Python Biomedical-knowledge-graph Resources

ElasticGNN This repository includes the official implementation of ElasticGNN in the paper "Elastic Graph Neural Networks" [ICML 2021]. Xiaorui Liu, W

PGExplainer This is a Tensorflow implementation of the paper: Parameterized Explainer for Graph Neural Network https://arxiv.org/abs/2011.04573 NeurIP

A collection of research papers and software related to explainability in graph machine learning.

Aspect-level Sentiment Classification Code and dataset for ACL2018 [paper] ‘‘Exploiting Document Knowledge for Aspect-level Sentiment Classification’’

Adaptive Segmentation Mask Attack This repository contains the implementation of the Adaptive Segmentation Mask Attack (ASMA), a targeted adversarial

PyKEEN PyKEEN (Python KnowlEdge EmbeddiNgs) is a Python package designed to train and evaluate knowledge graph embedding models (incorporating multi-m

Binance Report Bot The intent of this bot is to take a snapshot of your binance wallet, e.g. the current balances and store it for further plotting. I

ProSelfLC: CVPR 2021 ProSelfLC: Progressive Self Label Correction for Training Robust Deep Neural Networks For any specific discussion or potential fu

Logic Tensor Networks (LTN) Logic Tensor Network (LTN) is a neurosymbolic framework that supports querying, learning and reasoning with both rich data

VidLanKD Implementation of VidLanKD: Improving Language Understanding via Video-Distilled Knowledge Transfer by Zineng Tang, Jaemin Cho, Hao Tan, Mohi

CLIPPER: A Graph-Theoretic Framework for Robust Data Association Data association is a fundamental problem in robotics and autonomy. CLIPPER provides

Self-supervised Graph-level Representation Learning with Local and Global Structure Introduction This project is an implementation of ``Self-supervise

Heterogeneous INteract and aggreGatE (GraphHINGE) This is a pytorch implementation of GraphHINGE model. This is the experiment code in the following w

Box is a text-based visual programming language inspired by Unreal Engine blueprint function graphs. $ cat factorial.box ┌─ƒ(Factorial)───┐

GCResNet PyTorch implementation of Graph Convolutional Networks in Feature Space for Image Deblurring and Super-resolution, IJCNN 2021. The code will

This is my reading list for my PhD in AI, NLP, Deep Learning and more.

GPRGNN This is the source code for our ICLR2021 paper: Adaptive Universal Generalized PageRank Graph Neural Network. Hidden state feature extraction i

Physics-aware Difference Graph Networks for Sparsely-Observed Dynamics This repository is the official PyTorch implementation of "Physics-aware Differ

PLOME:Pre-training with Misspelled Knowledge for Chinese Spelling Correction (ACL2021) This repository provides the code and data of the work in ACL20

Data Efficient Stagewise Knowledge Distillation Table of Contents Data Efficient Stagewise Knowledge Distillation Table of Contents Requirements Image

Learning Canonical Representations for Scene Graph to Image Generation (ECCV 2020) Roei Herzig*, Amir Bar*, Huijuan Xu, Gal Chechik, Trevor Darrell, A

Graph-to-Graph Transformers Self-attention models, such as Transformer, have been hugely successful in a wide range of natural language processing (NL

DensePhrases DensePhrases is an extractive phrase search tool based on your natural language inputs. From 5 million Wikipedia articles, it can search

Graph4NLP Graph4NLP is an easy-to-use library for R&D at the intersection of Deep Learning on Graphs and Natural Language Processing (i.e., DLG4NLP).

Knowledge-Inheritance Source code paper: Knowledge Inheritance for Pre-trained Language Models (preprint). The trained model parameters (in Fairseq fo

Graph Transformer - Pytorch Implementation of Graph Transformer in Pytorch, for potential use in replicating Alphafold2. This was recently used by bot

Embedding Transfer with Label Relaxation for Improved Metric Learning Official PyTorch implementation of CVPR 2021 paper Embedding Transfer with Label

Python daily pills Daily knowledge pills to get better Python code. Why Does your Python code suffers of any of this symptoms? Incorrect Indentation I

U Net Lowered with Keras Complete U-net Implementation with keras Original Paper Link : https://arxiv.org/abs/1505.04597 Special Implementations : The

DeepCDR Cancer Drug Response Prediction via a Hybrid Graph Convolutional Network This work has been accepted to ECCB2020 and was also published in the

Query Embedding on Hyper-Relational Knowledge Graphs This repository contains the code used for the experiments in the paper Query Embedding on Hyper-

NodePiece - Compositional and Parameter-Efficient Representations for Large Knowledge Graphs NodePiece is a "tokenizer" for reducing entity vocabulary

FinGAT: A Financial Graph Attention Networkto Recommend Top-K Profitable Stocks This is our implementation for the paper: FinGAT: A Financial Graph At

Random Walk Graph Neural Networks This repository is the official implementation of Random Walk Graph Neural Networks. Requirements Code is written in

JittorVis - Visual understanding of deep learning model.

AWS_ORG_MAPPER This tool uses sso-oidc to authenticate to the AWS organization. Once authenticated the tool will attempt to enumerate all users and ro

GraphSum This repo contains the data and code for the G2G model in the paper: Extracting Summary Knowledge Graphs from Long Documents. The other basel

We present Graph Neural Diffusion (GRAND) that approaches deep learning on graphs as a continuous diffusion process and treats Graph Neural Networks (GNNs) as discretisations of an underlying PDE.

The final code for OGB Installation Requirements: ogb=1.3.1 torch=1.7.0 torch-geometric=1.7.0 torch-scatter=2.0.6 torch-sparse=0.6.9 Baseline models T

UmlsBERT: Clinical Domain Knowledge Augmentation of Contextual Embeddings Using the Unified Medical Language System Metathesaurus General info This is

LMs for biomedical KG completion This repository contains code to run the experiments described in: Scientific Language Models for Biomedical Knowledg

Graph Contrastive Learning Automated PyTorch implementation for Graph Contrastive Learning Automated [talk] [poster] [appendix] Yuning You, Tianlong C

This is the repo for the paper: Leveraging Two Types of Global Graph for Sequential Fashion Recommendation Requirements OS: Ubuntu 16.04 or higher ver

DSTC10 Track 2 - Knowledge-grounded Task-oriented Dialogue Modeling on Spoken Conversations This repository contains the data, scripts and baseline co

文字是人类用以记录和表达的最基本工具，也是信息传播的重要媒介。透过文字与符号，我们可以追寻人类文明的起源，可以传播知识与经验，读懂文字是认识与了解的第一步。对于人工智能而言，它的核心问题之一就是认知，而认知的核心则是语义理解。

Graphormer By Chengxuan Ying, Tianle Cai, Shengjie Luo, Shuxin Zheng*, Guolin Ke, Di He*, Yanming Shen and Tie-Yan Liu. This repo is the official impl

PyGAS: Auto-Scaling GNNs in PyG PyGAS is the practical realization of our G NN A uto S cale (GAS) framework, which scales arbitrary message-passing GN

Graph-to-Tree Learning for Solving Math Word Problems PyTorch implementation of Graph based Math Word Problem solver described in our ACL 2020 paper G

merlot MERLOT: Multimodal Neural Script Knowledge Models MERLOT is a model for learning what we are calling "neural script knowledge" -- representatio

English | 中文说明 CBLUE AI (Artificial Intelligence) is playing an indispensabe role in the biomedical field, helping improve medical technology. For fur

[TensorFlow] Protein Interface Prediction using Graph Convolutional Networks Unofficial TensorFlow implementation of Protein Interface Prediction usin

GSDN-F and GSDN-EF This repository provides a reference implementation of GSDN-F and GSDN-EF as described in the paper "Understanding Graph Neural Net

Degree-Quant This repo provides a clean re-implementation of the code associated with the paper Degree-Quant: Quantization-Aware Training for Graph Ne

Prior-Enhanced network with Meta-Prototypes (PEMP) This is the PyTorch implementation of PEMP. Overview of PEMP Meta-Prototypes & Adaptive Prototypes

ProcrustEs-KGE Paddle implementation for Highly Efficient Knowledge Graph Embedding Learning with Orthogonal Procrustes Analysis 🙈 A more detailed re

How Attentive are Graph Attention Networks? This repository is the official implementation of How Attentive are Graph Attention Networks?. The PyTorch

Visualizing Adapted Knowledge in Domain Transfer @inproceedings{hou2021visualizing, title={Visualizing Adapted Knowledge in Domain Transfer}, auth

SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization This is the code for our paper ``SumGNN: Multi-typed Drug

GCN-LPA This repository is the implementation of GCN-LPA (arXiv): Unifying Graph Convolutional Neural Networks and Label Propagation Hongwei Wang, Jur

Simple Spectral Graph Convolutional Overview This repo contains an example implementation of the Simple Spectral Graph Convolutional (S^2GC) model. Th

Grapy-ML: Graph Pyramid Mutual Learning for Cross-dataset Human Parsing This repository contains pytorch source code for AAAI2020 oral paper: Grapy-ML

Factor graphs + nonlinear optimization in JAX

OEIS explorer This is a tool for exploring two different kinds of relationships between sequences in the OEIS: mentions (links) of other sequences on

Show, Attend and Distill: Knowledge Distillation via Attention-based Feature Matching Official pytorch implementation of "Show, Attend and Distill: Kn

DeepFRI Deep functional residue identification Citing @article {Gligorijevic2019, author = {Gligorijevic, Vladimir and Renfrew, P. Douglas and Koscio

ReviewKD Distilling Knowledge via Knowledge Review Pengguang Chen, Shu Liu, Hengshuang Zhao, Jiaya Jia This project provides an implementation for the

If the compilation is successful, the evaluator of cpp implementation will be called automatically. Otherwise, the evaluator of python implementation will be called.

DDAMS This is the pytorch code for our IJCAI 2021 paper Dialogue Discourse-Aware Graph Model and Data Augmentation for Meeting Summarization [Arxiv Pr

An Unsupervised Graph-based Toolbox for Fraud Detection Introduction: UGFraud is an unsupervised graph-based fraud detection toolbox that integrates s

When2com: Multi-Agent Perception via Communication Graph Grouping This is the PyTorch implementation of our paper: When2com: Multi-Agent Perception vi

Expressive Power of Invariant and Equivaraint Graph Neural Networks In this repository, we show how to use powerful GNN (2-FGNN) to solve a graph alig

GCA Source code for Graph Contrastive Learning with Adaptive Augmentation (WWW 2021) For example, to run GCA-Degree under WikiCS, execute: python trai

language-models-are-knowledge-graphs-pytorch Language models are open knowledge graphs ( work in progress ) A non official reimplementation of Languag

python_graphs This package is for computing graph representations of Python programs for machine learning applications. It includes the following modu

PairRE Code for paper PairRE: Knowledge Graph Embeddings via Paired Relation Vectors. This implementation of PairRE for Open Graph Benchmak datasets (

Continuous Query Decomposition This repository contains the official implementation for our ICLR 2021 (Oral) paper, Complex Query Answering with Neura

Karate Club is an unsupervised machine learning extension library for NetworkX. Please look at the Documentation, relevant Paper, Promo Video, and Ext

SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks Molecular interaction networks are powerful resources for the discovery. While dee

Graph-Based Protein Design This repo contains code for Generative Models for Graph-Based Protein Design by John Ingraham, Vikas Garg, Regina Barzilay

SentiLARE: Sentiment-Aware Language Representation Learning with Linguistic Knowledge Introduction SentiLARE is a sentiment-aware pre-trained language

Desmos Bezier Renderer A simple image/video to Desmos graph converter run locally Sample Result Setup Install dependencies apt update apt install git

FedGraphNN: A Federated Learning System and Benchmark for Graph Neural Networks A Research-oriented Federated Learning Library and Benchmark Platform

Beyond Homophily in Graph Neural Networks: Current Limitations and Effective Designs Jiong Zhu, Yujun Yan, Lingxiao Zhao, Mark Heimann, Leman Akoglu,

Graph Evolving Meta-Learning for Low-resource Medical Dialogue Generation Code to be further cleaned... This repo contains the code of the following p

Introduction This is the PyTorch implementation for Adaptive Graph Representation Learning for Video Person Re-identification. Get started git clone h

Learning Knowledge Bases with Parameters for Task-Oriented Dialogue Systems This is the implementation of the paper: Learning Knowledge Bases with Par

End-to-End Optimization of Scene Layout Code release for: End-to-End Optimization of Scene Layout CVPR 2020 (Oral) Project site, Bibtex For help conta

PyKale is a PyTorch library for multimodal learning and transfer learning as well as deep learning and dimensionality reduction on graphs, images, texts, and videos. By adopting a unified pipeline-based API design, PyKale enforces standardization and minimalism, via reusing existing resources, reducing repetitions and redundancy, and recycling learning models across areas.

(Comet-) ATOMIC 2020: On Symbolic and Neural Commonsense Knowledge Graphs Paper Jena D. Hwang, Chandra Bhagavatula, Ronan Le Bras, Jeff Da, Keisuke Sa

This repository contains code to train and test GNN models for recommendation, mainly using the Deep Graph Library (DGL).

SpikeX is a collection of pipes ready to be plugged in a spaCy pipeline. It aims to help in building knowledge extraction tools with almost-zero effort.

AutoSF The code for our paper "AutoSF: Searching Scoring Functions for Knowledge Graph Embedding" and this paper has been accepted by ICDE2020. News:

MultiResUNet Rethinking the U-Net architecture for multimodal biomedical image segmentation This repository contains the original implementation of "M

Few-shot Graph Learning for Molecular Property Prediction Introduction This is the source code and dataset for the following paper: Few-shot Graph Lea

Knowledge Graph,Question Answering System，基于知识图谱和向量检索的医疗诊断问答系统

GraphMask This repository contains an implementation of GraphMask, the interpretability technique for graph neural networks presented in our ICLR 2021

libmaths libmaths was created not only as a learning experience for me, but as a way to make mathematical models in seconds for Python users using mat

Neighbor Averaging over Relation Subgraphs (NARS) NARS is an algorithm for node classification on heterogeneous graphs, based on scalable neighbor ave

Trove Trove is a research framework for building weakly supervised (bio)medical named entity recognition (NER) and other entity attribute classifiers

AMTML-KD: Adaptive Multi-teacher Multi-level Knowledge Distillation