Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining
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A full spaCy pipeline and models for scientific/biomedical documents.
- scientific-documents
- spacy
- custom-pipes
- nlp
A deep learning toolkit for healthcare AI: EHR (MIMIC, eICU, OMOP), clinical text, signals and imaging. 30+ models, reproducible pipelines.
- healthcare
- data-mining
- deep-learning
- preprocessing
TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.
A clinical decision-evidence benchmark: pull the one fact an answer rests on, and see whether the assistant's action moves with the evidence. Built on HealthBench.
Vision-Language Pathology Foundation Model - Nature Medicine
- bioimage-analysis
- bioimage-informatics
- conch
- foundation-model
U-Net Brain Tumor Segmentation
- tensorflow
- tensorlayer
- unet
- medical-imaging
Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
- histopathology-images
- microscopy
- sliding-windows
- medical-image-analysis
:hospital: Medical Text Mining and Information Extraction with spaCy
- natural-language-processing
- medical-natural-language-processing
- machine-learning
- metamap
PyTorch Connectomics: segmentation toolbox for EM connectomics
- computer-vision
- neuroscience
- connectomics
- pytorch
MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.
Modular, fast NLP framework, compatible with Pytorch and spaCy, offering tailored support for French clinical notes.
- nlp
- medical
- text-mining
- clinical-data-warehouse
OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.
A smorgasbord architecture for coreference resolution in biomedical text