Official repository for the ProteinGym benchmarks

Protein (language model) Benchmarking Collection - PBC

OTRec: Deep Learning Recommender for Disease-Target Drug Repurposing Predictions on Open Targets

A benchmark suite of five genomics tasks for evaluating DNA foundation models on long-range dependencies.

cz-benchmarks is a package for standardized evaluation and comparison of machine learning models for biological applications.

Provide with pre-build flash-attention package wheels on Linux and Windows platforms using GitHub Actions

A general purpose scientific writer

A lightweight and fast auto-ml library

[BabyLM@EMNLP 2025 - Challenge Award] Official Implementation: Masked Diffusion Language Models with Frequency-Informed Training

Functional sequence annotation, metamorphism and multifunctionality research over proteins

BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model | NeurIPS '25

GENERanno: A Genomic Foundation Model for Metagenomic Annotation

GENERator: A Long-Context Generative Genomic Foundation Model

Fallout 1 to 2 engine conversion

A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. Stored as pure Python. All in a modern, AI-native editor.

Publish coverage report as PR comment, and create a coverage badge & dashboard to display on the Readme for Python projects, all inside GitHub without third party servers

The Family of Diffusion Protein Language Models (DPLM)

PDLLMs: A group of tailored DNA large language models (LLMs) for analyzing plant genomes

Tools and scripts for experimenting with Transformers: Bert, T5...

GENA-LM is a transformer masked language model trained on human DNA sequence.

A research project exploring fine-tuning BERT-style models for text generation

TxGNN: Zero-shot prediction of therapeutic use with geometric deep learning and clinician centered design

Automatically uncover Interesting (novel, plausible, and useful) features in biomedical data by combining statistical filtering, literature mining, knowledge graphs and LLMs on UK BioBank tabular f…

Open-source offline translation library written in Python