xypan1232

alibi

Algorithms for explaining machine learning models

Graphormer

Graphormer is a general-purpose deep learning backbone for molecular modeling.

RoseTTAFold

This package contains deep learning models and related scripts for RoseTTAFold

awesome-explainable-graph-reasoning

A collection of research papers and software related to explainability in graph machine learning.

alphafold2

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

solo-learn

solo-learn: a library of self-supervised methods for visual representation learning powered by Pytorch Lightning

Awesome-explainable-AI

A collection of research materials on explainable AI/ML

papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

chainerrl

ChainerRL is a deep reinforcement learning library built on top of Chainer.

SMAC3

SMAC3: A Versatile Bayesian Optimization Package for Hyperparameter Optimization

pykg2vec

Python library for knowledge graph embedding and representation learning.

ColabDesign

Making Protein Design accessible to all via Google Colab!

bio_embeddings

Get protein embeddings from protein sequences

explainx

Explainable AI framework for data scientists. Explain & debug any blackbox machine learning model with a single line of code. We are looking for co-authors to take this project forward. Reach out @ ms8909@nyu.edu

LiGAN

Deep generative models of 3D grids for structure-based drug discovery

visual-attribution

Pytorch Implementation of recent visual attribution methods for model interpretability

BioPhi

BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.

AbNumber

Convenience Python APIs for antibody numbering using ANARCI

bento-tools

A Python toolkit for subcellular analysis of spatial transcriptomics data

antiberta

Public repository describing training and testing of AntiBERTa.

MetaNN

MetaModule provides extensions of PyTorch Module for meta learning

antibody-2019

DeepSynergy

fingeRNAt

Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.

CustOmics

A deep-learning framework for multi-omics integration

STIM

Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.

scikit-multimodallearn

This Python package implements algorithms for multiviews (multimodals) learning

DGAPN

This repository implements Distilled Graph Attention Policy Network (DGAPN), a curiosity-driven reinforcement learning model to generate novel graph-structured chemical representations.

dl-rna

FactorizableLibrary

Code and data for factorizable libraries