SAIL

SAIL-Lab统一代码库

Motivation

创建这个项目的动机最早来源于实验室组内成员相互Debug代码的时候遇到的麻烦。由于整个小组内所做的课题非常类似，而借鉴的代码都是来自不同的人写的，尽管大部分的时候都使用Pytorch，但是每个人写的特征计算流程、数据预处理流程、模型训练流程、模型推理流程、性能评估流程千差万别，这非常不利于组内的科研交流，因此萌生了写一套完整的、统一的代码库，同时也便于实验室后续的同学继续研究相关课题。

除此之外，还有下列的一些原因帮助推动该代码库持续不断的完善和更新。

实验室内部对于特征计算以及模型性能评估的理解有所差异甚至出现错误，并且延续了多个年级的研究生。
当希望尝试加入新的计算特征时发现要对原始代码进行大规模的改动。
组内所研究的药物分子、晶体分子以及蛋白质分子属于规模复杂程度不同的图，但是很多对于药物分子有效的工程技巧未必适用于另外两者。
无法避免的batch size=1的问题。

该项目作为我的硕士毕业论文的展望与延伸部分，会持续进行更新，并且在实验室允许的范围内进行开源。

TODO

下面展示的模型代码复现主要方向为SAIL-Lab药物分子、晶体分子以及蛋白质分子相关研究的模型。

CMPNN

根据Moleculenet中收集的数据集，增加Quantum Mechanics系列和Biophysics系列中提到的数据集结果。
根据OGB中收集的数据集，增加结果。

CoMPT

代码进度0%

CrystalNet

检查重现代码的性能与原始实现性能相差较大的问题。
检查由于GRU带来的晶胞图与超晶胞图性能不一致问题。

DeepANIS

代码进度0%

GraphPPIS

增加性能结果日志。

GraphSite

代码进度60%

GraphSol

增加S.cerevisiae数据集的结果。
增加DeepSol数据集的结果。

SPROF

代码进度95%
加速Paper中超大模型的运行时间，减少消耗的显存。

Thank you

如果你觉得本项目对你的科研进展有所帮助的话，请给本项目一个star，谢谢！

Hi,

Thanks for open sourcing your wonderful work, "Learning Attributed Graph Representations with Communicative Message Passing Transformer." I found a potential bug in your in_scores cross-attention computation. It seems problematic when the edge feature matrix is not symmetric.

Please see my reproduction at: https://colab.research.google.com/drive/1LLMc9Ue47MoHrTDqJgM-rMMLUacgXM_R?usp=sharing

And by einsum definition, the Eq. (8) and your code seem inconsistent. I could understand the Eq. (8), where the broadcast of node/token embedding for M_i is along the column axis. But your code implementation is not the same as such. https://github.com/jcchan23/SAIL/blob/878c59e9f1b4e6df3e2424c8213c1df25459e950/Repeat/CoMPT/model_node.py#L181-L182

Any help is appreciated.

Many thank, Qi

Code reimplementation of some papers published in SAIL-Lab

Related tags

Overview

SAIL

Motivation

TODO

CMPNN

CoMPT

CrystalNet

DeepANIS

GraphPPIS

GraphSite

GraphSol

SPROF

Thank you

You might also like...

New armachat based on Raspberry Pi PICO an Circuitpython code

Code for the onshape macropad.

♟️ QR Code display for P4wnP1 (SSH, VNC, any text / URL)

This repo uses a stereo camera and gray-code-based structured light to realize dense 3D reconstruction.

Example code to sending USB Gadget multimedia keys via Python

Example Python code for building RPi-controlled robotic systems

Code and build instructions for Snap, a simple Raspberry Pi and LED machine to show you how expensive the electricyty is at the moment

Doughskript interpreter for converting simple command sequences into executable Arduino C++ code.

Sail is a free CLI tool to deploy, manage and scale WordPress applications in the DigitalOcean cloud.

text_recognition_toolbox: The reimplementation of a series of classical scene text recognition papers with Pytorch in a uniform way.

Repository of conference publications and source code for first-/ second-authored papers published at NeurIPS, ICML, and ICLR.

The papers published in top-tier AI conferences in recent years.

The tl;dr on a few notable transformer/language model papers + other papers (alignment, memorization, etc).

arxiv-sanity, but very lite, simply providing the core value proposition of the ability to tag arxiv papers of interest and have the program recommend similar papers.

Code for the AI lab course 2021/2022 of the University of Verona

Train neural network for semantic segmentation (deep lab V3) with pytorch in less then 50 lines of code

All the code and files related to the MI-Lab of UE19CS305 course in sem 5

This repository contains the code for the python introduction lab

[ECCV 2020] Reimplementation of 3DDFAv2, including face mesh, head pose, landmarks, and more.

Comments

Potential bug in the CoMPT attention implementation

Owner

Jianwen Chen

🎃 Some spooky code samples to hack yourself a pumpkin 👻

Testing out some (stolen) DMA code for RP2040 Micropython

Minimal and clean dashboard to visualize some stats of Pi-Hole with an E-Ink display attached to your Raspberry Pi

Run this code to blink your ThinkPad LED with a hidden mysterious Morse code! ;)

Raspberry Pi Pico support for VS Code

This repository contains all the code and files needed to simulate the notspot quadrupedal robot using Gazebo and ROS.

Simple Python script to decode and verify an European Health Certificate QR-code

Python code written to utilize the Korlan usb2can hardware to send and receive data over the can-bus on a 2008 Nissan 350z

Example code and projects for FeatherS2 and FeatherS2 Neo

This repository hosts the code for Stanford Pupper and Stanford Woofer, Raspberry Pi-based quadruped robots that can trot, walk, and jump.