Python Biomedical-knowledge-graph Resources

PyNode Next A complete rewrite of PyNode for the modern era. Up to five times faster than the original PyNode. PyNode Next allows you to easily create

This repository contains sample code scripts for creating awesome data visualizations from scratch using different python libraries (such as matplotli

Transcript Analysis - Graph + NLP This program extracts insights from Zoom Meeting Transcripts (.vtt) using TigerGraph and NLTK. In order to run this

DAG_Generator Random Directed Acyclic Graph Generator verison1.0 简介 工作流通常由DAG（有向无环图）来定义，其中每个计算任务$T_i$由一个顶点(node,task,vertex)表示。同时，任务之间的每个数据或控制依赖性由一条加权

title emoji colorFrom colorTo sdk app_file pinned decontextualizer 📤 green gray streamlit main.py false Decontextualizer As a second step in improvin

Multimodal Trajectory Prediction Conditioned on Lane-Graph Traversals This repository contains code for "Multimodal trajectory prediction conditioned

Graph Convolutional Networks with Dual Message Passing for Subgraph Isomorphism Counting and Matching This repository is an official implementation of

Neointerface - Neo4j made easy for Python programmers! A Python interface to use the Neo4j graph database, and simplify its use. class NeoInterface: C

HyFactor Graph-based architectures are becoming increasingly popular as a tool for structure generation. Here, we introduce a novel open-source archit

ForceAtlas2 for Python A port of Gephi's Force Atlas 2 layout algorithm to Python 2 and Python 3 (with a wrapper for NetworkX and igraph). This is the

gdsclient NOTE: This is a work in progress and many GDS features are known to be missing or not working properly. This repo hosts the sources for gdsc

gdsclient This repo hosts the sources for gdsclient, a Python wrapper API for operating and working with the Neo4j Graph Data Science (GDS) library. g

deepGCFX PyTorch implementation for our AAAI 2022 Paper "Graph-wise Common Latent Factor Extraction for Unsupervised Graph Representation Learning" Pr

Graph Convolutional Networks with Dual Message Passing for Subgraph Isomorphism Counting and Matching This repository is an official implementation of

Fonduer is a Python package and framework for building knowledge base construction (KBC) applications from richly formatted data. Note that Fonduer is

ReFine: Multi-Grained Explainability for GNNs This is the official code for Towards Multi-Grained Explainability for Graph Neural Networks (NeurIPS 20

SSL_OSC Graph Self-Supervised Learning for Optoelectronic Properties of Organic Semiconductors

Documentation | External Resources | Datasets | Examples ChemicalX is a deep learning library for drug-drug interaction, polypharmacy side effect and

KiwiDB HTTP graph database built in Python 3. Reference Format References are strings in the format: {refIDENTIFIER@GROUP} Authentication Currently, t

Target Adaptive Context Aggregation for Video Scene Graph Generation This is a PyTorch implementation for Target Adaptive Context Aggregation for Vide

ICCV'21 Context-aware Scene Graph Generation with Seq2Seq Transformers Authors: Yichao Lu*, Himanshu Rai*, Cheng Chang*, Boris Knyazev†, Guangwei Yu,

Graph Notebook: easily query and visualize graphs The graph notebook provides an easy way to interact with graph databases using Jupyter notebooks. Us

Cog - Embedded Graph Database for Python cogdb.io New release: 2.0.5! Installing Cog pip install cogdb Cog is a persistent embedded graph database im

Edge-augmented Graph Transformer Introduction This is the official implementation of the Edge-augmented Graph Transformer (EGT) as described in https:

Pretrained Language Model This repository provides the latest pretrained language models and its related optimization techniques developed by Huawei N

LUKE (Language Understanding with Knowledge-based Embeddings) is a new pre-trained contextualized representation of words and entities based on transf

Knover Knover is a toolkit for knowledge grounded dialogue generation based on PaddlePaddle. Knover allows researchers and developers to carry out eff

CGPN This is the repository for the NeurIPS-21 paper [Contrastive Graph Poisson Networks: Semi-Supervised Learning with Extremely Limited Labels]. Req

PyContinual (An Easy and Extendible Framework for Continual Learning) Easy to Use You can sumply change the baseline, backbone and task, and then read

Gihan Jayatilaka*, Jameel Hassan*, Suren Sritharan*, Janith Senananayaka, Harshana Weligampola, et. al., 2021. Holistic Interpretation of Public Scenes Using Computer Vision and Temporal Graphs to Identify Social Distancing Violations. arXiv preprint.

Decentralised graph database management system To get started clone the repo, and run the command below. python3 database.py Now, create a new termina

Docker Network Graph Visualize the relationship between Docker networks and containers as a neat graphviz graph. Example Usage usage: docker-net-graph

Hierarchical Clustering: O(1)-Approximation for Well-Clustered Graphs This repository contains code to accompany the paper "Hierarchical Clustering: O

Dual Correlation Reduction Network An official source code for paper Deep Graph Clustering via Dual Correlation Reduction, accepted by AAAI 2022. Any

Sparse Structure Learning via Graph Neural Networks for inductive document classification Make graph dataset create co-occurrence graph for datasets.

How to apply? Create your config.ini file following the example provided in config.ini Choose one of the options below to run: Run with Python3 pip in

Sleep_Staging_Knowledge Distillation This codebase implements knowledge distillation approach for ECG based sleep staging assisted by EEG based sleep

Lightweight-Deep-CNN-for-Natural-Image-Matting-via-Similarity-Preserving-Knowledge-Distillation Introduction Accepted at IEEE Signal Processing Letter

SHGNN: Structure-Aware Heterogeneous Graph Neural Network The source code and dataset of the paper: SHGNN: Structure-Aware Heterogeneous Graph Neural

Lambekseq "Everyone who failed Greek or Latin hates it." This package is for proving theorems in Categorial grammars (CG) and constructing semantic gr

RDFLib RDFLib is a pure Python package for working with RDF. RDFLib contains most things you need to work with RDF, including: parsers and serializers

PyG (PyTorch Geometric) is a library built upon PyTorch to easily write and train Graph Neural Networks (GNNs) for a wide range of applications related to structured data.

# 1. Installing Maven & Pandas First, please install Java (JDK11) and Python 3 if they are not already. Next, make sure that Maven (for importing J

LUNAR Official Implementation of "LUNAR: Unifying Local Outlier Detection Methods via Graph Neural Networks" Adam Goodge, Bryan Hooi, Ng See Kiong and

Contents AnonyGAN Installation Dataset Preparation Generating Images Using Pretrained Model Train and Test New Models Evaluation Acknowledgments Citat

Mask-invariant Face Recognition through Template-level Knowledge Distillation This is the official repository of "Mask-invariant Face Recognition thro

Monte Carlo python simulation Install linux dependencies sudo apt update sudo apt install build-essential \ software-properties-commo

KIDA: Knowledge Inheritance in Data Aggregation This project releases our 1st place solution on NeurIPS2021 ML4CO Dual Task. Slide and model weights a

CogniPy for Pandas - In-memory Graph Database and Knowledge Graph with Natural Language Interface Whats in the box Reasoning, exploration of RDF/OWL,

WSDM 2022 Large-scale Temporal Graph Link Prediction - Baseline and Initial Test Set WSDM Cup Website link Link to this challenge This branch offers A

HetGAN Implementation of Heterogeneous Graph Attention Network This is the code repository of paper "Prediction of Metro Ridership During the COVID-19

BT-Unet: A-Self-supervised-learning-framework-for-biomedical-image-segmentation-using-Barlow-Twins Deep learning has brought most profound contributio

Knowledge Graph Embeddings and Chemical Effect Prediction, 2020. Scripts and outputs related to the paper Prediction of Adverse Biological Effects of

Enhancing Column Generation by a Machine-Learning-BasedPricing Heuristic for Graph Coloring (to appear at AAAI 2022) We propose a machine-learning-bas

AKGNN The source code for Adaptive Kernel Graph Neural Network at AAAI2022. Please cite our paper if you think our work is helpful to you: @inproceedi

Wikidated Wikidated 1.0 is a dataset of Wikidata’s full revision history, which encodes changes between Wikidata revisions as sets of deletions and ad

DiffMG This repository contains the code for our KDD 2021 Research Track paper: DiffMG: Differentiable Meta Graph Search for Heterogeneous Graph Neura

Introduction K-PLUG: Knowledge-injected Pre-trained Language Model for Natural Language Understanding and Generation in E-Commerce. Installation PyTor

Learning From Multiple Experts: Self-paced Knowledge Distillation for Long-tailed Classification Implementation of "Learning From Multiple Experts: Se

A toolkit for computational pathology and machine learning. View documentation Please cite our paper Installation There are several ways to install Pa

PyCRE Conflict-aware Inference of Python Compatible Runtime Environments with Domain Knowledge Graph, ICSE 2022 Dependencies This project is developed

KIDA: Knowledge Inheritance in Data Aggregation This project releases our 1st place solution on NeurIPS2021 ML4CO Dual Task. Slide and model weights a

LUNAR Official Implementation of "LUNAR: Unifying Local Outlier Detection Methods via Graph Neural Networks" Adam Goodge, Bryan Hooi, Ng See Kiong and

CRGNN Paper ： Improving the Training of Graph Neural Networks with Consistency Regularization Environments Implementing environment: GeForce RTX™ 3090

An interactive visualization system designed to helps domain experts responsibly edit Generalized Additive Models (GAMs). For more information, check

Junction Tree Variational Autoencoder for Molecular Graph Generation Official implementation of our Junction Tree Variational Autoencoder https://arxi

MINERVA Meandering In Networks of Entities to Reach Verisimilar Answers Code and models for the paper Go for a Walk and Arrive at the Answer - Reasoni

CCasGNN A new framework, collaborative cascade prediction based on graph neural networks (CCasGNN) to jointly utilize the structural characteristics,

Graph Neural Controlled Differential Equations for Traffic Forecasting Setup Python environment for STG-NCDE Install python environment $ conda env cr

ADD: Frequency Attention and Multi-View based Knowledge Distillation to Detect Low-Quality Compressed Deepfake Images Binh M. Le & Simon S. Woo, "ADD:

Graph WaveNet for brain network analysis This is the implementation of the Graph WaveNet model used in our manuscript: S. Wein , A. Schüller, A. M. To

CRGNN Paper ： Improving the Training of Graph Neural Networks with Consistency Regularization Environments Implementing environment: GeForce RTX™ 3090

This project is no longer maintained. If you are interested in taking over the project, email [email protected]. Welcome to django-knowledge! django-

README Needs to be improved Prerequisites Need to have graphiz installed on the machine. Refer to https://graphviz.readthedocs.io/en/stable/manual.htm

Federated learning on graph, especially on graph neural networks (GNNs), knowledge graph, and private GNN.

Papers about explainability of GNNs

CBio-NAMER CBioNAMER (Nested nAMed Entity Recognition for Chinese Biomedical Text) is our method used in CBLUE (Chinese Biomedical Language Understand

subgraph-extractor Extracts data from the database for a graph-node and stores it in parquet files Installation For developing, it's recommended to us

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

ASCII Graph Plotter Plots the graph of a function with ASCII characters. See the change log here. Developed by InformaticFreak (c) 2021 How to use py

Graph Posterior Network This is the official code repository to the paper Graph Posterior Network: Bayesian Predictive Uncertainty for Node Classifica

Convert ONNX model graph to Keras model format.

CTO (Call Tree Overviewer) CTO (Call Tree Overviewer) is an IDA plugin for creating a simple and efficiant function call tree graph. It can also summa

CAPGNN Source code and dataset of the paper "Contrastive Adaptive Propagation Graph Neural Networks forEfficient Graph Learning" Paper URL: https://ar

TC-GNN (Running Sparse GNN on Dense Tensor Core on Ampere GPU) Cite this project and paper. @inproceedings{TC-GNN, title={TC-GNN: Accelerating Spars

Open-CyKG: An Open Cyber Threat Intelligence Knowledge Graph Model Description Open-CyKG is a framework that is constructed using an attenti

Decoupled Spatial-Temporal Graph Neural Networks Code for our paper: Decoupled Dynamic Spatial-Temporal Graph Neural Network for Traffic Forecasting.

Permutation Invariant Graph Generation via Score-Based Generative Modeling This repo contains the official implementation for the paper Permutation In

farabio is a minimal PyTorch toolkit for out-of-the-box deep learning support in biomedical imaging. For further information, see Wikis and Docs.

Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures Code for the Multiplex Molecular Graph Neural Network (M

Efficient Graph Similarity Computation - (EGSC) This repo contains the source code and dataset for our paper: Slow Learning and Fast Inference: Effici

Reminder ST-GCN has transferred to MMSkeleton, and keep on developing as an flexible open source toolbox for skeleton-based human understanding. You a

slam-playground Educational 2D SLAM implementation based on ICP and Pose Graph How to use: Use keyboard arrow keys to navigate robot. Press 'r' to vie

To run a generation experiment (either conceptnet or atomic), follow these instructions: First Steps First clone, the repo: git clone https://github.c

K-BERT Sorce code and datasets for "K-BERT: Enabling Language Representation with Knowledge Graph", which is implemented based on the UER framework. R

LUKE (Language Understanding with Knowledge-based Embeddings) is a new pre-trained contextualized representation of words and entities based on transf

KEPLER: A Unified Model for Knowledge Embedding and Pre-trained Language Representation Source code for TACL 2021 paper KEPLER: A Unified Model for Kn

This repository contains code for: Fusion-in-Decoder models Distilling Knowledge from Reader to Retriever Dependencies Python 3 PyTorch (currently tes

FKD: A Fast Knowledge Distillation Framework for Visual Recognition Official PyTorch implementation of paper A Fast Knowledge Distillation Framework f

DOC | Quick Start | 中文 Breaking News !! 🔥 🔥 🔥 OGB-LSC KDD CUP 2021 winners announced!! (2021.06.17) Super excited to announce our PGL team won TWO