Stars
Auton Survival - an open source package for Regression, Counterfactual Estimation, Evaluation and Phenotyping with Censored Time-to-Events
Pytorch implementation for t-SNE with cuda to accelerate
DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models
Deep functional residue identification
The resources of LucaOne, including: the model code, training scripts, embedding inference code, and trained checkpoints.
The aim of this project is to perform a face swap on a youtube video almost automatically.
[ICLR 2024] EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations
Generative Models for Graph-Based Protein Design
Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding
Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)
Extension for 3D Slicer that allows the application to be used from Jupyter notebook
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network
A partially latent flow matching model for the joint generation of a protein’s amino acid sequence and full atomistic structure, including both the backbone and side chain.
RNA-seq prediction with deep convolutional neural networks.
A Protein Large Language Model for Multi-Task Protein Language Processing
Nature Methods: RhoFold+, Accurate RNA 3D structure prediction using a language model-based deep learning approach
Bench-marking classification tools for scRNA-seq data
Regression Transformer (2023; Nature Machine Intelligence)
Neural Networks for Protein Sequence Alignment
Starter pack for NeurIPS LLM Efficiency Challenge 2023.
Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
[ISMB 2025] DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models
ESM-GearNet for Protein Structure Representation Learning (https://arxiv.org/abs/2303.06275)