Repository Index

Official repository for the Boltz biomolecular interaction models

• binding-prediction
• drug-discovery
• protein-structure

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

• pytorch
• protein-structure
• alphafold2

Chai-1, SOTA model for biomolecular structure prediction

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

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

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

• workflow-execution
• workflow
• cloud
• hpc

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

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

R package for detecting doublets in single-cell RNA sequencing data

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

• bioinformatics
• taxonomy
• cross-platform
• lineage

Sequential regulatory activity predictions with deep convolutional neural networks.

Reference mapping for single-cell genomics

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

Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star

• dna
• language-model
• variant-effect-prediction
• genomics

RNA-seq prediction with deep convolutional neural networks.

Bi-Directional Equivariant Long-Range DNA Sequence Modeling

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

• cancer-genomics
• cnv-detection
• single-cell
• phylogeny

A Network Integration Approach for Drug-Target Interaction Prediction

OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.

🏃 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

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

Interpretable bilinear attention network with domain adaptation improves drug-target prediction.

Accurate and efficient spot detection for microscopy data

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

Learning cell communication from spatial graphs of cells

• tensorflow
• gnn
• glm
• cvae