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attentionxml

Implementation for "AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification"

baal

Library to enable Bayesian active learning in your research or labeling work.

basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

bioinfor-deepatt

DeepATT, a hybrid deep neural network method for identifying functional effects of DNA sequences.

chexpert-labeler

CheXpert NLP tool to extract observations from radiology reports.

clinical-longformer

clinicalbert

repository for Publicly Available Clinical BERT Embeddings

clinicalbert-1

ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission (CHIL 2020 Workshop)

compact-transformers

[Preprint] Escaping the Big Data Paradigm with Compact Transformers, 2021

cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

coronavirus_exploration

Clustering analysis and classification of coronavirus sequence data and metadata.

cxr-implant-finder

CheXpert-based automated pipeline for implant detection from a free-text input.

deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications

deepsilencer

A deep convolutional neural network for the accurate prediction of silencers

dl-for-genomics

Selections from CS185-Deep Learning for Genomics, Brown University

dna-transformer

dnabert

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

embeddingrecycling

Embedding Recycling for Language models

enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

esm

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

exploring-t5

A repo to explore different NLP tasks which can be solved using T5

exploringrnaseq

facial-similarity-with-siamese-networks-in-pytorch

Implementing Siamese networks with a contrastive loss for similarity learning

fainhd

fairseq

Facebook AI Research Sequence-to-Sequence Toolkit written in Python.

fastsk

Bioinformatics 2020: FastSK: Fast and Accurate Sequence Classification by making gkm-svm faster and scalable. https://fastsk.readthedocs.io/en/master/

fbgan

genesis

Deep Exploration Networks - Diverse Deep Generative Models for DNA, RNA and Protein Sequences

geometric_shapes

gnn-based-diag

A repository for the 02-740 Bioimage Informatics course project on GNN-based cancer detection and classification.