Biomedical Informatics Research and Data Science @ Dartmouth

3dMRISegmentation

Code for NeuroImage: Clinical paper "Automatic post-stroke lesion segmentation on MR images using 3D residual convolutional neural network."

cell-heterogeneity-emtscore

deepslide

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.

DifficultyTranslation

Code for "Difficulty Translation in Histopathology Images" full paper at Artificial Intelligence in Medicine (AIME) 2020.

HealthTranscriptAnnotator

Annotates concepts in patient-physician office visit transcripts.

HistoGAN

Code for "Generative Image Translation for Data Augmentation in Colorectal Histopathology Images" full paper at ML4H Workshop at NeurIPS 2019.

medical-image-preprocessing

Functions for pre-processing large images

MORE

Code for "Multi-Ontology Refined Embeddings (MORE): A Hybrid Multi-Ontology and Corpus-based Semantic Representation Model for Biomedical Concepts" in the Journal of Biomedical Informatics.

Slide2Graph

Graph Convolutional Networks for Whole-Slide Analysis in PyTorch

titan-rtx-benchmark

BMIRDS/deepslide

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.

BMIRDS/HistoGAN

Code for "Generative Image Translation for Data Augmentation in Colorectal Histopathology Images" full paper at ML4H Workshop at NeurIPS 2019.

BMIRDS/3dMRISegmentation

Code for NeuroImage: Clinical paper "Automatic post-stroke lesion segmentation on MR images using 3D residual convolutional neural network."

BMIRDS/medical-image-preprocessing

Functions for pre-processing large images

BMIRDS/MORE

Code for "Multi-Ontology Refined Embeddings (MORE): A Hybrid Multi-Ontology and Corpus-based Semantic Representation Model for Biomedical Concepts" in the Journal of Biomedical Informatics.

BMIRDS/titan-rtx-benchmark

BMIRDS/Slide2Graph

Graph Convolutional Networks for Whole-Slide Analysis in PyTorch

BMIRDS/DifficultyTranslation

Code for "Difficulty Translation in Histopathology Images" full paper at Artificial Intelligence in Medicine (AIME) 2020.

BMIRDS/cell-heterogeneity-emtscore

BMIRDS/HealthTranscriptAnnotator

Annotates concepts in patient-physician office visit transcripts.