Python Biomedical Resources

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

SOFIMA SOFIMA (Scalable Optical Flow-based Image Montaging and Alignment) is a tool for stitching, aligning and warping large 2d, 3d and 4d microscopy

SciFive SciFive provided a Text-Text framework for biomedical language and natural language in NLP. Under the T5's framework and desrbibed in the pape

Hyper-Convolution Networks for Biomedical Image Segmentation Code for our WACV 2022 paper "Hyper-Convolution Networks for Biomedical Image Segmentatio

Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.

This is a Kaggle competition in which we have to identify if the given lesion image is malignant or not for Melanoma which is a type of skin cancer.

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

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

Biomedical Entity Linking This repo provides the code for the paper BERT might be Overkill: A Tiny but Effective Biomedical Entity Linker based on Res

A set of Python codes for the generation of biomedical ontologies from the MeSH keywords of the PubMed scholarly publications

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

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

BERN2 We present BERN2 (Advanced Biomedical Entity Recognition and Normalization

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

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

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

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

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

Tools for curating biomedical training data for large-scale language modeling

Introduction The field of connectomics aims to reconstruct the wiring diagram of the brain by mapping the neural connections at the level of individua

RobustBioNLP Improving the robustness and performance of biomedical NLP models through adversarial training In this repository you can find suppliment

Medical Image Segmentation with Guided Attention This repository contains the code of our paper: "'Multi-scale self-guided attention for medical image

Deep Learning Tutorial for Kaggle Ultrasound Nerve Segmentation competition, using Keras This tutorial shows how to use Keras library to build deep ne

Flexible-CLmser: Regularized Feedback Connections for Biomedical Image Segmentation The skip connections in U-Net pass features from the levels of enc

waltlabtools A collection of tools for biomedical research assay analysis in Python. Key Features Analysis for assays such as digital ELISA, including

BMVC 2021 BI-GConv: Boundary-Aware Input-Dependent Graph Convolution for Biomedical Image Segmentation Necassary Dependencies: PyTorch 1.2.0 Python 3.

MedMNIST Project (Website) | Dataset (Zenodo) | Paper (arXiv) | MedMNIST v1 (ISBI'21) Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Bili

Kimimaro: Skeletonize Densely Labeled Images # Produce SWC files from volumetric images. kimimaro forge labels.npy --progress # writes to ./kimimaro_o

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

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

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

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

Adaptive Segmentation Mask Attack This repository contains the implementation of the Adaptive Segmentation Mask Attack (ASMA), a targeted adversarial

U Net Lowered with Keras Complete U-net Implementation with keras Original Paper Link : https://arxiv.org/abs/1505.04597 Special Implementations : The

LMs for biomedical KG completion This repository contains code to run the experiments described in: Scientific Language Models for Biomedical Knowledg

English | 中文说明 CBLUE AI (Artificial Intelligence) is playing an indispensabe role in the biomedical field, helping improve medical technology. For fur

SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization This is the code for our paper ``SumGNN: Multi-typed Drug

MultiResUNet Rethinking the U-Net architecture for multimodal biomedical image segmentation This repository contains the original implementation of "M

Trove Trove is a research framework for building weakly supervised (bio)medical named entity recognition (NER) and other entity attribute classifiers

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

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

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