ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
Repository Index
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TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
- drug-repurposing
- deep-learning
- drug-target-interactions
- toolkit
Precision Medicine Knowledge Graph (PrimeKG)
- knowledge-graph
- precision-medicine
- therapeutics
- bioinformatics
Pathology Foundation Model - Nature Medicine
- foundation
- foundation-model
- histopathology
- mahmoodlab
Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star
- dna
- language-model
- variant-effect-prediction
- genomics
Deep Reinforcement Learning for de-novo Drug Design
- deeplearning
- reinforcement-learning
- cheminformatics
- molecular-modeling
MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)
A python Two Source Energy Balance model for estimation of evapotranspiration with remote sensing data
- source-energy-balance
- canopy
- soil
- radiometric-temperatures
🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
- disentanglement
- drug-discovery
- genomics
- perturbation
Optimising chemical reactions using machine learning
- chemistry
- machine-learning
- optimization
- bayesian-optimization
A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design
- protein
- protein-sequences
- protein-design
- representation-learning
PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.
Research experiments exploring uncommon quant techniques.
- analysis
- jupyter-notebook
- python
- quant
Classification and Gradient-based Localization of Chest Radiographs using PyTorch.
- fine-tuning
- vgg16
- resnet18
- densenet121
High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
UV-first benchmark for protein-ligand docking with reproducible annotation, pocket similarity, and HPC workflows.
- benchmark
- bioinformatics
- cheminformatics
- computational-chemistry
:game_die: Neutrino research
- physics
- neutrino
- neutrino-oscillations
Interpretable drug response prediction with graph neural networks over drugs, cell lines, and genes.