PaccMann

All

23 repositories

paccmann_datasets
Public
pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/
bioinformatics pytorch rdkit chemoinformatics smiles python deep-learning
Python
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MIT License
•7•27•0•0•Updated Oct 6, 2024Oct 6, 2024
chemical_representation_learning_for_toxicity_prediction
Public
Chemical representation learning paper in Digital Discovery
deep-learning chemoinformatics qsar property-prediction toxicity-prediction pytorch
Jupyter Notebook
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MIT License
•15•56•0•0•Updated May 22, 2024May 22, 2024
paccmann_generator
Public
Generative models for transcriptomic-driven or protein-driven molecular design (PaccMann^RL).
deep-reinforcement-learning generative-model vae drug-discovery molecule-generation
Python
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MIT License
•7•9•0•0•Updated May 22, 2024May 22, 2024
transcriptomic_signature_sampling
Public
Python
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MIT License
•0•2•0•0•Updated May 22, 2024May 22, 2024
paccmann_predictor
Public
PyTorch implementation of bimodal neural networks for drug-cell (pharmarcogenomics) and drug-protein (proteochemometrics) interaction prediction
pharmacogenomics drug-interaction drug-sensitivity proteochemometrics deep-learning pytorch
Python
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MIT License
•18•46•0•0•Updated May 21, 2024May 21, 2024
paccmann.github.io
Public
PaccMann website
HTML
•0•0•0•0•Updated May 17, 2024May 17, 2024
fdsa
Public
A fully differentiable set autoencoder
deep-learning multimodal-data set-autoencoder
Python
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MIT License
•3•17•0•1•Updated Apr 3, 2024Apr 3, 2024
paccmann_gp
Public
PyTorch/skopt based implementation of Bayesian optimization with Gaussian processes - build to optimize latent spaces of VAEs to generate molecules with desired properties
machine-learning generative-model chemoinformatics gaussian-processes bayesian-optimization
Python
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MIT License
•5•11•0•0•Updated Mar 23, 2024Mar 23, 2024
TITAN
Public
Code for "T Cell Receptor Specificity Prediction with Bimodal Attention Networks" (https://doi.org/10.1093/bioinformatics/btab294, ISMB 2021)
immunology tcr-epitope compound-protein-interaction protein-ligand deep-learning
Jupyter Notebook
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MIT License
•6•29•1•0•Updated Aug 4, 2023Aug 4, 2023
paccmann_chemistry
Public
Generative models of chemical data for PaccMann^RL
generative-model vae drug-discovery molecule-generation deep-learning
Python
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MIT License
•8•14•0•0•Updated Jun 2, 2023Jun 2, 2023
paccmann_kinase_binding_residues
Public
Comparison of active site and full kinase sequences for drug-target affinity prediction and molecular generation. Full paper: https://pubs.acs.org/doi/10.1021/acs.jcim.1c00889
knn protein-ligand-interactions kinases active-sites proteochemometrics machine-learning
Python
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MIT License
•6•35•0•0•Updated Oct 3, 2022Oct 3, 2022
guacamol_baselines
Public archive
Baselines models for GuacaMol benchmarks
Python
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MIT License
•33•0•0•0•Updated Feb 11, 2022Feb 11, 2022
moses
Public archive
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models
Python
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MIT License
•243•0•0•0•Updated Feb 10, 2022Feb 10, 2022
paccmann_rl
Public
Code pipeline for the PaccMann^RL in iScience: https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6
deep-learning drug-discovery transcriptomics generative-models drug-sensitivity de-novo-drug-design
MIT License
•9•31•1•0•Updated Feb 10, 2022Feb 10, 2022
tape
Public
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
Python
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BSD 3-Clause "New" or "Revised" License
•129•0•0•0•Updated Feb 9, 2022Feb 9, 2022
guacamol
Public archive
Benchmarks for generative chemistry
Python
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MIT License
•84•1•0•0•Updated Jan 28, 2022Jan 28, 2022
paccmann_proteomics
Public
PaccMann models for protein language modeling
pytorch transformer protein-language-model
Python
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MIT License
•8•40•1•0•Updated Nov 10, 2021Nov 10, 2021
paccmann_sarscov2
Public
Code for paper on automation of discovery and synthesis of targeted molecules: https://iopscience.iop.org/article/10.1088/2632-2153/abe808
deep-learning drug-discovery sars-cov-2 de-novo-drug-design proteochemometrics computer-aided-synthesis-planning accelerated-discovery
MIT License
•6•19•0•0•Updated Sep 18, 2021Sep 18, 2021
paccmann_omics
Public
Generative models for transcriptomics profiles and proteins
generative-model vae proteomics transcriptomics variational-autoencoder deep-learning
Python
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MIT License
•3•8•0•0•Updated Sep 17, 2021Sep 17, 2021
paccmann_polymer
Public
Graph-regularized VAE and the impact of topology on learned representations
deep-learning vae manifold-learning gnn graph-regularized-vae pytorch
Python
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MIT License
•1•2•0•0•Updated Sep 17, 2021Sep 17, 2021
paccmann_predictor_tf
Public
Tensorflow implementation of PaccMann (drug sensitivity prediction)
deep-learning cancer tensorflow drug-response-prediction drug-sensitivity
Python
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MIT License
•22•3•0•0•Updated Sep 17, 2021Sep 17, 2021
reinvent_models
Public
PaccMann fork of Reinvent Models
Python
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MIT License
•1•2•0•0•Updated Sep 6, 2021Sep 6, 2021
docs
Public
Documentation for PaccMann service
Ruby
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MIT License
•1•0•0•0•Updated Apr 3, 2020Apr 3, 2020