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alphafold

Open source code for AlphaFold.

ample-theme

A theme for Emacs providing dark, light, and flat versions.

bern2

BERN2: an advanced neural biomedical namedentity recognition and normalization tool

bio-transformers

bio-transformers is a wrapper on top of the ESM/Protbert model, trained on millions on proteins and used to predict embeddings.

biobert

BioBERT: a pre-trained biomedical language representation model

bioelectra

BioELECTRA

biopython

Official git repository for Biopython (originally converted from CVS)

borb

borb is a library for reading, creating and manipulating PDF files in python.

colbert

ColBERT: Contextualized Late Interaction over BERT (SIGIR'20)

cord

CORD: A Consolidated Receipt Dataset for Post-OCR Parsing

cosine

This is the code for our paper `Fine-Tuning Pre-trained Language Model with Weak Supervision: A Contrastive-Regularized Self-Training Approach' (In Proc. of NAACL-HLT 2021).

dataprofiler

What's in your data? Extract schema, statistics and entities from datasets

deepimmuno

Deep-learning empowered prediction and generation of immunogenic epitopes for T cell immunity

deeptcr

Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data

doctr

docTR by Mindee (Document Text Recognition) - a seamless, high-performing & accessible library for OCR-related tasks powered by Deep Learning.

electra

ELECTRA: Pre-training Text Encoders as Discriminators Rather Than Generators

electra_pytorch

Pretrain and finetune ELECTRA with fastai and huggingface. (Results of the paper replicated !)

emacs-python-black

Emacs package to reformat Python using black-macchiato

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

fds

Fast Data Science, AKA fds, is a CLI for Data Scientists to version control data and code at once, by conveniently wrapping git and dvc

icdar-2019-sroie

ICDAR 2019 Robust Reading Challenge on Scanned Receipts OCR and Information Extraction

lit

The Language Interpretability Tool: Interactively analyze NLP models for model understanding in an extensible and framework agnostic interface.

mhcvizpipe

A reporting pipeline for visualization of immunopeptidomics MS data.

mtl-bioinformatics-2016

pandasgui

A GUI for Pandas DataFrames

pke

Python Keyphrase Extraction module

plotly-resampler

Visualize large time-series data in plotly

pmtnet

Deep Learning the T Cell Receptor Binding Specificity of Neoantigen

prime

PRedictor of IMmunogenic Epitopes

prottrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.