Python Biomedical-knowledge-graph Resources

GNNLens2 is an interactive visualization tool for graph neural networks (GNN).

DGCNN is the author's re-implementation of Dynamic Graph CNN, which achieves state-of-the-art performance on point-cloud-related high-level tasks including category classification, semantic segmentation and part segmentation.

Student Helping Teacher: Teacher Evolution via Self-Knowledge Distillation (TESKD) By Zheng Li[1,4], Xiang Li[2], Lingfeng Yang[2,4], Jian Yang[2], Zh

IGMTF The source code and data of the paper "Instance-wise Graph-based Framework for Multivariate Time Series Forecasting". Requirements The framework

RNG-KBQA: Generation Augmented Iterative Ranking for Knowledge Base Question Answering Authors: Xi Ye, Semih Yavuz, Kazuma Hashimoto, Yingbo Zhou and

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

GLaRA: Graph-based Labeling Rule Augmentation for Weakly Supervised Named Entity Recognition

This is the source code for: Context-aware Entity Typing in Knowledge Graphs.

Splitter ⠀⠀ A PyTorch implementation of Splitter: Learning Node Representations that Capture Multiple Social Contexts (WWW 2019). Abstract Recent inte

ConvE Convolutional 2D Knowledge Graph Embeddings resources. Paper: Convolutional 2D Knowledge Graph Embeddings Used in the paper, but do not use thes

Graphlevel-SSL Overview Apply Graph Self-Supervised Learning methods to graph-level task(TUDataset, MolculeNet Dataset). It is unified framework to co

Dynamic Attentive Graph Learning for Image Restoration This repository is for GATIR introduced in the following paper: Chong Mou, Jian Zhang, Zhuoyuan

Attention Transfer PyTorch code for "Paying More Attention to Attention: Improving the Performance of Convolutional Neural Networks via Attention Tran

SE Aggregation This is the implementation for Rethinking High-order Graph Convolutional Networks. Here we show the codes for citation networks as an e

BioLAMA BioLAMA is biomedical factual knowledge triples for probing biomedical LMs. The triples are collected and pre-processed from three sources: CT

Pretraining summarization models using a corpus of nonsense

AAGCN-ACSA EMNLP 2021 Introduction This repository was used in our paper: Beta Distribution Guided Aspect-aware Graph for Aspect Category Sentiment An

Pyan takes one or more Python source files, performs a (rather superficial) static analysis, and constructs a directed graph of the objects in the combined source, and how they define or use each other. The graph can be output for rendering by GraphViz or yEd.

obsidiantools is a Python package for getting structured metadata about your Obsidian.md notes and analysing your vault.

DeepPanoContext (DPC) [Project Page (with interactive results)][Paper] DeepPanoContext: Panoramic 3D Scene Understanding with Holistic Scene Context G

This is an open-source toolkit for Heterogeneous Graph Neural Network(OpenHGNN) based on DGL [Deep Graph Library] and PyTorch.

This repository contains the code for the paper in Findings of EMNLP 2021: "EfficientBERT: Progressively Searching Multilayer Perceptron via Warm-up Knowledge Distillation".

ROSITA News & Updates (24/08/2021) Release the demo to perform fine-grained semantic alignments using the pretrained ROSITA model. (15/08/2021) Releas

CTR-GCN This repo is the official implementation for Channel-wise Topology Refinement Graph Convolution for Skeleton-Based Action Recognition. The pap

MVGCN MVGCN: a novel multi-view graph convolutional network (MVGCN) framework for link prediction in biomedical bipartite networks. Developer: Fu Hait

STaCK: Sentence Ordering with Temporal Commonsense Knowledge This repository contains the pytorch implementation of the paper STaCK: Sentence Ordering

Adaptive Graph Convolution for Point Cloud Analysis This repository contains the implementation of AdaptConv for point cloud analysis. Adaptive Graph

DKPNet ICCV 2021 Variational Attention: Propagating Domain-Specific Knowledge for Multi-Domain Learning in Crowd Counting Baseline of DKPNet is availa

Conceptarium A fluid medium for storing, relating, and surfacing thoughts. Read more... Instructions The conceptarium takes up about 1GB RAM when runn

Graph2Pix: A Graph-Based Image to Image Translation Framework Installation Install the dependencies in env.yml $ conda env create -f env.yml $ conda a

Single Node Injection Attack against Graph Neural Networks This repository is our Pytorch implementation of our paper: Single Node Injection Attack ag

ANEMONE A PyTorch implementation of "ANEMONE: Graph Anomaly Detection with Multi-Scale Contrastive Learning", CIKM-21 Dependencies python==3.6.1 dgl==

代码地址： https://github.com/Sharpiless/yolov5-knowledge-distillation 教师模型： python train.py --weights weights/yolov5m.pt \ --cfg models/yolov5m.ya

近年来，图计算在搜索、推荐和风控等场景中获得显著的效果，但也面临超大规模异构图训练，与现有的深度学习框架Tensorflow和PyTorch结合等难题。 Galileo（伽利略）是一个图深度学习框架，具备超大规模、易使用、易扩展、高性能、双后端等优点，旨在解决超大规模图算法在工业级场景的落地难题，提

✨A Python framework to explore, label, and monitor data for NLP projects

Interactive Machine Comprehension with Dynamic Knowledge Graphs Implementation for the EMNLP 2021 paper. Dependencies apt-get -y update apt-get instal

PocketNet This is the official repository of the paper: PocketNet: Extreme Lightweight Face Recognition Network using Neural Architecture Search and M

ZSL-KG is a general-purpose zero-shot learning framework with a novel transformer graph convolutional network (TrGCN) to learn class representa

GraphKer Open Source Tool - Cybersecurity Graph Database in Neo4j |G|r|a|p|h|K|e|r| { open source tool for a cybersecurity graph database in neo4j } W

COTREC Codes for CIKM'21 paper 'Self-Supervised Graph Co-Training for Session-based Recommendation'. Requirements: Python 3.7, Pytorch 1.6.0 Best Hype

MWPToolkit is a PyTorch-based toolkit for Math Word Problem (MWP) solving. It is a comprehensive framework for research purpose that integrates popular MWP benchmark datasets and typical deep learning-based MWP algorithms.

Poplar Implementation of Bundle Adjustment using Gaussian Belief Propagation on Graphcore's IPU Implementation of CVPR 2020 paper: Bundle Adjustment o

PSPNet-logits and feature-distillation Introduction This repository is based on PSPNet and modified from semseg and Pixelwise_Knowledge_Distillation_P

SGLKT-VisDial Pytorch Implementation for the paper: Reasoning Visual Dialog with Sparse Graph Learning and Knowledge Transfer Gi-Cheon Kang, Junseok P

GraphGT: Machine Learning Datasets for Graph Generation and Transformation Dataset Website | Paper Installation Using pip To install the core environm

Differentiable Factor Graph Optimization for Learning Smoothers Overview Status Setup Datasets Training Evaluation Acknowledgements Overview Code rele

This project is a collection of the open source pytorch code for knowledge distillation, especially for the perception tasks, including semantic segmentation, depth estimation, object detection and instance segmentation.

DomainWordsDict, Chinese words dict that contains more than 68 domains, which can be used as text classification、knowledge enhance task。涵盖68个领域、共计916万词的专业词典知识库，可用于文本分类、知识增强、领域词汇库扩充等自然语言处理应用。

Using a predicted aligned error matrix corresponding to an AlphaFold2 model , returns a series of lists of residue indices, where each list corresponds to a set of residues clustering together into a pseudo-rigid domain.

Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study Codes for [Preprint] Bag of Tricks for Training Deeper Graph

Filtration Curves for Graph Representation This repository provides the code from the KDD'21 paper Filtration Curves for Graph Representation. Depende

MERIT A PyTorch implementation of our IJCAI-21 paper Multi-Scale Contrastive Siamese Networks for Self-Supervised Graph Representation Learning. Depen

Graph-Based Local Trajectory Planner The graph-based local trajectory planner is python-based and comes with open interfaces as well as debug, visuali

SpiderFoot Neo4j Tools Import, visualize, and analyze SpiderFoot OSINT data in Neo4j, a graph database Step 1: Installation NOTE: This installs the sf

SIGIR2021-EGLN The implement of paper "Enhanced Graph Learning for Collaborative Filtering via Mutual Information Maximization" Neural graph based Col

Extract knowledge from raw text This repository is a nearly copy-paste of "From Text to Knowledge: The Information Extraction Pipeline" with some cosm

Torch-RGCN Torch-RGCN is a PyTorch implementation of the RGCN, originally proposed by Schlichtkrull et al. in Modeling Relational Data with Graph Conv

README.md shall be finished soon. WSSGG 0 Overview 1 Installation 1.1 Faster-RCNN 1.2 Language Parser 1.3 GloVe Embeddings 2 Settings 2.1 VG-GT-Graph

Improving Graph Neural Network Expressivity via Subgraph Isomorphism Counting Official PyTorch implementation of the paper: Improving Graph Neural Net

Named Entity Recognition with Small Strongly Labeled and Large Weakly Labeled Data arXiv This is the code base for weakly supervised NER. We provide a

Graph ConvNets in PyTorch October 15, 2017 Xavier Bresson http://www.ntu.edu.sg/home/xbresson https://github.com/xbresson https://twitter.com/xbresson

Graph Convolutional Networks in PyTorch PyTorch implementation of Graph Convolutional Networks (GCNs) for semi-supervised classification [1]. For a hi

PanGraphViewer -- show panenome graph in an easy way Table of Contents Versions and dependences Desktop-based panGraphViewer Library installation for

Graph Convolutional Networks for Hyperspectral Image Classification Danfeng Hong, Lianru Gao, Jing Yao, Bing Zhang, Antonio Plaza, Jocelyn Chanussot T

Heterogeneous Graph Benchmark Revisiting, benchmarking, and refining Heterogeneous Graph Neural Networks. Roadmap We organize our repo by task, and on

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

News The code of MCTrans has been released. if you are interested in contributing to the standardization of the medical image analysis community, plea

A powerful and flexible machine learning platform for drug discovery

CG-MuAlign A reference implementation for "Collective Multi-type Entity Alignment Between Knowledge Graphs", published in WWW 2020. If you find our pa

GNNGuard: Defending Graph Neural Networks against Adversarial Attacks Authors: Xiang Zhang ([email protected]), Marinka Zitnik (marinka@hms.

PyGCL is an open-source library for graph contrastive learning (GCL), which features modularized GCL components from published papers, standardized evaluation, and experiment management.

中文开放信息抽取系统, open-information-extraction-system, build open-knowledge-graph(SPO, subject-predicate-object) by pyltp(version==3.4.0)

PyGCL: Graph Contrastive Learning for PyTorch PyGCL is an open-source library for graph contrastive learning (GCL), which features modularized GCL com

knowledge-neurons An open source repository replicating the 2021 paper Knowledge Neurons in Pretrained Transformers by Dai et al., and extending the t

Versatile Generative Language Model This is the implementation of the paper: Exploring Versatile Generative Language Model Via Parameter-Efficient Tra

FunMatch-Distillation TF2 implementation of knowledge distillation using the "function matching" hypothesis from the paper Knowledge distillation: A g

knowledge-neurons An open source repository replicating the 2021 paper Knowledge Neurons in Pretrained Transformers by Dai et al., and extending the t

HKD Code for ICCV 2021 paper "Distilling Holistic Knowledge with Graph Neural Networks" cifia-100 result The implementation of compared methods are ba

A PyTorch Implementation of GGNN This is a PyTorch implementation of the Gated Graph Sequence Neural Networks (GGNN) as described in the paper Gated G

Deep Learning for Physical Processes: Integrating Prior Scientific Knowledge: Official Pytorch implementation of ICLR 2018 paper Deep Learning for Phy

ConvE Convolutional 2D Knowledge Graph Embeddings resources. Paper: Convolutional 2D Knowledge Graph Embeddings Used in the paper, but do not use thes

GNN4Traffic - This is the repository for the collection of Graph Neural Network for Traffic Forecasting

DataFree A benchmark of data-free knowledge distillation from paper "Contrastive Model Inversion for Data-Free Knowledge Distillation" Authors: Gongfa

TilinGNN: Learning to Tile with Self-Supervised Graph Neural Network (SIGGRAPH 2020) About The goal of our research problem is illustrated below: give

Open-source tool for exploring, labeling, and monitoring data for AI projects

Graph Wavelet Neural Network ⠀⠀ A PyTorch implementation of Graph Wavelet Neural Network (ICLR 2019). Abstract We present graph wavelet neural network

Attention Walk ⠀⠀ A PyTorch Implementation of Watch Your Step: Learning Node Embeddings via Graph Attention (NIPS 2018). Abstract Graph embedding meth

SGCN ⠀ A PyTorch implementation of Signed Graph Convolutional Network (ICDM 2018). Abstract Due to the fact much of today's data can be represented as

Scalable Incomplete Network Embedding ⠀⠀ A PyTorch implementation of Scalable Incomplete Network Embedding (ICDM 2018). Abstract Attributed network em

GAM ⠀⠀ A PyTorch implementation of Graph Classification Using Structural Attention (KDD 2018). Abstract Graph classification is a problem with practic

TuckER: Tensor Factorization for Knowledge Graph Completion This codebase contains PyTorch implementation of the paper: TuckER: Tensor Factorization f

SimGNN ⠀⠀⠀ A PyTorch implementation of SimGNN: A Neural Network Approach to Fast Graph Similarity Computation (WSDM 2019). Abstract Graph similarity s

APPNP ⠀ A PyTorch implementation of Predict then Propagate: Graph Neural Networks meet Personalized PageRank (ICLR 2019). Abstract Neural message pass

MixHop and N-GCN ⠀ A PyTorch implementation of "MixHop: Higher-Order Graph Convolutional Architectures via Sparsified Neighborhood Mixing" (ICML 2019)

Splitter ⠀⠀ A PyTorch implementation of Splitter: Learning Node Representations that Capture Multiple Social Contexts (WWW 2019). Abstract Recent inte

CapsGNN ⠀⠀ A PyTorch implementation of Capsule Graph Neural Network (ICLR 2019). Abstract The high-quality node embeddings learned from the Graph Neur

SEAL ⠀⠀⠀ A PyTorch implementation of Semi-Supervised Graph Classification: A Hierarchical Graph Perspective (WWW 2019) Abstract Node classification an

ClusterGCN ⠀⠀ A PyTorch implementation of "Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks" (KDD 2019). A

On the Bottleneck of Graph Neural Networks and its Practical Implications This is the official implementation of the paper: On the Bottleneck of Graph

Library | Paper | Slack We released two versions of OAG-BERT in CogDL package. OAG-BERT is a heterogeneous entity-augmented academic language model wh