Code for the ProteinMPNN paper
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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
Wrapper for RDKit's RunReactants to improve stereochemistry handling
scPerturb: A resource and a python/R tool for single-cell perturbation data
- cite-seq
- database
- perturbation
- scatac-seq
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
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
Integrated pipeline for multiplexed image analysis
- multiplexed-imaging
- python
PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
- epigenomics
- pattern-search
- data-visualization
- interactive-machine-learning
Research experiments exploring uncommon quant techniques.
- analysis
- jupyter-notebook
- python
- quant
Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
- foundation-models
- gpt
- single-cell
High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations