MULTI-evolve: a machine learning-guided end-to-end framework for engineering hyperactive multi-mutant proteins

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

Spacer: Towards Engineered Scientific Inspiration

Paper2Agent is a multi-agent AI system that automatically transforms research papers into interactive AI agents with minimal human input.

Codebase for Germinal, a broadly enabling generative pipeline for efficient generation of epitope-targeted de novo antibodies.

This is the official code repository for the paper NeurIPS 2024 spotlight paper "Kermut: Composite kernel regression for protein variant effects".

A template for starting reproducible Python machine-learning projects with hardware acceleration. Find an example at https://github.com/CLAIRE-Labo/no-representation-no-trust

🧬 Advanced hybrid language model for directed protein evolution. (NeurIPS 2024)

BioNeMo Framework: For building and adapting AI models in drug discovery at scale

Pretraining infrastructure for multi-hybrid AI model architectures

Genome modeling and design across all domains of life

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Protein Structure Transformer (PST): Endowing pretrained protein language models with structural knowledge

tsl: a PyTorch library for processing spatiotemporal data.

Official repository for the paper "Filling the G_ap_s: Multivariate Time Series Imputation by Graph Neural Networks" (ICLR 2022)

Official repository for the paper "Learning to Reconstruct Missing Data from Spatiotemporal Graphs with Sparse Observations" (NeurIPS 2022)

A deep learning-based tool to identify splice variants

Strelka2 germline and somatic small variant caller

A one page , two asymmetric column resume template in XeTeX that caters to an undergraduate Computer Science student

Repository for the Sequoia phylogeny reconstruction pipeline

Calculates the Variant Allele Fraction of variants in VCF files

MMseqs2: ultra fast and sensitive search and clustering suite

Repository for StripedHyena, a state-of-the-art beyond Transformer architecture

Biological foundation modeling from molecular to genome scale

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.