Python Medical-knowledge-graph Resources

Disclaimer This code is provided for research and development use only. This code is not intended for use in clinical decision-making or for any other

LinkBERT: A Knowledgeable Language Model Pretrained with Document Links This repo provides the model, code & data of our paper: LinkBERT: Pretraining

01_Python_Introduction Introduction 👋 Python is a modern, robust, high level programming language. It is very easy to pick up even if you are complet

Python Decision Tree and Random Forest Decision Tree A Decision Tree is one of the popular and powerful machine learning algorithms that I have learne

DeltaConv [Paper] [Project page] Code for the SIGGRAPH 2022 paper "DeltaConv: Anisotropic Operators for Geometric Deep Learning on Point Clouds" by Ru

Multi-Graph Fusion Networks for Urban Region Embedding (IJCAI-22) This is the implementation of Multi-Graph Fusion Networks for Urban Region Embedding

Drug Interaction Prediction with Tigerlily Documentation | Example Notebook | Youtube Video | Project Report Tigerlily is a TigerGraph based system de

Structured Sparse R-CNN for Direct Scene Graph Generation Our paper Structured Sparse R-CNN for Direct Scene Graph Generation has been accepted by CVP

Causality-inspired Single-source Domain Generalization for Medical Image Segmentation Arxiv preprint Repository under construction. Might still be bug

MedMCQA MedMCQA : A Large-scale Multi-Subject Multi-Choice Dataset for Medical domain Question Answering A large-scale, Multiple-Choice Question Answe

PrimeKG Website | bioRxiv Paper | Harvard Dataverse Precision Medicine Knowledge Graph (PrimeKG) presents a holistic view of diseases. PrimeKG integra

Graph Stochastic Attention (GSAT) The official implementation of GSAT for our paper: Interpretable and Generalizable Graph Learning via Stochastic Att

SignLangGNN When GNNs 💜 MediaPipe. This is a starter project where I tried to implement some traditional image classification problem i.e. the ASL si

GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation [OpenReview] [arXiv] [Code] The official implementation of GeoDiff: A Geome

CAKE ACL 2022: CAKE: A Scalable Commonsense-Aware Framework For Multi-View Knowledge Graph Completion Introduction This is the PyTorch implementation

PyGOD is a Python library for graph outlier detection (anomaly detection). This exciting yet challenging field has many key applications, e.g., detect

PyGCL is a PyTorch-based open-source Graph Contrastive Learning (GCL) library, which features modularized GCL components from published papers, standa

LEAR The implementation our EMNLP 2021 paper "Enhanced Language Representation with Label Knowledge for Span Extraction". See below for an overview of

AMRBART An implementation for ACL2022 paper "Graph Pre-training for AMR Parsing and Generation". You may find our paper here (Arxiv). Requirements pyt

MKGFormer Code for the SIGIR 2022 paper "Hybrid Transformer with Multi-level Fusion for Multimodal Knowledge Graph Completion" Model Architecture Illu

medical by LAION This repository will be a summary and outlook on all our open, medical, AI advancements. See the medical-general channel in the medic

What is this? This is where I'll be collecting resources related to the Study Group on Dr. Justin Thaler's Proofs Arguments And Zero Knowledge Book. T

DeepGNN Overview DeepGNN is a framework for training machine learning models on large scale graph data. DeepGNN contains all the necessary features in

OD-Rec Codes for SIGIR'22 Paper 'On-Device Next-Item Recommendation with Self-Supervised Knowledge Distillation' Paper, saved teacher models and Andro

Intention Adaptive Graph Neural Network (IAGNN) This is the official repository of paper Intention Adaptive Graph Neural Network for Category-Aware Se

Twingrind This project brings profiling to TwinCAT PLCs. The general idea of the implementation is as follows. Twingrind is a TwinCAT library that inc

Diversifying Commonsense Reasoning Generation on Knowledge Graph Introduction -- This is the pytorch implementation of our ACL 2022 paper "Diversifyin

Ensemble Knowledge Guided Sub-network Search and Fine-tuning for Filter Pruning This repository is official Tensorflow implementation of paper: Ensemb

Project: Text Analysis - This project aims to conduct a text information retrieval and text mining on medical research publication regarding Covid19 -

SDM - Lab 1 @ UPC 👨🏻‍💻 Table of contents Introduction Property Graph Dataset 1. Introduction This repo is all about what we have done in SDM lab 1

On-the-Fly Adaptation Official Pytorch Code base for On-the-Fly Test-time Adaptation for Medical Image Segmentation Paper Introduction One major probl

On Size-Oriented Long-Tailed Graph Classification of Graph Neural Networks We provide the code (in PyTorch) and datasets for our paper "On Size-Orient

Multi-view graph embedding clustering network: Joint self-supervision and block diagonal representation Simple implementation of our paper MVGC. The d

Commit Bot Automatically generate GitHub activity! We've all wanted to be the developer that commits every day, but that requires a lot of work. Let's

Source code for "Finding Valid Adjustments under Non-ignorability with Minimal DAG Knowledge" Reference: Abhin Shah, Karthikeyan Shanmugam, Kartik Ahu

SGMC: Spectral Graph Matrix Completion Code for AAAI21 paper "Scalable and Explainable 1-Bit Matrix Completion via Graph Signal Learning". Data Format

GraphLily: A Graph Linear Algebra Overlay on HBM-Equipped FPGAs GraphLily is the first FPGA overlay for graph processing. GraphLily supports a rich se

Locally Differentially Private Distributed Deep Learning via Knowledge Distillation (LDP-DL) A preprint version of our paper: Link here This is a samp

Graph Data Science: an abstraction layer in Python for building knowledge graphs, integrated with popular graph libraries – atop Pandas, RDFlib, pySHACL, RAPIDS, NetworkX, iGraph, PyVis, pslpython, pyarrow, etc.

TGIN Tensorflow implementation of our method: "Triangle Graph Interest Network for Click-through Rate Prediction". Files in the folder dataset/ electr

MarkovGNN This is the official PyTorch-Geometric implementation of MarkovGNN paper under the title "MarkovGNN: Graph Neural Networks on Markov Diffusi

TorchMD-net TorchMD-Net provides state-of-the-art graph neural networks and equivariant transformer neural networks potentials for learning molecular

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

Code for CCA-SSG model proposed in the NeurIPS 2021 paper From Canonical Correlation Analysis to Self-supervised Graph Neural Networks.

FAST is an open-source cross-platform framework with the main goal of making it easier to do high-performance processing and visualization of medical images on heterogeneous systems utilizing both multi-core CPUs and GPUs. To achieve this, FAST use modern C++, OpenCL and OpenGL.

The project has set itself the goal of analyzing the thoughts and interaction of Italian users through the social posts expressed through the Twitter platform on the day of the entry into force of the new measures. In particular, we want to research the reference hubs present on the network, but also the sentiment and emotions of peoples with respect to the new limitations.

Create a semantic search engine with a neural network (i.e. BERT) whose knowledge base can be updated. This engine can later be used for downstream tasks in NLP such as Q&A, summarization, generation, and natural language understanding (NLU).

Rank-One Model Editing (ROME) This repository provides an implementation of Rank-One Model Editing (ROME) on auto-regressive transformers (GPU-only).

Large-scale Knowledge Graph Construction with Prompting across tasks (predictive and generative), and modalities (language, image, vision + language, etc.)

Multi-atlas segmentation (MAS) is a promising framework for medical image segmentation. Generally, MAS methods register multiple atlases, i.e., medical images with corresponding labels, to a target image;

FIRA is a learning-based commit message generation approach, which first represents code changes via fine-grained graphs and then learns to generate commit messages automatically.

A small python package that allows the user to look up common medical abbreviations.

BoxPlotGraphAutomation Automatization of BoxPlot graph usin Python / Excel. This file is an automation of BoxPlot-Graph using python graph library mat

A Graph Learning library for Humans These novel algorithms include but are not limited to: A graph construction and graph searching class can be found

HAIS_2GNN: 3D Visual Grounding with Graph and Attention This repository is for the HAIS_2GNN research project. Tao Gu, Yue Chen Introduction The motiv

A tool to get a minimalist view of any architecture This tool has only be tested with the models included in this repo. Therefore, I can't guarantee t

This is the repository for codes for ML, domain generation, graph generation of Asymmetric Buckling Columns (ABC) dataset in the paper "Learning Mechanically Driven Emergent Behavior with Message Passing Neural Networks".

Graph Coloring - Weighted Vertex Coloring Problem This project proposes several local searches and an MCTS algorithm for the weighted vertex coloring

DCSAU-Net: A Deeper and More Compact Split-Attention U-Net for Medical Image Segmentation By Qing Xu, Wenting Duan and Na He Requirements pytorch==1.1

Code Impementation for "Mold into a Graph: Efficient Bayesian Optimization over Mixed Spaces" This repo contains the implementation of GEBO algorithm.

Posterior temperature optimized Bayesian models for inverse problems in medical imaging Max-Heinrich Laves*, Malte Tölle*, Alexander Schlaefer, Sandy

Graph Convolution Simulator (GCS) Source code for "Understanding Knowledge Integration in Language Models with Graph Convolutions" Requirements: PyTor

Python-AmongUsProblem Project in which we modelise an Among Us problem using graph theories. The rules are as following: Total of 100 players 10 playe

TGraM Multi-Object Tracking in Satellite Videos with Graph-Based Multi-Task Modeling, Qibin He, Xian Sun, Zhiyuan Yan, Beibei Li, Kun Fu Abstract Rece

Expense Tracker is a very good tool to keep track of your expenseditures and the total money you saved.

LabGraph is a a Python-first framework used to build sophisticated research systems with real-time streaming, graph API, and parallelism.

Iterative refinement graph neural network for antibody sequence-structure co-des

GraphNLI: A Graph-based Natural Language Inference Model for Polarity Prediction in Online Debates Vibhor Agarwal, Sagar Joglekar, Anthony P. Young an

Equivariant Subgraph Aggregation Networks (ESAN) This repository contains the official code of the paper Equivariant Subgraph Aggregation Networks (IC

Hatchet Hatchet is a Python-based library that allows Pandas dataframes to be indexed by structured tree and graph data. It is intended for analyzing

DIR-GNN "Discovering Invariant Rationales for Graph Neural Networks" (ICLR 2022)

Live Demo (currently not running, on it) Espial is an engine for automated organization and discovery in knowledge bases. It can be adapted to run wit

Medical natural language parsing and utility library A natural language medical

TorchGRL TorchGRL is the source code for our paper Graph Convolution-Based Deep Reinforcement Learning for Multi-Agent Decision-Making in Mixed Traffi

GNN_PPI Codes and models for the paper "Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction". Lear

1st place solution in CCF BDCI 2021 ULSEG challenge This is the source code of the 1st place solution for ultrasound image angioma segmentation task (

machine-learning-with-graphs My solutions for Stanford University course CS224W: Machine Learning with Graphs Fall 2021 colabs Course materials can be

Medical-Insurance-Project-OOP Python Classes: Medical Insurance Project using Object Oriented Programming Concepts Classes are an incredibly useful pr

GenGNN: A Generic FPGA Framework for Graph Neural Network Acceleration Stefan Abi-Karam*, Yuqi He*, Rishov Sarkar*, Lakshmi Sathidevi, Zihang Qiao, Co

Tracking Progress in Question Answering over Knowledge Graphs Table of contents Question Answering Systems with Descriptions The QA Systems Table cont

SegTransVAE: Hybrid CNN - Transformer with Regularization for medical image segmentation This repo is the official implementation for SegTransVAE. Seg

miseval: a metric library for Medical Image Segmentation EVALuation The open-source and free to use Python package miseval was developed to establish

OntoProtein This is the implement of the paper "OntoProtein: Protein Pretraining With Ontology Embedding". OntoProtein is an effective method that mak

On Evaluation Metrics for Graph Generative Models Authors: Rylee Thompson, Boris Knyazev, Elahe Ghalebi, Jungtaek Kim, Graham Taylor This is the offic

GNDC For submission to IEEE TKDE. Overview Here we provide the implementation of GND-Nets (Graph Neural Diffusion Networks) in TensorFlow. The reposit

Author Name Disambiguation with Knowledge Graph Embeddings using Literals This is the repository for the master thesis project on Knowledge Graph Embe

HistoKT: Cross Knowledge Transfer in Computational Pathology Exciting News! HistoKT has been accepted to ICASSP 2022. HistoKT: Cross Knowledge Transfe

An Analysis on Ensemble Learning optimized Medical Image Classification with Deep Convolutional Neural Networks Novel and high-performance medical ima

GreaseLM: Graph REASoning Enhanced Language Models This repo provides the source code & data of our paper "GreaseLM: Graph REASoning Enhanced Language

TGRNet: A Table Graph Reconstruction Network for Table Structure Recognition Xue, Wenyuan, et al. "TGRNet: A Table Graph Reconstruction Network for Ta

STAR_KGC This repo contains the source code of the paper accepted by WWW'2021. "Structure-Augmented Text Representation Learning for Efficient Knowled

CSKG: The CommonSense Knowledge Graph CSKG is a commonsense knowledge graph that combines seven popular sources into a consolidated representation: AT

LSHFM.detection This is the PyTorch source code for Distilling Knowledge by Mimicking Features. And this project contains code for object detection wi

Graph Analysis From Scratch Goal In this notebook we wanted to implement some functionalities to analyze a weighted graph only by using algorithms imp

Roam to Logseq The script loads a json export of a Roam graph and cleans it up f

Toward Model Interpretability in Medical NLP LING380: Topics in Computational Linguistics Final Project James Cross ([email protected]) and Daniel Kim

STonKGs STonKGs is a Sophisticated Transformer that can be jointly trained on biomedical text and knowledge graphs. This multimodal Transformer combin

This repo supplements our Survey on Transformers in Medical Imaging Fahad Shamshad, Salman Khan, Syed Waqas Zamir, Muhammad Haris Khan, Munawar Hayat,

Introduction: X-Ray Report Generation This repository is for our EMNLP 2021 paper "Automated Generation of Accurate & Fluent Medical X-ray Reports". O

RATCHET: RAdiological Text Captioning for Human Examined Thoraxes RATCHET is a Medical Transformer for Chest X-ray Diagnosis and Reporting. Based on t