Repository Index

Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining

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

• scientific-documents
• spacy
• custom-pipes
• nlp

StarDist - Object Detection with Star-convex Shapes

• bioimage-analysis
• cell-segmentation
• nuclei-segmentation
• object-detection

Plant phenotyping with image analysis

• science
• bioinformatics
• image-analysis
• plant-phenotyping

Precision Medicine Knowledge Graph (PrimeKG)

• knowledge-graph
• precision-medicine
• therapeutics
• bioinformatics

Segment Anything for Microscopy

• microscopy-images
• segment-anything
• segmentation
• cell-segmentation

Vision-Language Pathology Foundation Model - Nature Medicine

• bioimage-analysis
• bioimage-informatics
• conch
• foundation-model

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

Apache cTAKES is a Natural Language Processing (NLP) platform for clinical text.

• clinical
• nlp
• bioinformatics
• ai

A tool for cell instance aware segmentation in densely packed 3D volumetric images

• segmentation
• deep-learning
• bioinformatics
• neural-network

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

• computational-biology
• bioinformatics
• graph-convolution
• deep-learning

Tool for segmentation in bioimaging

• napari
• bioimage-analysis

A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources

• bioimage-analysis
• cell-classification
• computer-vision
• digital-pathology