Repository Index

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

• drug-repurposing
• deep-learning
• drug-target-interactions
• toolkit

Official Repository for the Uni-Mol Series Methods

• molecular-modeling
• pre-trained-model
• pretraining
• deep-learning

Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models

• machine-learning
• generative-models
• drug-discovery
• benchmark

Foundation Models for Genomics & Transcriptomics

• genomics
• deep-learning
• transformer
• dna

:four_leaf_clover: Evolutionary optimization library for Go (genetic algorithm, partical swarm optimization, differential evolution)

• go
• optimization
• parallel
• machine-learning

Precision Medicine Knowledge Graph (PrimeKG)

• knowledge-graph
• precision-medicine
• therapeutics
• bioinformatics

Python package for graph neural networks in chemistry and biology

• deep-learning
• graph-neural-networks
• dgl
• cheminformatics

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)

• deep-learning
• pytorch
• deep-chemistry
• graph-neural-network

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

• kmer
• dnabert-model
• kmer-format
• gpu

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

• computational-chemistry
• computational-biology
• deep-learning
• deep-neural-networks

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

• deep-learning
• protein-sequences
• protein-structure
• semi-supervised-learning

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

• deep-learning
• chemistry
• neural-network
• biology

DiffSharp: Differentiable Functional Programming

• machine-learning
• tensor
• dotnet
• autodiff

Module for statistical learning, with a particular emphasis on time-dependent modelling

• machine-learning
• python
• point-process
• optimization

🎯 A comprehensive gradient-free optimization framework written in Python

• metaheuristics
• optimization
• optimization-algorithms
• python

Vision-Language Pathology Foundation Model - Nature Medicine

• bioimage-analysis
• bioimage-informatics
• conch
• foundation-model

A Euclidean diffusion model for structure-based drug design.

• ddpm
• drug-design
• equivariance
• generative-model

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq

Large collection of number systems providing custom arithmetic for mixed-precision algorithm development and optimization for AI, Machine Learning, Computer Vision, Signal Processing, CAE, EDA, control, optimization, estimation, and approximation.

• arithmetic
• integer-arithmetic
• fixed-point-arithmetic
• rational-arithmetic

A blazing fast matrix library for Elixir/Erlang with C implementation using CBLAS.

• matrix
• cblas
• linear-algebra
• machine-learning

Graph-linked unified embedding for single-cell multi-omics data integration

• bioinformatics
• deep-learning
• single-cell
• single-cell-multiomics

Tools for computational pathology

• machine-learning
• digital-pathology
• computational-pathology
• biomedical-image-processing

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

Reference mapping for single-cell genomics

• single-cell
• deep-learning
• rna-seq-analysis
• data-integration