2019 Jaganathan Predicting Splicing from Primary Sequence with Deep Learning
2019 He The practical implementation of artificial intelligence technologies in medicine
2019 Kriegescorte Neural network models and deep learning - a primer for biologists
2019 Esteva A guide to deep learning in healthcare
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2018 Yu Visible Machine Learning for Biomedicine Cell
2018 Brown GuacaMol: Benchmarking Models for de Novo Molecular Design J. Chem. Inf. Model.
2018 Sellwood Artificial intelligence in drug discovery
2018 Yu Artificial intelligence in healthcare
2018 Pérez Simulations meet machine learning in structural biology
2018 Zou A primer on deep learning in genomics
2018 Ching Opportunities and obstacles for deep learning in biology and medicine
2018 Greene Opportunities and obstacles for deep learning in biology and medicine
2018 Wainberg Deep learning in biomedicine
2018 Zitnik Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities
2018 Telenti Deep learning of genomic variation and regulatory network data
2018 Yue Deep Learning for Genomics: A Concise Overview
2018 Camacho Next-Generation Machine Learning for Biological Networks
2018 Jung Machine Learning: Basic Principles
2018 Chen The rise of deep learning in drug discovery. A summary of the latest applications of deep learning to bioactivity and reaction predictions, and image analysis
2018 Lo Machine learning in chemoinformatics and drug discovery
2018 Segler Planning chemical syntheses with deep neural networks and symbolic AI
2018 Sundaram Predicting the clinical impact of human mutation with deep neural networks
2018 Zhou Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk
2018 Teschendorff Avoiding common pitfalls in machine learning omic data science
2018 Colwell Statistical and machine learning approaches to predicting protein–ligand interactions
2018 Yang Machine learning in protein engineering
2018 Coley Machine Learning in Computer-Aided Synthesis Planning
2018 Goh Deep Learning for Computational Chemistry
2018 Wu MoleculeNet: a benchmark for molecular machine learning
2018 Salim Synthetic Patient Generation: A Deep Learning Approach Using Variational Autoencoders
2018 Butler Machine learning for molecular and materials science
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2017 Altae-Tran Low Data Drug Discovery with One-Shot Learning. Learning with little data in drug discovery
2017 Ransundar Is Multitask Deep Learning Practical for Pharma?
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2016 Angermueller Deep learning for computational biology
2016 Mamoshina Applications of Deep Learning in Biomedicine
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2015 Park Deep learning for regulatory genomics
2015 LeCun Deep learning

Other:

Books

Authors Title / Link
Nielsen Neural Networks and Deep Learning
James, Witten, Hastie and Tibshirani An Introduction to Statistical Learning with Applications in R
Hastie, Tibshirani and Friedman The Elements of Statistical Learning: Data Mining, Inference, and Prediction
Goodfellow, Bengio and Courville Deep Learning

Courses

Provider Title / Link
Parr and Howard How to explain gradient boosting
Machine learning for kids projects
Data flair Machine learning tutorials and Artificial Intelligence tutorials
MIT Introduction to Deep Learning
fast.ai Deep learning and machine learning courses
Coursera Deep Learning Specialization
University of Cambridge An Introduction to Machine Learning: github and book
Data School In-depth introduction to machine learning in 15 hours of expert videos
Shirin Glander Introduction to Machine Learning with R

Resources

Implementations:

Language Library Description
Python scikit-learn machine learning
Python PyTorch deep learning, Facebook
Python Keras deep learning
Python TensorFlow deep learning, Google
Python Theano deep learning
Python DragoNN deep learning for genomics
Python Macau Bayesian factorization
R h2o machine and deep learning
R mlr machine learning
R caret machine learning
R randomForest Breiman and Cutler's Random Forests for Classification and Regression
Java WEKA machine learning

Repositories:

Title / Link Description
Kipoi machine and deep learning models in genomics

Blogs:

Cheat sheets:

CRAN Task Views:

References

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