awesome-small-molecule-ml

Machine Learning Resources

A curated collection of resources and papers related to machine learning in small-molecule drug discovery

A curated list of resources for machine learning for small-molecule drug discovery

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Awesome Small Molecule Machine Learning / Papers / Survey papers and books
Critical assessment of AI in drug discovery Walters and Barzilay, 2021.
Deep Learning for Molecules and Materials White, 2021.
Defining and Exploring Chemical Spaces Coley, 2020.
Learning Molecular Representations for Medicinal Chemistry Chuang et al, 2020.
Applications of Deep Learning in Molecule Generation and Molecular Property Prediction Walters and Barzilay, 2020.
Transfer Learning for Drug Discovery Cai et al, 2020.

Awesome Small Molecule Machine Learning / Papers / Representation, transfer learning, and few-shot learning
SELFIES and the future of molecular string representations Krenn et al, 2022.
Molecular Contrastive Learning of Representations via Graph Neural Networks Wang et al, 2022. . [ ]
ChemBERTa-2: Towards Chemical Foundation Models Ahmad et al, 2021. . [ ]
E(n) Equivariant Graph Neural Networks Satorras et al, 2021. . [ ]
FS-Mol: A Few-Shot Learning Dataset of Molecules Stanley et al, 2021. . [ ]
ATOM3D: Tasks On Molecules in Three Dimensions Townshend et al, 2021.
X-MOL: large-scale pre-training for molecular understanding and diverse molecular analysis Xue et al, 2021. . [ ]
Do Transformers Really Perform Bad for Graph Representation? (Graphormer paper) Ying et al, 2021. . [ ]
Attention-Based Learning on Molecular Ensembles Chuang and Keiser, 2020.
Inductive transfer learning for molecular activity prediction: Next-Gen QSAR Models with MolPMoFiT Li and Fourches, 2020. . [ ]
Molecule Attention Transformer Maziarka et al, 2020. . [ ]
Meta-Learning GNN Initializations for Low-Resource Molecular Property Prediction Nguyen et al., 2020. [ ]
Self-Supervised Graph Transformer on Large-Scale Molecular Data (GROVER paper) Rong et al., 2020. . [ ]
Strategies for Pre-training Graph Neural Networks Hu et al, 2019. . [ ]
Analyzing Learned Molecular Representations for Property Prediction (Chemprop) Yang et al, 2019. . [ ]
PotentialNet for Molecular Property Prediction Feinberg et al, 2018.
Low Data Drug Discovery with One-Shot Learning Altae-Tran et al, 2017.

Awesome Small Molecule Machine Learning / Papers / Generative algorithms
Flow Network based Generative Models for Non-Iterative Diverse Candidate Generation Bengio et al, 2021. . [ ]
Molecular generation by Fast Assembly of (Deep)SMILES fragments Berenger and Tsuda, 2021. . [ ]
Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design Gao et al, 2021. . [ ]
R-group replacement database for medicinal chemistry Takeuchi et al, 2021.
Deep Generative Models for 3D Linker Design Imrie et al, 2020. . [ ]
Hierarchical Generation of Molecular Graphs using Structural Motifs Jin et al, 2020. . [ ]
CReM: chemically reasonable mutations framework for structure generation Polishchuk, 2020. . [ ]
GuacaMol: Benchmarking Models for de Novo Molecular Design Brown, 2019. . [ ]
MolecularRNN: Generating realistic molecular graphs with optimized properties Popova et al, 2019.
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation You et al, 2019. . [ ]
Optimization of Molecules via Deep Reinforcement Learning Zhou et al, 2019. . [ ] [ ]
Junction Tree Variational Autoencoder for Molecular Graph Generation Jin et al, 2018. . [ ]
De Novo Design of Bioactive Small Molecules by Artificial Intelligence Merk et al, 2018.

Awesome Small Molecule Machine Learning / Papers / Hit finding and potency prediciton
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Stärk et al, 2022. . [ ]
A practical guide to large-scale docking Bender et al, 2021.
DOCKSTRING: easy molecular docking yields better benchmarks for ligand design García-Ortegón et al, 2021. . [ ] [ ]
Accelerating high-throughput virtual screening through molecular pool-based active learning Graff et al, 2021. . [ ]
Deep Docking: A Deep Learning Platform for Augmentation of Structure Based Drug Discovery Gentile et al, 2020. . [ ]
Adding Stochastic Negative Examples into Machine Learning Improves Molecular Bioactivity Prediction Cáceres et al, 2020.
Ultra-large library docking for discovering new chemotypes Lin et al, 2019.

Awesome Small Molecule Machine Learning / Papers / ADME and toxicity prediction
A Graph Neural Network Approach to Molecule Carcinogenicity Prediction Fradkin et al, 2022.
CardioTox net: a robust predictor for hERG channel blockade based on deep learning meta-feature ensembles Karim et al, 2021. . [ ]
Validating ADME QSAR Models Using Marketed Drugs Siramshetty et al, 2021.
Bayer’s in silico ADMET platform: a journey of machine learning over the past two decades Göller et al, 2020.
DeepHIT: a deep learning framework for prediction of hERG-induced cardiotoxicity Ryu et al, 2020. . [ ]
Deep Learning-Based Prediction of Drug-Induced Cardiotoxicity Cai et al, 2019. . [ ]
Support Vector Machine model for hERG inhibitory activities based on the integrated hERG database using descriptor selection by NSGA-II Ogura et al, 2019. . [ ]
In Silico Absorption, Distribution, Metabolism, Excretion, and Pharmacokinetics (ADME-PK): Utility and Best Practices Lombardo et al, 2018.

Awesome Small Molecule Machine Learning / Papers / Synthetic accessability and retrosynthetic planning
Data augmentation and pretraining for template-based retrosynthetic prediction in computer-aided synthesis planning Fortunato et al, 2020.
Reinforcement Learning for Bioretrosynthesis Koch et al, 2020.
Learning Graph Models for Retrosynthesis Prediction Somnath et al, 2020.
Retrosynthesis Prediction with Conditional Graph Logic Network Dai et al, 2019. . [ ]
SCScore: Synthetic Complexity Learned from a Reaction Corpus Coley et al, 2018. . [ ] [ ]

Awesome Small Molecule Machine Learning / Papers / DNA-encoded libraries (DELs)
Machine Learning on DNA-Encoded Library Count Data Using an Uncertainty-Aware Probabilistic Loss Function Lim et al, 2022. . [ ]
Machine Learning on DNA-Encoded Libraries: A New Paradigm for Hit Finding McCloskey et al, 2020.

Awesome Small Molecule Machine Learning / Papers / Visualization and interpretability
ChemInformatics Model Explorer (CIME): Exploratory analysis of chemical model explanations Humer et al, 2021. . [ ]
Benchmarks for interpretation of QSAR models Matveieva and Polishchuk, 2021. . [ ]
Integrating the Structure–Activity Relationship Matrix Method with Molecular Grid Maps and Activity Landscape Models for Medicinal Chemistry Applications Atsushi et al, 2019.
Finding Constellations in Chemical Space Through Core Analysis Naveja and Medina-Franco, 2019.

Awesome Small Molecule Machine Learning / Papers / MS/MS prediction
MassFormer: Tandem Mass Spectrum Prediction for Small Molecules using Graph Transformers Young et al, 2023. . [ ]
Prefix-Tree Decoding for Predicting Mass Spectra from Molecules Goldman el al, 2023. . [ ]
3DMolMS: prediction of tandem mass spectra from 3D molecular conformations Hong et al, 2023. . [ ]
CFM-ID 4.0: More Accurate ESI-MS/MS Spectral Prediction and Compound Identification Wang et al, 2021.
Rapid Prediction of Electron–Ionization Mass Spectrometry Using Neural Networks Wei et al, 2019. . [ ]

Awesome Small Molecule Machine Learning / Data sets
ADME@NCATS
AMED Cardiotoxicity Database
BindingDB
ChEMBL
DrugBank
DrugMatrix
Enamine Real database
hERG Central
MoleculeNet
MONA: DB of Mass spec + other readouts
NPASS database of natural products
PubChem
The Open Reaction Database
Therapeutic Data Commons
Zinc

Awesome Small Molecule Machine Learning / Frameworks, Libraries, and Software Tools
AutoDock Vina
BioPandas
Chemprop 1,827 11 months ago
DeepChem [ ]
Open Babel
pdb-tools
PyTorch Geometric
rd_filters 132 about 2 years ago
Small-World Search
TorchDrug

Awesome Small Molecule Machine Learning / Blogs
Hyperparameter Space
Is Life Worth Living
Practical Cheminformatics
RDKit Blog

Awesome Small Molecule Machine Learning / Twitter
Regina Barzilay
Bob the Grumpy Med Chemist
John Chodera
Connor W. Coley
Greg Landrum
pen(Taka)
Bharath Ramsundar
Marwin Segler
Patrick Walters
Awesome Cheminformatics 707 over 1 year ago
Awesome Drug Discovery 42 almost 4 years ago
Awesome Explainable Graph Reasoning 1,949 over 3 years ago
Awesome Python Chemistry 1,152 about 1 year ago
deeplearning-biology 2,026 about 1 year ago

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