Qi Liu

gitfs. Version controlled file system

alisthelper. Alist Helper is an application developed using Flutter, designed to simplify the use of the desktop version of alist. It can manage alist, allowing you to easily start and stop the alist program.

tweepy. Twitter for Python!

SciencePlots. Matplotlib styles for scientific plotting

Wooey. A Django app that creates automatic web UIs for Python scripts.

nicegui. Create web-based user interfaces with Python. The nice way.

text2video. 半个神器👉一键文本转视频的工具

autocut. 用文本编辑器剪视频

GPTCelltype. HTML

LLMBook-zh.github.io. 《大语言模型》作者：赵鑫，李军毅，周昆，唐天一，文继荣

simple-evals. Python

pytorch-llama. LLaMA 2 implemented from scratch in PyTorch

safe-rlhf. Safe RLHF: Constrained Value Alignment via Safe Reinforcement Learning from Human Feedback

DeepSpeed. DeepSpeed is a deep learning optimization library that makes distributed training and inference easy, efficient, and effective.

aligner. [NeurIPS 2024 Oral] Aligner: Efficient Alignment by Learning to Correct

peft. 🤗 PEFT: State-of-the-art Parameter-Efficient Fine-Tuning.

direct-preference-optimization. Reference implementation for DPO (Direct Preference Optimization)

LaTeX-OCR. pix2tex: Using a ViT to convert images of equations into LaTeX code.

awesome-diffusion-model-in-rl. A curated list of Diffusion Model in RL resources (continually updated)

ImageReward. [NeurIPS 2023] ImageReward: Learning and Evaluating Human Preferences for Text-to-image Generation

google-research. Google Research

Diff4RLSurvey. This repository contains a collection of resources and papers on Diffusion Models for RL, accompanying the paper "Diffusion Models for Reinforcement Learning: A Survey"

open_clip. An open source implementation of CLIP.

CLIP. CLIP (Contrastive Language-Image Pretraining), Predict the most relevant text snippet given an image

BabyStories-UTSA. Python

Deep-Reinforcement-Learning-Algorithms-with-PyTorch. PyTorch implementations of deep reinforcement learning algorithms and environments

ddpo-pytorch. Reproduction of DDPO paper (RLHF for diffusion)

DRLX. Diffusion Reinforcement Learning Library

LLMs-from-scratch. Implement a ChatGPT-like LLM in PyTorch from scratch, step by step

evaluate. 🤗 Evaluate: A library for easily evaluating machine learning models and datasets.

ddpo. Code for the paper "Training Diffusion Models with Reinforcement Learning"

RL_Tutorial. Reinforcement Learning Tutorial (强化学习教程)

openrl. Unified Reinforcement Learning Framework

ml-agents. The Unity Machine Learning Agents Toolkit (ML-Agents) is an open-source project that enables games and simulations to serve as environments for training intelligent agents using deep reinforcement learning and imitation learning.

colabcode. Run VSCode (codeserver) on Google Colab or Kaggle Notebooks

Gymnasium. A standard API for single-agent reinforcement learning environments, with popular reference environments and related utilities (formerly Gym)

TextRL. Implementation of ChatGPT RLHF (Reinforcement Learning with Human Feedback) on any generation model in huggingface's transformer (blommz-176B/bloom/gpt/bart/T5/MetaICL)

PaLM-rlhf-pytorch. Implementation of RLHF (Reinforcement Learning with Human Feedback) on top of the PaLM architecture. Basically ChatGPT but with PaLM

trlx. A repo for distributed training of language models with Reinforcement Learning via Human Feedback (RLHF)

RL4LMs. A modular RL library to fine-tune language models to human preferences

LLMsPracticalGuide. A curated list of practical guide resources of LLMs (LLMs Tree, Examples, Papers)

trl. Train transformer language models with reinforcement learning.

PanglaoDB. metadata and data from the database

scib. Benchmarking analysis of data integration tools

scimilarity. A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.

scEval. Codes for paper: Evaluating the Utilities of Large Language Models in Single-cell Data Analysis.

pertpy. Single-cell perturbation analysis

cellot. Learning Single-Cell Perturbation Responses using Neural Optimal Transport

CPA. The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

scBERT. Python

CellPLM. Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.

LandMark. Python

InternLM. Official release of InternLM series (InternLM, InternLM2, InternLM2.5, InternLM3).

openai-python. The official Python library for the OpenAI API

solara-examples. Some simple apps in solara

reacton. A pure Python port of React for ipywidgets

wanderlust. Wanderlust OpenAI example using Solara

chatgpt-ui. A ChatGPT web client that supports multiple users, multiple languages, and multiple database connections for persistent data storage. Provides Docker images and quick deployment scripts.

awesome_LLMs_interview_notes. LLMs interview notes and answers:该仓库主要记录大模型（LLMs）算法工程师相关的面试题和参考答案

evals. Evals is a framework for evaluating LLMs and LLM systems, and an open-source registry of benchmarks.

singlecell_gpt. Python

neurips-2023-scripts. Scripts associated with the 2023 Open Problems competition

single-cell-models. Model zoo and study notes for single cell data analysis.

flash-attention. Fast and memory-efficient exact attention

accelerate. 🚀 A simple way to launch, train, and use PyTorch models on almost any device and distributed configuration, automatic mixed precision (including fp8), and easy-to-configure FSDP and DeepSpeed support

scFoundation. Jupyter Notebook

datasets. 🤗 The largest hub of ready-to-use datasets for AI models with fast, easy-to-use and efficient data manipulation tools

scFormer. Python

IFP-RNN. A molecule generative model used interaction fingerprint (docking pose) as constraints.

SWIT. Python

cellxgene-census. CZ CELLxGENE Discover Census

gdown. Google Drive public file downloader when curl/wget fails.

scVI-data. datasets for scVI

anndata. Annotated data.

scvi-tools. Deep probabilistic analysis of single-cell and spatial omics data

plotly.py. The interactive graphing library for Python :sparkles:

nbviewer. nbconvert as a web service: Render Jupyter Notebooks as static web pages

scGPT. Jupyter Notebook

MolGAN-pytorch. Pytroch implementation of MolGAN: An implicit generative model for small molecular graphs (https://arxiv.org/abs/1805.11973)

improved_wgan_training. Code for reproducing experiments in "Improved Training of Wasserstein GANs"

AlphaDrug. AlphaDrug: Protein Target Specific De Novo Molecular Generation

matplotlib-venn. Area-weighted venn-diagrams for Python/matplotlib

rcsbsearch. Python interface for the RCSB search API.

GEARS. GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

ConPLex. Adapting protein language models and contrastive learning for highly-accurate drug-target interaction prediction.

pymol-open-source. Open-source foundation of the user-sponsored PyMOL molecular visualization system.

MGCVAE. Code for "MGCVAE: Multi-Objective Inverse Design via Molecular Graph Conditional Variational Autoencoder" (https://doi.org/10.1021/acs.jcim.2c00487)

onnx. Open standard for machine learning interoperability

graph-generation. GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models

GraphINVENT. Graph neural networks for molecular design.

netron. Visualizer for neural network, deep learning and machine learning models

molecular-vae. Pytorch implementation of the paper "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules"

self-instruct. Aligning pretrained language models with instruction data generated by themselves.

constrained-graph-variational-autoencoder. Sample code for Constrained Graph Variational Autoencoders

molecule-generation. Implementation of MoLeR: a generative model of molecular graphs which supports scaffold-constrained generation

MolVAE. Molecule Generation and Translation Framework. This is a joint PyTorch implementation of three papers in VAE-based molecule generation and translation including JTVAE, V-JTNN-GAN, HierVAE and HierVGNN

Reinvent. Python

chemprop. Message Passing Neural Networks for Molecule Property Prediction

pytorch_structure2vec. pytorch implementation of structure2vec (https://arxiv.org/abs/1603.05629)

graphnn. Training computational graph on top of structured data (string, graph, etc)

grobid. A machine learning software for extracting information from scholarly documents

moflow. MoFlow: an invertible flow model for generating molecular graphs

MolGAN. Tensorflow implementation of MolGAN: An implicit generative model for small molecular graphs

ConfVAE-ICML21. An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming (ICML'21)

target-id-by-WGCNA. Target Identification Using the WGCNA Method

R-Tutor. R语言学习资料

Zutilo. Zotero plugin providing some additional editing features

vae_tutorial. Caffe code to accompany my Tutorial on Variational Autoencoders

neurips2021_multimodal_topmethods. Python

egnn. Python

3D-Generative-SBDD. 💊 A 3D Generative Model for Structure-Based Drug Design (NeurIPS 2021)

planetoid. Semi-supervised learning with graph embeddings

graphsage-simple. Simple reference implementation of GraphSAGE.

GraphSAGE. Representation learning on large graphs using stochastic graph convolutions.

ccf-deadlines. ⏰ Agenticly track worldwide conference deadlines (Website, Python Cli, Wechat Applet)

protein-ligand-benchmark. Protein-Ligand Benchmark Dataset for Free Energy Calculations

ProLIF. Interaction Fingerprints for protein-ligand complexes and more

p2rank. P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

plip. Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361

practical_cheminformatics_tutorials. Practical Cheminformatics Tutorials

nglview. Jupyter widget to interactively view molecular structures and trajectories

dataset. Code to help download and extract the dockstring dataset.

benchmarks. Official repository for dockstring-based benchmarks.

dockstring. A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discovery.

AutoDock-Vina. AutoDock Vina

Protein-Ligand-Interaction-Graphs. Jupyter Notebook

oddt. Open Drug Discovery Toolkit

onionnet. A multiple-layer inter-molecular contact features based deep neural network for protein-ligand binding affinity prediction

pypdb. A Python API for the RCSB Protein Data Bank (PDB)

mustard. mustard - Machine learning Using Svms To Analyse Rdf Data

Source-Code-Notebook. 关于一些经典论文源码的逐行中文笔记

gae. Implementation of Graph Auto-Encoders in TensorFlow

biopython. Official git repository for Biopython (originally converted from CVS)

PyTorchStepByStep. Official repository of my book: "Deep Learning with PyTorch Step-by-Step: A Beginner's Guide"

PyMySQL. MySQL client library for Python

psycopg2. PostgreSQL database adapter for the Python programming language

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

teachopencadd. TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

examples. A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.

PyTorch-VAE. A Collection of Variational Autoencoders (VAE) in PyTorch.

pytorch-template. My PyTorch project template (for Kaggle and research)

the-incredible-pytorch. The Incredible PyTorch: a curated list of tutorials, papers, projects, communities and more relating to PyTorch.

zotero-night. Night theme for Zotero UI and PDF

mml-book.github.io. Companion webpage to the book "Mathematics For Machine Learning"

fcd_torch. Fréchet ChemNet Distance on PyTorch

moses. Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models

zotero-pdf-preview. Preview Zotero attachments in the library view.

zotero-better-notes. Everything about note management. All in Zotero.

zotero-citationcounts. Zotero plugin for auto-fetching citation counts from various sources

pytorch-lightning. Pretrain, finetune ANY AI model of ANY size on 1 or 10,000+ GPUs with zero code changes.

pytorch-sentiment-analysis. Tutorials on getting started with PyTorch and TorchText for sentiment analysis.

AutoDock-GPU. AutoDock for GPUs and other accelerators

tablexplore. Table analysis and plotting application written in PySide2/PyQt5

PyQt5-Apps. :paperclip:Some useful apps based on PyQt5. | 谷歌翻译、bilibili视频下载、华科电费查询、猫耳FM音频下载、无损音乐下载、华科图书馆查询、词云生成器etc.

pyqt5pandas. PyQt5 Meets Pandas

selfies. Robust representation of semantically constrained graphs, in particular for molecules in chemistry

mamba. The Fast Cross-Platform Package Manager

marp-themes. Custom themes for Marp Next

fairseq. Facebook AI Research Sequence-to-Sequence Toolkit written in Python.

Graphormer. Graphormer is a general-purpose deep learning backbone for molecular modeling.

rust. Empowering everyone to build reliable and efficient software.

book. The Rust Programming Language

analysis-ik. 🚌 The IK Analysis plugin integrates Lucene IK analyzer into Elasticsearch and OpenSearch, support customized dictionary.

jieba. 结巴中文分词

snorkel. A system for quickly generating training data with weak supervision

vscode-sftp. Super fast sftp/ftp extension for VS Code

cmder. Lovely console emulator package for Windows

fastapi. FastAPI framework, high performance, easy to learn, fast to code, ready for production

openbabel. Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

redoc. 📘 OpenAPI/Swagger-generated API Reference Documentation

rdkit. The official sources for the RDKit library

tmap. A very fast visualization library for large, high-dimensional data sets.

LIMO. generative model for drug discovery

mdBook. Create book from markdown files. Like Gitbook but implemented in Rust

transformers. 🤗 Transformers: the model-definition framework for state-of-the-art machine learning models in text, vision, audio, and multimodal models, for both inference and training.

cryodrgn_empiar. Shell

bolei_awesome_posters. CVPR and NeurIPS poster examples and templates

ete. Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

scikit-bio. scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

mpnn. Open source implementation of "Neural Message Passing for Quantum Chemistry"

graph_datasets. Data for "Understanding Isomorphism Bias in Graph Data Sets" paper.

irida-galaxy-deploy. :whale: Deploying IRIDA and Galaxy all in one server/VM using Docker or Terraform

ChemTreeMap. An Interactive Map of Biochemical Similarity in Molecular Datasets. The document: http://chemtreemap.readthedocs.org/en/latest/ . The project website:

pyGPGO. Bayesian optimization for Python

ogb. Benchmark datasets, data loaders, and evaluators for graph machine learning

machine-learning-notes. My continuously updated Machine Learning, Probabilistic Models and Deep Learning notes and demos (2000+ slides) 我不间断更新的机器学习，概率模型和深度学习的讲义(2000+页)和视频链接

bayesian-belief-networks. Pythonic Bayesian Belief Network Package, supporting creation of and exact inference on Bayesian Belief Networks specified as pure python functions.

pyem. Python programs for electron microscopy

opencv-python. Automated CI toolchain to produce precompiled opencv-python, opencv-python-headless, opencv-contrib-python and opencv-contrib-python-headless packages.

PaddleHelix. Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

lime. Lime: Explaining the predictions of any machine learning classifier

examples. Example deep learning projects that use wandb's features.

deepchem. Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

Cryo-RAlib. Jupyter Notebook

relion. Image-processing software for cryo-electron microscopy

skorch. A scikit-learn compatible neural network library that wraps PyTorch

AutoViz. Automatically Visualize any dataset, any size with a single line of code. Created by Ram Seshadri. Collaborators Welcome. Permission Granted upon Request.

PytorchGeometricTutorial. Pytorch Geometric Tutorials

cryodrgn. Neural networks for cryo-EM reconstruction

gnn-model-explainer. gnn explainer