Python Biomedical-knowledge-graph Resources

FairEdit Relevent Publication FairEdit: Preserving Fairness in Graph Neural Networks through Greedy Graph Editing

TBSG: Tree-based Search Graph for Approximate Nearest Neighbor Search. TBSG is a graph-based algorithm for ANNS based on Cover Tree, which is also an

DeepKE is a knowledge extraction toolkit supporting low-resource and document-level scenarios for entity, relation and attribute extraction. We provide comprehensive documents, Google Colab tutorials, and online demo for beginners.

SimReg: A Simple Regression Based Framework for Self-supervised Knowledge Distillation Source code for the paper "SimReg: Regression as a Simple Yet E

1 MAGNN This repo is the official implementation for Multi-Scale Adaptive Graph Neural Network for Multivariate Time Series Forecasting. 1.1 The frame

VisionKG: Vision Knowledge Graph Official Repository of VisionKG by Anh Le-Tuan, Trung-Kien Tran, Manh Nguyen-Duc, Jicheng Yuan, Manfred Hauswirth and

PPGNet: Learning Point-Pair Graph for Line Segment Detection PyTorch implementation of our CVPR 2019 paper: PPGNet: Learning Point-Pair Graph for Line

TransferNet: Learning Transferrable Knowledge for Semantic Segmentation with Deep Convolutional Neural Network Created by Seunghoon Hong, Junhyuk Oh,

Dynamic Stock Industrial Classification Use graph-based analysis to re-classify stocks and experiment different re-classification methodologies to imp

Dagon - An Asynchronous Task Graph Execution Engine Dagon is a job execution sys

Simple implementation of Equivariant GNN A short implementation of E(n) Equivariant Graph Neural Networks for HOMO energy prediction. Just 50 lines of

This is the course project of AI3602: Data Mining of SJTU. Group Members include Jinghao Feng, Mingyang Jiang and Wenzhong Zheng.

Table of Contents Introduction Installation Examples Pre-trained models Quick start using colab JARVIS-ALIGNN webapp Peformances on a few datasets Use

BERN2 We present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by

Graph-to-3D This is the official implementation of the paper Graph-to-3d: End-to-End Generation and Manipulation of 3D Scenes Using Scene Graphs | arx

merlot_reserve Code release for "MERLOT Reserve: Neural Script Knowledge through Vision and Language and Sound" MERLOT Reserve (in submission) is a mo

ReceptiveFieldAnalysisToolbox This is RFA-Toolbox, a simple and easy-to-use library that allows you to optimize your neural network architectures usin

Intel® Neural Compressor targeting to provide unified APIs for network compression technologies, such as low precision quantization, sparsity, pruning, knowledge distillation, across different deep learning frameworks to pursue optimal inference performance.

Graph-based CTR prediction This is a repository designed for graph-based CTR prediction methods, it includes our graph-based CTR prediction methods: F

Security audit Python project dependencies against security advisory databases.

Knowledge Informed Machine Learning using a Weibull-based Loss Function Exploring the concept of knowledge-informed machine learning with the use of a

PYGON A Graph Neural Network Tool for Recovering Dense Sub-graphs in Random Dense Graphs. Installation This code requires to install and run the graph

BERN2 We present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by

Intro Real-time object detection and classification. Paper: version 1, version 2. Read more about YOLO (in darknet) and download weight files here. In

GraphFPN: Graph Feature Pyramid Network for Object Detection Download graph-FPN-main.zip For training , run: python train.py For test with Graph_fpn

FlatGCN This is the official Pytorch-version code of FlatGCN (Flattened Graph Convolutional Networks for Recommendation, submitted to ICASSP2022). Req

This application aims to read all wifi passwords and visualizes the complexity in graph formation by taking into account several criteria and help you generate new random passwords.

Distilling-the-Knowledge-in-a-Neural-Network This is an implementation of a part of the paper "Distilling the Knowledge in a Neural Network" (https://

Distilling-the-knowledge-in-neural-network Teaches a student network from the knowledge obtained via training of a larger teacher network This is an i

GAT - Graph Attention Network (PyTorch) 💻 + graphs + 📣 = ❤️ This repo contains a PyTorch implementation of the original GAT paper ( 🔗 Veličković et

Skeletal-GNN Code for "Learning Skeletal Graph Neural Networks for Hard 3D Pose Estimation" ICCV'21 Various deep learning techniques have been propose

Spatio-Temporal Dynamic Inference Network for Group Activity Recognition The source codes for ICCV2021 Paper: Spatio-Temporal Dynamic Inference Networ

Scene Graph Generation Object Detections Ground truth Scene Graph Generated Scene Graph In this visualization, woman sitting on rock is a zero-shot tr

BERN2 We present BERN2 (Advanced Biomedical Entity Recognition and Normalization

Documentation | Paper [JMLR] | Tutorials | Benchmarks | Examples DIG: Dive into Graphs is a turnkey library for graph deep learning research. Why DIG?

HKDnet Paper Title: "Heterogeneous Knowledge Distillation for Simultaneous Infrared-Visible Image Fusion and Super-Resolution" Email: 18186470991@163.

Introduction This is a crawler I wrote in Python using the APIs of Telethon months ago. This tool was not intended to be publicly available for a numb

Predico Disease Prediction system based on symptoms provided by patient- using Python-Django & Machine Learning

d o t m o t i f Find graph motifs using intuitive notation DotMotif is a library that identifies subgraphs or motifs in a large graph. It looks like t

Knowledge Repo The Knowledge Repo project is focused on facilitating the sharing of knowledge between data scientists and other technical roles using

U-Net Implementation By Christopher Ley This is my interpretation and implementation of the famous paper "U-Net: Convolutional Networks for Biomedical

Multi-level Disentanglement Graph Neural Network (MD-GNN) This is a PyTorch implementation of the MD-GNN, and the code includes the following modules:

✔️ Linux ✔️ OS X ❌ Windows (#39) Welcome to graph-app-kit Turn your graph data into a secure and interactive visual graph app in 15 minutes! Why This

mask-uncertainty-in-HSI This repository contains the testing code and pre-trained models for the paper Calibrated Hyperspectral Image Reconstruction v

Fast-Partial-Ranking-MNL This repo provides a PyTorch implementation for the CopulaGNN models as described in the following paper: Fast Learning of MN

cluster-link-prediction This repository provides some of the code implemented and the data used for the work proposed in "A Cluster-Based Trip Predict

Mammoth - An Extendible (General) Continual Learning Framework for Pytorch NEWS STAY TUNED: We are working on an update of this repository to include

Glyth Graph Revision for 0.01 A simple, yet versatile, package for graphing equations on a 2-dimensional text canvas List of contents: Brief Introduct

A collection of graph classification methods, covering embedding, deep learning, graph kernel and factorization papers

Total number of Spanning Trees in a Graph This is a python script just written f

Pure Python web server - PyProject A blogging platform written in pure python (n

Pytorch implementation of paper Semi-supervised Knowledge Transfer for Deep Learning from Private Training Data

Strongly local p-norm-cut algorithms for semi-supervised learning and local graph clustering

Confidence-based Graph Convolutional Networks for Semi-Supervised Learning Source code for AISTATS 2019 paper: Confidence-based Graph Convolutional Ne

Neural Structured Learning in TensorFlow Neural Structured Learning (NSL) is a new learning paradigm to train neural networks by leveraging structured

Graph-based joint model with Nonignorable Missingness (GNM) This is a Keras implementation of the GNM model in paper ’Graph-Based Semi-Supervised Lear

G3NN This repo provides a pytorch implementation for the 4 instantiations of the flexible generative framework as described in the following paper: A

Graph Contrastive Learning with Augmentations PyTorch implementation for Graph Contrastive Learning with Augmentations [poster] [appendix] Yuning You*

CCGL: Contrastive Cascade Graph Learning This repo provides a reference implementation of Contrastive Cascade Graph Learning (CCGL) framework as descr

GitHub Activity Generator A script that helps you instantly generate a beautiful GitHub Contributions Graph for the last year. Before 😐 😶 😒 After ?

GCC: Graph Contrastive Coding for Graph Neural Network Pre-Training Original implementation for paper GCC: Graph Contrastive Coding for Graph Neural N

GRACE The official PyTorch implementation of deep GRAph Contrastive rEpresentation learning (GRACE). For a thorough resource collection of self-superv

GMI (Graphical Mutual Information) Graph Representation Learning via Graphical Mutual Information Maximization (Peng Z, Huang W, Luo M, et al., WWW 20

SelfGNN A PyTorch implementation of "SelfGNN: Self-supervised Graph Neural Networks without explicit negative sampling" paper, which will appear in Th

Pretraining on Dynamic Graph Neural Networks Our article is PT-DGNN and the code is modified based on GPT-GNN Requirements python 3.6 Ubuntu 18.04.5 L

DGI Deep Graph Infomax (Veličković et al., ICLR 2019): https://arxiv.org/abs/1809.10341 Overview Here we provide an implementation of Deep Graph Infom

Unsupervised Attributed Multiplex Network Embedding (DMGI) Overview Nodes in a multiplex network are connected by multiple types of relations. However

Heterogeneous-Deep-Graph-Infomax Parameter Setting: HDGI-A: Node-level dimension: 16 Attention head: 4 Semantic-level attention vector: 8 learning rat

Subg-Con Sub-graph Contrast for Scalable Self-Supervised Graph Representation Learning (Jiao et al., ICDM 2020): https://arxiv.org/abs/2009.10273 Over

Graph-InfoClust-GIC [PAKDD 2021] PAKDD'21 version Graph InfoClust: Maximizing Coarse-Grain Mutual Information in Graphs Preprint version Graph InfoClu

MC Outpost A Python server and client application that tracks player session times and server status About MC Outpost provides a session graph and ser

PyMeasure scientific package PyMeasure makes scientific measurements easy to set up and run. The package contains a repository of instrument classes a

Block Modeling-Guided Graph Convolutional Neural Networks This repository contains the demo code of the paper: Block Modeling-Guided Graph Convolution

InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization Authors: Fan-yun Sun, Jordan Hoffm

NeoDTI NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions (Bioinformatics).

SelfTask-GNN A PyTorch implementation of "Self-supervised Learning on Graphs: Deep Insights and New Directions". [paper] In this paper, we first deepe

Graph-Bert Source code of "Graph-Bert: Only Attention is Needed for Learning Graph Representations". Please check the script.py as the entry point. We

Pretrain-Recsys This is our Tensorflow implementation for our WSDM 2021 paper: Bowen Hao, Jing Zhang, Hongzhi Yin, Cuiping Li, Hong Chen. Pre-Training

SLAPS-GNN This repo contains the implementation of the model proposed in SLAPS: Self-Supervision Improves Structure Learning for Graph Neural Networks

G-Bert Pre-training of Graph Augmented Transformers for Medication Recommendation Intro G-Bert combined the power of Graph Neural Networks and BERT (B

GPT-GNN: Generative Pre-Training of Graph Neural Networks GPT-GNN is a pre-training framework to initialize GNNs by generative pre-training. It can be

Self-supervised Auxiliary Learning with Meta-paths for Heterogeneous Graphs This repository is the implementation of SELAR. Dasol Hwang* , Jinyoung Pa

deeper_insights_into_GCNs Deeper insights into graph convolutional networks for semi-supervised learning References data and utils.py come from Implem

Reference Code for AAAI-20 paper "Multi-Stage Self-Supervised Learning for Graph Convolutional Networks on Graphs with Few Labels" Please refer to htt

Self-supervised edge features for improved Graph Neural Network training Data availability: Here is a link to the raw data for the organoids dataset.

DrRepair: Learning to Repair Programs from Error Messages This repo provides the source code & data of our paper: Graph-based, Self-Supervised Program

Implementation for the papers: Self-Supervised Hyperboloid Representations from Logical Queries over Knowledge Graphs, Nurendra Choudhary, Nikhil Rao,

There is More than Meets the Eye: Self-Supervised Multi-Object Detection and Tracking with Sound by Distilling Multimodal Knowledge MM-DistillNet is a

Knowledge Bridging for Empathetic Dialogue Generation This is the official implementation for paper Knowledge Bridging for Empathetic Dialogue Generat

SAG-DTA The code is the implementation for the paper 'SAG-DTA: Prediction of Drug–Target Affinity Using Self-Attention Graph Network'. Requirements py

Cross Domain Facial Expression Recognition Benchmark Implementation of papers: Cross-Domain Facial Expression Recognition: A Unified Evaluation Benchm

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

UMLS-Graph Build a medical knowledge graph based on Unified Language Medical System (UMLS) Requisite Install MySQL Server 5.6 and import UMLS data int

MS Graph API authentication example with Fast API What it is & does This is a simple python service/webapp, using FastAPI with server side rendering,

LynxKite is a complete graph data science platform for very large graphs and other datasets. It seamlessly combines the benefits of a friendly graphical interface and a powerful Python API.

Weak-supervised Visual Geo-localization via Attention-based Knowledge Distillation Introduction WAKD is a PyTorch implementation for our ICPR-2022 pap

pysal/spaghetti SPAtial GrapHs: nETworks, Topology, & Inference Spaghetti is an open-source Python library for the analysis of network-based spatial d

tfgraphviz tfgraphviz is a module to visualize a TensorFlow's data flow graph like TensorBoard using Graphviz. tfgraphviz enables to provide a visuali

Logo by Zhuoning Yuan LibAUC: A Machine Learning Library for AUC Optimization Website | Updates | Installation | Tutorial | Research | Github LibAUC a

Build an Amazon SageMaker Pipeline to Transform Raw Texts to A Knowledge Graph This repository provides a pipeline to create a knowledge graph from ra