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annotated_deep_learning_paper_implementations

🧑‍🏫 60 Implementations/tutorials of deep learning papers with side-by-side notes 📝; including transformers (original, xl, switch, feedback, vit, ...), optimizers (adam, adabelief, sophia, ...), gans(cyclegan, stylegan2, ...), 🎮 reinforcement learning (ppo, dqn), capsnet, distillation, ... 🧠

antibody-ml-resources

This repository collates tools and publications that use Machine-learning with antibody sequences and structures.

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

biopython

Official git repository for Biopython (converted from CVS)

clean

CLEAN: a contrastive learning model for high-quality functional prediction of proteins

cpython

The Python programming language

crewai

Framework for orchestrating role-playing, autonomous AI agents. By fostering collaborative intelligence, CrewAI empowers agents to work together seamlessly, tackling complex tasks.

deepfri

Deep functional residue identification

deeppurpose

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

deeprank-gnn

Graph Network for protein-protein interface

deepzf

epitope-prediction

esm

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

esm-gearnet

ESM-GearNet for Protein Structure Representation Learning (https://arxiv.org/abs/2303.06275)

esm3

eve

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

grelu

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

knowledgebase

recipes that save time

langchain-experiments

Building Apps with LLMs

llm-applications

A comprehensive guide to building RAG-based LLM applications for production.

localpdb

Python package to manage protein structures and their annotations

proteinnpt

Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"

protkit

A Unified Approach to Protein Engineering

protlearn

A Python package for extracting protein sequence features

pt-lm-gnn

pydicom

Read, modify and write DICOM files with python code

pymolfold

Protein folding in Pymol

pyrosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

pytorch_experiments