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@molML Molecular Machine Learning

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    27 repositories

    • batchAL-benchmark-study-paper

      Public
      A Systematic Approach to Batch Active Learning for Material Optimization paper repository
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 25, 2026Aug 25, 2026

    • MolFaith

      Public
      MolFaith is a benchmark for evaluating the faithfulness of feature-attribution methods in molecular machine learning.
      Jupyter Notebook
      •
      MIT License
      •0•8•0•0•Updated Aug 10, 2026Aug 10, 2026

    • molforge

      Public
      A configurable pipeline for molecular data processing, curation, and conformer generation
      Python
      •
      MIT License
      •1•6•1•0•Updated Aug 6, 2026Aug 6, 2026

    • molforge-paper

      Public
      MolForge: Building Reproducible Molecular Datasets at Speed and Scale
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 24, 2026Jul 24, 2026

    • ChemLint

      Public
      A molecular machine learning MCP server that enables LLMs to handle molecular data
      Python
      •
      MIT License
      •8•29•1•0•Updated Jun 29, 2026Jun 29, 2026

    • STRIPES

      Public
      STRIPES: a physically interpretable symbolic language encoding protein–ligand interaction dynamics from MD simulations for similarity analysis and de novo molec…
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 25, 2026Jun 25, 2026

    • acer

      Public
      Towards Generalizable Protein-ligand Co-folding with ACER (Adaptive Co-folding via pocket Exploration and pose Ranking)
      0•3•0•0•Updated Jun 1, 2026Jun 1, 2026

    • JointMolecularModel

      Public
      Using a joint AE and property prediction model to estimate OOD molecules and quantify uncertainty
      Python
      •2•28•0•0•Updated Apr 25, 2026Apr 25, 2026

    • intro-to-chemical-language-modelling

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Apr 24, 2026Apr 24, 2026

    • self-driving-lab-for-coacervate-property-optimization

      Public
      Self-Driving Laboratory for Multicomponent Coacervate Property Optimization
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 19, 2026Jan 19, 2026

    • jungle-of-generative-drug-discovery

      Public
      The official codebase of the paper "The Jungle of Generative Drug Discovery: Traps, Treasures, and Ways Out""
      deep-learningchemistrycheminformatics
      deep-learningchemistrycheminformaticsevaluationdrug-discoveryde-novo-drug-design
      Python
      •
      MIT License
      •1•4•0•0•Updated Jan 19, 2026Jan 19, 2026

    • molbox

      Public
      A molecular database system built on Parquet for storing molecules with multiple conformers and properties
      Python
      •1•3•0•0•Updated Nov 28, 2025Nov 28, 2025

    • DNA-origami-stability-prediction

      Public
      Predicting DNA origami stability in physiological media using experimentally validated data and machine learning.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 1, 2025Oct 1, 2025

    • activeML-navigation-of-condensate-phases

      Public
      Automated navigation of condensate phase behavior, focusing on phase boundaries, with active machine learning.
      Python
      •
      MIT License
      •1•3•0•0•Updated Sep 29, 2025Sep 29, 2025

    • fragSMILES4reaction

      Public
      The official codebase for the reproducible experiments of the paper "Enhancing deep chemical reaction prediction with advanced chirality and fragment representa…
      deep-learningrxnchemical-language-models
      deep-learningrxnchemical-language-models
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • fantasticSMILESaugmentation

      Public
      Novel ways of augmenting SMILES for generative deep learning
      Python
      •
      MIT License
      •0•6•0•0•Updated Aug 1, 2025Aug 1, 2025

    • deep-cocrystal

      Public
      The official codebase of the paper "Deep Supramolecular Language Processing for Co-crystal Prediction"
      deep-learningchemistrycheminformatics
      deep-learningchemistrycheminformaticsdrug-discoveryconvolutional-neural-networkssmiles-strings
      PureBasic
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      Other
      •1•8•0•0•Updated Jun 21, 2025Jun 21, 2025

    • peptidy

      Public
      The official codebase of peptidy, a peptide processing tool for machine learning.
      machine-learningdeep-learningdrug-discovery
      machine-learningdeep-learningdrug-discoverypeptides
      Python
      •
      MIT License
      •2•38•0•0•Updated Apr 25, 2025Apr 25, 2025

    • 14-3-3-bindsite

      Public
      Python
      •1•0•0•0•Updated Apr 17, 2025Apr 17, 2025

    • chemical-language-processing-for-bioactivity-prediction

      Public
      The official codebase for the paper "A Hitchhiker's Guide to Deep Chemical Language Processing for Bioactivity Prediction"
      deep-learningguidedrug-discovery
      deep-learningguidedrug-discoveryselfiessmiles-stringsbioactivity-prediction
      Python
      •3•12•0•0•Updated Mar 26, 2025Mar 26, 2025

    • RUSH

      Public
      Official implementation of RuSH (Scaffold Hopping with Generative Reinforcement Learning). Includes ScaffoldFinder algorithm for 2D decoration identification, 3…
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•23•0•0•Updated Feb 20, 2025Feb 20, 2025

    • MoleculeACE

      Public
      A tool for evaluating the predictive performance on activity cliff compounds of machine learning models
      Python
      •
      MIT License
      •27•219•3•0•Updated Feb 15, 2025Feb 15, 2025

    • traversing_chem_space

      Public
      Small molecules discovery with different active deep learning strategies. Codebase for the paper: "Traversing chemical space with active deep learning for low-d…
      Python
      •
      MIT License
      •7•28•0•0•Updated Aug 18, 2024Aug 18, 2024

    • s4-for-de-novo-drug-design

      Public
      The official codebase of the paper "Chemical language modeling with structured state space sequence models"
      deep-learningchemistrycheminformatics
      deep-learningchemistrycheminformaticss4state-space-modelssmiles-stringsde-novo-drug-designchemical-language-models
      HTML
      •
      MIT License
      •9•90•0•1•Updated Aug 1, 2024Aug 1, 2024

    • Nano_Particles_Active_Learning

      Public
      Formulating Nanoparticles with Bayesian active learning. Codebase for the paper "Machine learning-guided high throughput nanoparticle design" (Digital Discovery…
      Python
      •
      MIT License
      •2•7•0•0•Updated May 29, 2024May 29, 2024

    • de-novo-design-with-lstm

      Public
      Python
      •0•1•0•0•Updated Jan 31, 2024Jan 31, 2024

    • BME_data_analysis

      Public
      CSS
      •
      MIT License
      •0•0•0•0•Updated Jun 2, 2023Jun 2, 2023
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