Jie Huang's repositories
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, ... 🧠
awesome-deep-learning-4-life-sciences
A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).
BMBL-analysis-notebooks
A collection of bioinformatics data analysis notebooks focused on providing examples of current best practices in single-cell analysis.
cellrank
CellRank: dynamics from multi-view single-cell data. See the docs:
cellxgenedp
R interface to the cellxgene data portal
cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
ChuanhuChatGPT
GUI for ChatGPT API and many LLMs
d2l-zh
《动手学深度学习》：面向中文读者、能运行、可讨论。中英文版被70多个国家的500多所大学用于教学。
deepmind-research
This repository contains implementations and illustrative code to accompany DeepMind publications
dify
Dify is an open-source LLM app development platform. It has the core tech required to build AI-native apps, including RAG, agent capabilities, model management, observability and more, packaged into one intuitive interface.
DNABERT_S
DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models
EasyPubMed
EasyPubMed is an extension to make new PubMed easy to use
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
flash-attention
Fast and memory-efficient exact attention
OrthoSLC
OrthoSLC: A pipeline to get Orthologous Genes using Reciprocal Best Blast Hit (RBBH) Single Linkage Clustering, indenpendent of relational database management system
ProtTrans
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
Qwen-Audio
The official repo of Qwen-Audio (通义千问-Audio) chat & pretrained large audio language model proposed by Alibaba Cloud.
ReLSO-Guided-Generative-Protein-Design-using-Regularized-Transformers
a Transformer-based neural network for generating highly optimized protein sequences called Regularized Latent Space Optimization (RELSO)
Scientific-LLM-Survey
Scientific Large Language Models: A Survey on Biological & Chemical Domains
SingleCellNotes
Links to interesting courses, tutorials, papers, software etc. related to single-cell omics data analysis
taxonkit
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
Ternary
Create ternary plots in R
timm
PyTorch image models, scripts, pretrained weights -- ResNet, ResNeXT, EfficientNet, EfficientNetV2, NFNet, Vision Transformer, MixNet, MobileNet-V3/V2, RegNet, DPN, CSPNet, and more
TVBox_live
TVbox直播接口，互联网直播源检索，验证提取高速直播源
Tvlist-awesome-m3u-m3u8
直播源相关资源汇总 📺 💯 IPTV、M3U —— 勤洗手、戴口罩，祝愿所有人百毒不侵
Uni-Fold
An open-source platform for developing protein models beyond AlphaFold.
Uni-Mol
Official Repository for the Uni-Mol Series Methods