biomedical

A full spaCy pipeline and models for scientific/biomedical documents.

Chinese Biomedical Language Understanding Evaluation benchmark (ChineseBLUE)

🧫 A curated list of resources relevant to doing Biomedical Information Extraction (including BioNLP)

BioGrakn Knowledge Graph

Full abstract relation extraction from biological texts with bi-affine relation attention networks

SleepEEGNet: Automated Sleep Stage Scoring with Sequence to Sequence Deep Learning Approach

Workshop (6 hours): Deep learning in R using Keras. Building & training deep nets, image classification, transfer learning, text analysis, visualization

SCIRun is a Problem Solving Environment, for modeling, simulation and visualization of scientific problems. This is version 5, the upgraded version of SCIRun v4.

MedType: Improving Medical Entity Linking with Semantic Type Prediction

A software package for statistically significant shapelet mining

Flexible and powerful platform for biomedical information extraction from text

Code for the paper Biomedical Event Extraction with Hierarchical Knowledge Graphs

Small Animal Magnetic Resonance Imaging via Python.

Weakly supervised medical named entity classification

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

PDD Graph : Bridging MIMIC-III and Linked Data Cloud

Biomedical Visualization and Analysis Framework

Medical Relations and Entities Extraction

Named Entity Recognition with Small Strongly Labeled and Large Weakly Labeled Data

Collection of various biomedical data models in parseable formats.

Research data management in biomedical and machine learning applications

Behavioral data analysis and plotting in Python.

Repository used to collect biomedical corpus on the Internet!

Improving Biomedical Pretrained Language Models with Knowledge [BioNLP 2021]

Table compiling the list of biomedically-related corpora available for named entity recognition (and some also suitable for association detection). This has been published as part of the paper: Dieter Galea, Ivan Laponogov, Kirill Veselkov; Exploiting and assessing multi-source data for supervised biomedical named entity recognition, Bioinformatics, bty152, https://doi.org/10.1093/bioinformatics/bty152 . If you would like to add other (or your) corpora, please submit a pull request and I'll happily approve it.

A collection of tools for manipulation of morphological features in patient-specific geometries

Biomedical Segmentation with PyTorch and different Convolutional Neural Network Architectures.

Atrial Fibrillation Detection Blood Pressure Monitor (Oscillometric Method)

Multi-modal Image Registration And Connectivity anaLysis

PyTorch toolkit for biomedical imaging 🤖 🛠️ ❤️