Mudman14

CRPBsites

Code for my paper on"Prediction of RBP binding sites on circRNAs using a LSTM-based deep sequence learning architecture"

getcontacts

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

RNAonGraph

A repository for neural representational learning of RNA secondary structures

pygcn

Graph Convolutional Networks in PyTorch

GAT

Graph Attention Networks (https://arxiv.org/abs/1710.10903)

SLSTM

Reproduce ACL 2018 paper "Sentence-State LSTM for Text Representation" in Pytorch

DeepCIP

A deep learning method for the prediction of internal ribosome entry sites (IRES) of circRNAs

dgl

Python package built to ease deep learning on graph, on top of existing DL frameworks.

UTR-LM

ML2022-Spring

**Official** 李宏毅 (Hung-yi Lee) 機器學習 Machine Learning 2022 Spring

UFold

labs

Rmd source files for the HarvardX series PH525x

Smart5UTR

MTAE-based 5UTR design model

flash-attention

Fast and memory-efficient exact attention

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

Deeprank-GNN

Graph Network for protein-protein interface

RoseTTAFold-All-Atom

rf_diffusion_all_atom

Public RFDiffusionAA repo

PCMol

Multi-target de novo molecular generator conditioned on AlphaFold's latent protein embeddings.

GPro

hyena-dna

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

mamba

Mamba SSM architecture

Spike-Driven-Transformer-V2

Offical implementation of "Spike-driven Transformer V2: Meta Spiking Neural Network Architecture Inspiring the Design of Next-generation Neuromorphic Chips" (ICLR2024)

bonito

A PyTorch Basecaller for Oxford Nanopore Reads

cs229-2018-autumn

All notes and materials for the CS229: Machine Learning course by Stanford University

UCB

Original PyTorch implementation of Uncertainty-guided Continual Learning with Bayesian Neural Networks, ICLR 2020

LanczosNetwork

Lanczos Network, Graph Neural Networks, Deep Graph Convolutional Networks, Deep Learning on Graph Structured Data, QM8 Quantum Chemistry Benchmark, ICLR 2019

GPTs

leaked prompts of GPTs

arc

Adaptive and Reliable Classification: efficient conformity scores for multi-class classification problems