Python Biomedical-knowledge-graph Resources

My Body is a Cage: the Role of Morphology in Graph-Based Incompatible Control

Cornell Biomedical Knowledge Hub (CBKH) CBKG integrates data from 18 publicly available biomedical databases. The current version of CBKG contains a t

QA-GNN: Question Answering using Language Models and Knowledge Graphs This repo provides the source code & data of our paper: QA-GNN: Reasoning with L

DomainCAT (Domain Connectivity Analysis Tool) Domain Connectivity Analysis Tool is used to analyze aggregate connectivity patterns across a set of dom

Comprehensive and Rigorous Framework for Reproducible Recommender Systems Evaluation

peartree 🍐 🌳 peartree is a library for converting GTFS feed schedules into a representative directed network graph. The tool uses Partridge to conve

OSMnet Tools for the extraction of OpenStreetMap (OSM) street network data. Intended to be used in tandem with Pandana and UrbanAccess libraries to ex

K-Adapter: Infusing Knowledge into Pre-Trained Models with Adapters This repository is the implementation of the paper "K-Adapter: Infusing Knowledge

PyTorch code for the paper "Curriculum Graph Co-Teaching for Multi-target Domain Adaptation" (CVPR2021) This repo presents PyTorch implementation of M

STAR-FC This code is the implementation for the CVPR 2021 paper "Structure-Aware Face Clustering on a Large-Scale Graph with 10^7 Nodes" 🌟 🌟 . 🎓 Re

FAU Implementation of the paper: Facial Action Unit Intensity Estimation via Semantic Correspondence Learning with Dynamic Graph Convolution. Yingruo

LifelongReID Offical implementation of our Lifelong Person Re-Identification via Adaptive Knowledge Accumulation in CVPR2021 by Nan Pu, Wei Chen, Yu L

Undistillable: Making A Nasty Teacher That CANNOT teach students "Undistillable: Making A Nasty Teacher That CANNOT teach students" Haoyu Ma, Tianlong

NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

Knowledge Distillation for BERT Unsupervised Domain Adaptation Official PyTorch implementation | Paper Abstract A pre-trained language model, BERT, ha

DNA This repository provides the code of our paper: Blockwisely Supervised Neural Architecture Search with Knowledge Distillation. Illustration of DNA

Rethinking Graph Neural Architecture Search from Message-passing Intro The GNAS can automatically learn better architecture with the optimal depth of

DensePhrases DensePhrases provides answers to your natural language questions from the entire Wikipedia in real-time. While it efficiently searches th

SiamGAT 1. Environment setup This code has been tested on Ubuntu 16.04, Python 3.5, Pytorch 1.2.0, CUDA 9.0. Please install related libraries before r

A Critical Assessment of State-of-the-Art in Entity Alignment This repository contains the source code for the paper A Critical Assessment of State-of

FRSKD Official implementation for Refine Myself by Teaching Myself : Feature Refinement via Self-Knowledge Distillation (CVPR-2021) Requirements Pytho

Spectral Temporal Graph Neural Network for Multivariate Time-series Forecasting This repository is the official implementation of Spectral Temporal Gr

skggm : Gaussian graphical models using the scikit-learn API In the last decade, learning networks that encode conditional independence relationships

cuGraph - GPU Graph Analytics The RAPIDS cuGraph library is a collection of GPU accelerated graph algorithms that process data found in GPU DataFrames

CoMatch: Semi-supervised Learning with Contrastive Graph Regularization (Salesforce Research) This is a PyTorch implementation of the CoMatch paper [B

QC-DGM This is the official PyTorch implementation and models for our CVPR 2021 paper: Deep Graph Matching under Quadratic Constraint. It also contain

Deep GNN, Shallow Sampling Hanqing Zeng, Muhan Zhang, Yinglong Xia, Ajitesh Srivastava, Andrey Malevich, Rajgopal Kannan, Viktor Prasanna, Long Jin, R

Open Semantic Search https://opensemanticsearch.org Integrated search server, ETL framework for document processing (crawling, text extraction, text a

Commonsense Knowledge Base Completion with Structural and Semantic Context Code for the paper Commonsense Knowledge Base Completion with Structural an

FiGNN for CTR prediction The code and data for our paper in CIKM2019: Fi-GNN: Modeling Feature Interactions via Graph Neural Networks for CTR Predicti

DeepSphere-Weather - Deep Learning on the sphere for weather/climate applications. The code in this repository provides a scalable and flexible framew

Implicit Graph Neural Networks This repository is the official PyTorch implementation of "Implicit Graph Neural Networks". Fangda Gu*, Heng Chang*, We

Learning Intents behind Interactions with Knowledge Graph for Recommendation This is our PyTorch implementation for the paper: Xiang Wang, Tinglin Hua

tf-fsvd TensorFlow Implementation of Functional Singular Value Decomposition for paper Fast Graph Learning with Unique Optimal Solutions Cite If you f

SuperGAT Official implementation of Self-supervised Graph Attention Networks (SuperGAT). This model is presented at How to Find Your Friendly Neighbor

skggm : Gaussian graphical models using the scikit-learn API In the last decade, learning networks that encode conditional independence relationships

Welcome to Spektral Spektral is a Python library for graph deep learning, based on the Keras API and TensorFlow 2. The main goal of this project is to

Documentation | Paper | Colab Notebooks | External Resources | OGB Examples PyTorch Geometric (PyG) is a geometric deep learning extension library for

Little Ball of Fur is a graph sampling extension library for Python. Please look at the Documentation, relevant Paper, Promo video and External Resour

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

EGNN - Pytorch Implementation of E(n)-Equivariant Graph Neural Networks, in Pytorch. May be eventually used for Alphafold2 replication. This

Localization Distillation for Object Detection This repo is based on mmDetection. This is the code for our paper: Localization Distillation

E(n)-Equivariant Transformer (wip) Implementation of E(n)-Equivariant Transformer, which extends the ideas from Welling's E(n)-Equivariant G

django-wiki Django support The below table explains which Django versions are supported. Release Django Upgrade from 0.7.x 2.2, 3.0, 3.1 0.5 or 0.6 0.

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

Predicting Patient Outcomes with Graph Representation Learning This repository contains the code used for Predicting Patient Outcomes with Graph Repre

Notion Graph View Export Notion pages to a Roam Research like graph view.

A PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf 2021). Abstract In this work we propose Pathfind

HyperTag HyperTag helps humans intuitively express how they think about their files using tags and machine learning.

This is the official PyTorch implementation of our paper: "Joint Object Detection and Multi-Object Tracking with Graph Neural Networks". Our project website and video demos are here.

A command line stock market / portfolio tracker originally insipred by Ericm's Stonks program, featuring unicode for incredibly high detailed graphs even in a terminal.

HyperTag helps humans intuitively express how they think about their files using tags and machine learning. Represent how you think using tags. Find what you look for using semantic search for your text documents (yes, even PDF's) and images.

Plots is a graph plotting app for GNOME. Plots makes it easy to visualise mathematical formulae. In addition to basic arithmetic operations, it supports trigonometric, hyperbolic, exponential and logarithmic functions, as well as arbitrary sums and products.Plots is designed to integrate well with the GNOME desktop and takes advantage of modern hardware using OpenGL, and currently supports OpenGL 3.3+.

This repository contains custom pipes and models related to using spaCy for scientific documents. In particular, there is a custom tokenizer that adds

PyTextRank PyTextRank is a Python implementation of TextRank as a spaCy pipeline extension, used to: extract the top-ranked phrases from text document

plotly.py Latest Release User forum PyPI Downloads License Data Science Workspaces Our recommended IDE for Plotly’s Python graphing library is Dash En

This is a Pytorch implementation of the paper: Self-Supervised Graph Transformer on Large-Scale Molecular Data.

This repository contains custom pipes and models related to using spaCy for scientific documents. In particular, there is a custom tokenizer that adds

PyTextRank PyTextRank is a Python implementation of TextRank as a spaCy pipeline extension, used to: extract the top-ranked phrases from text document

plotly.py Latest Release User forum PyPI Downloads License Data Science Workspaces Our recommended IDE for Plotly’s Python graphing library is Dash En

Overview | Tutorials | Examples | Installation | FAQ | How to Cite Welcome to ktrain News and Announcements 2020-11-08: ktrain v0.25.x is released and

vprof vprof is a Python package providing rich and interactive visualizations for various Python program characteristics such as running time and memo

THE PROJECT IS ARCHIVED Forks: https://github.com/orsinium/forks DepHell -- project management for Python. Why it is better than all other tools: Form

This project is no longer maintained March 2020 Update: Please go see the amazing Pysa tutorial that should get you up to speed finding security vulne

Neo4j Bolt Driver for Python This repository contains the official Neo4j driver for Python. Each driver release (from 4.0 upwards) is built specifical

jsonpickle jsonpickle is a library for the two-way conversion of complex Python objects and JSON. jsonpickle builds upon the existing JSON encoders, s

OpenGraph is a module of python for parsing the Open Graph Protocol, you can read more about the specification at http://ogp.me/ Installation $ pip in

Django Facebook by Thierry Schellenbach (mellowmorning.com) Status Django and Facebook are both rapidly changing at the moment. Meanwhile, I'm caught

This is a simple graph database in SQLite, inspired by "SQLite as a document database".

Graph Transformer Architecture Source code for the paper "A Generalization of Transformer Networks to Graphs" by Vijay Prakash Dwivedi and Xavier Bres

SAINT-pytorch A Simple pyTorch implementation of "Towards an Appropriate Query, Key, and Value Computation for Knowledge Tracing" based on https://arx

🚀 Gated Graph Transformers Gated Graph Transformers for graph-level property prediction, i.e. graph classification and regression. Associated article

CyGNet This repository reproduces the AAAI'21 paper “Learning from History: Modeling Temporal Knowledge Graphs with Sequential Copy-Generation Network

Adjacent Attention Network An implementation of a simple transformer that is equivalent to graph neural network where the message passing is done with

Context Matters: Graph-based Self-supervised Representation Learning for Medical Images Official PyTorch implementation for paper Context Matters: Gra

Facebook Python SDK This client library is designed to support the Facebook Graph API and the official Facebook JavaScript SDK, which is the canonical

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

StellarGraph Machine Learning Library StellarGraph is a Python library for machine learning on graphs and networks. Table of Contents Introduction Get

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

Little Ball of Fur is a graph sampling extension library for Python. Please look at the Documentation, relevant Paper, Promo video and External Resour

Documentation | External Resources | Datasets PyTorch Geometric Temporal is a temporal (dynamic) extension library for PyTorch Geometric. The library

vprof vprof is a Python package providing rich and interactive visualizations for various Python program characteristics such as running time and memo

Pythonic Data Structures and Algorithms Minimal and clean example implementations of data structures and algorithms in Python 3. Contributing Thanks f