[EMNLP 2021] SimCSE: Simple Contrastive Learning of Sentence Embeddings https://arxiv.org/abs/2104.08821

A lightweight platform-accelerated library for biological motif scanning using position weight matrices.

Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all

Deep functional residue identification

Official repository for the Boltz-1 biomolecular interaction model

AlphaFold 3 inference pipeline.

A trainable PyTorch reproduction of AlphaFold 3.

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Genome assembly evaluation tool

Official Implemetation of DPLM (ICML'24) - Diffusion Language Models Are Versatile Protein Learners

User friendly and accurate binder design pipeline

Deep networks for protein functional inference

A runtime for writing reliable asynchronous applications with Rust. Provides I/O, networking, scheduling, timers, ...

Chai-1, SOTA model for biomolecular structure prediction

MinHash, LSH, LSH Forest, Weighted MinHash, HyperLogLog, HyperLogLog++, LSH Ensemble and HNSW

Efficient Triton Kernels for LLM Training

PLM based active learning model for protein engineering

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

Protein Sequence Annotation with Language Models

Joint embedding of protein sequence and structure with discrete and continuous compressions of protein folding model latent spaces. https://www.biorxiv.org/content/10.1101/2024.08.06.606920v1

Rank homologous protein sequences based on a regressor trained on experimental measures

SIMD partial order alignment tool/library

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.

deep learning gene finder

Official release of the ProGen models