Repository Index

A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

• cookiecutter-data-science
• cookiecutter
• cookiecutter-template
• data-science

Biological foundation modeling from molecular to genome scale

Hopsworks - Data-Intensive AI platform with a Feature Store

• feature-store
• aws
• azure
• data-science

Brian is a free, open source simulator for spiking neural networks.

• python
• neuroscience
• science
• differential-equations

Self-contained Japanese Morphological Analyzer written in pure Go

• japanese
• tokenizer
• nlp-library
• japanese-language

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

• deep-learning
• protein-sequences
• protein-structure
• semi-supervised-learning

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

Phoebus is a distributed framework for large scale graph processing written in Erlang.

Convert a number to an approximated text expression: from '0.23' to 'less than a quarter'.

• natural-language-generation
• clojure
• number-to-words
• number-to-text

Collection of mathematical morphology methods and plugins for ImageJ

• image-processing
• image-analysis
• imagej
• fiji

An NLP library for Uralic languages such as Finnish, Skolt Sami, Moksha and so on. Also supporting some non-Uralic languages such as Spanish, French, Arabic, Swedish, Norwegian, Russian and English. LLMs, FSTs and More!

• nlp-library
• uralic-languages
• finnish
• sami

RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation

• biological-images
• root
• painter
• segmentation

Predicting Cell Health with Morphological Profiles

• carpenter-lab
• morphological-profiling
• crispr
• cell-painting