bioc | pypi | Package Usage | Ecosyste.ms: Repos

shiva16/cervello.v2

An open sourced query engine for brainarchitecture.org project to extract functional relation between two brain regions from a corpus of scientific articles in neuroscience.

==1.1.dev3 requirements.txt

Size: 12.6 MB - Last synced: 9 months ago - Pushed: over 1 year ago

rythmm24/Search-Tool

Search tool to extract functional relationship between the two given mouse brain regions

==1.1.dev3 requirements.txt

Size: 12.6 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

lazappi/openproblems Fork of openproblems-bio/openproblems

Formalizing and benchmarking open problems in single-cell genomics

* docker/openproblems-r-base/r_requirements.txt
* docker/openproblems-r-extras/r_requirements.txt

Size: 90.5 MB - Last synced: 9 months ago - Pushed: about 1 year ago

ysmiura/ifcc

The code of Improving Factual Completeness and Consistency of Image-to-text Radiology Report Generation

==1.3.4 setup.py

Size: 28.9 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

IndoNLP/nusa-crowd

A collaborative project to collect datasets in Indonesian languages.

==1.3.7 requirements.txt

Size: 2.48 MB - Last synced: 26 days ago - Pushed: 5 months ago

bernaljg/covid19-classification

Testing Document Classification on COVID-19 Literature using the LitCovid dataset and the Hedwig library.

==1.3.5 requirements.txt

Size: 52.4 MB - Last synced: 11 months ago - Pushed: 11 months ago

dki-lab/covid19-classification

Document Classification on COVID-19 Literature using the LitCovid collection and the Hedwig library.

==1.3.5 requirements.txt

Size: 52.5 MB - Last synced: about 1 month ago - Pushed: 4 months ago

leonweber/pedl

Search the biomedical literature for protein interactions and protein associations

* requirements.txt

Size: 11.3 MB - Last synced: 10 days ago - Pushed: 6 months ago

yfpeng/PMCFigureX

* requirements.txt

Size: 120 KB - Last synced: about 1 month ago - Pushed: 8 months ago

coder318/sodner

==1.0 requirements.txt

Size: 70.3 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

RudrakshTuwani/emotion-classification

==1.1.dev2 requirements.txt

Size: 1000 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

danielStrobl/SingleCellOpenProblems Fork of openproblems-bio/openproblems

Formalizing and benchmarking open problems in single-cell genomics

* docker/openproblems-r-base/r_requirements.txt
* docker/openproblems-r-extras/r_requirements.txt

Size: 77.4 MB - Last synced: 11 months ago - Pushed: about 1 year ago

Nick1AA/Federated-Learning-in-Healthcare

This repository compares the performance of FedAvg and FedMA on the CheXpert dataset.

==1.1.dev3 environment.yml

Size: 803 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

Auto-CORPus pipeline developed by a University of Leicester and Imperial College London collaboration to standardize text and table data extracted from full text publications. See Open Access publication at: https://doi.org/10.3389/fdgth.2022.788124.

==1.3.7 requirements.txt

Size: 54.4 MB - Last synced: 2 months ago - Pushed: 2 months ago

bionlplab/drugprot_biocreative_vii2021

CU-UD: text-mining drug and chemical-protein interactions with ensembles of BERT-based models

* requirements.txt

Size: 110 KB - Last synced: about 1 month ago - Pushed: about 2 years ago

unik00/GraphLSTM

* requirements.txt

Size: 24.2 MB - Last synced: 10 months ago - Pushed: over 2 years ago

bigscience-workshop/biomedical

Tools for curating biomedical training data for large-scale language modeling

==2.0.post4 dev-requirements.txt
==2.0.post4 requirements.txt

Size: 25.4 MB - Last synced: 2 days ago - Pushed: 2 months ago

jantrienes/chexpert-labeler Fork of stanfordmlgroup/chexpert-labeler

CheXpert NLP tool to extract observations from radiology reports.

==1.1.dev3 environment.yml

Size: 59.6 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

ncbi-nlp/DeepRel

A convolutional neural network model for relation extraction.

==1.0.dev32 requirements.txt

Size: 277 KB - Last synced: 10 days ago - Pushed: about 1 year ago

em3ndez/chexpert-labeler Fork of stanfordmlgroup/chexpert-labeler

CheXpert NLP tool to extract observations from radiology reports.

==1.1.dev3 environment.yml

Size: 59.6 KB - Last synced: about 1 month ago - Pushed: over 1 year ago

openproblems-bio/openproblems

Formalizing and benchmarking open problems in single-cell genomics

* docker/openproblems-r-base/r_requirements.txt
* docker/openproblems-r-extras/r_requirements.txt

Size: 73.1 MB - Last synced: 10 days ago - Pushed: 4 months ago

Feat-FeAR/GATTACA_beta

Reproducible DEA... in times before bioTEA

* src/resources/r_requirements.txt

Size: 37.8 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

JungeAlexander/kbase_db_api

1.3.6 poetry.lock

Size: 727 KB - Last synced: 9 months ago - Pushed: almost 3 years ago

foxlf823/Multi-Filter-Residual-Convolutional-Neural-Network

Multi-Filter Residual Convolutional Neural Network for Text Classification

==1.0 requirements.txt

Size: 67.4 KB - Last synced: about 1 year ago - Pushed: about 3 years ago

Iamfinethanksu/nusa-crowd Fork of IndoNLP/nusa-crowd

A collaborative project to collect datasets in Indonesian languages.

==1.3.7 requirements.txt

Size: 1.53 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

facebookresearch/bio-lm 📦

We evaluate many models used for biomedical and clinical nlp tasks, and train new models that perform much better.

* requirements.txt

Size: 49.8 KB - Last synced: 3 months ago - Pushed: almost 3 years ago

jakelever/kindred

A Python biomedical relation extraction package that uses a supervised approach (i.e. needs training data).

>=1.3.1 requirements.readthedocs.txt
>=1.3.1 requirements.txt

Size: 2.38 MB - Last synced: 1 day ago - Pushed: about 1 year ago

bionlplab/negbio2

High-performance tool for negation and uncertainty detection in radiology reports

==1.3.2 requirements3.txt

Size: 194 KB - Last synced: 20 days ago - Pushed: 20 days ago

yana-xuyan/nusa-crowd Fork of IndoNLP/nusa-crowd

A collaborative project to collect datasets in Indonesian languages.

==1.3.7 requirements.txt

Size: 1.43 MB - Last synced: 8 months ago - Pushed: over 1 year ago

wenliangdai/nusa-crowd Fork of IndoNLP/nusa-crowd

A collaborative project to collect datasets in Indonesian languages.

==1.3.7 requirements.txt

Size: 1.38 MB - Last synced: 10 months ago - Pushed: over 1 year ago

rayendito/nusa-crowd Fork of IndoNLP/nusa-crowd

A collaborative project to collect datasets in Indonesian languages.

==1.3.7 requirements.txt

Size: 1.43 MB - Last synced: almost 1 year ago - Pushed: over 1 year ago

SBRG/lifelike 📦

Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.

==1.3.7 appserver/Pipfile
==1.3.7 appserver/Pipfile.lock

Size: 54.1 MB - Last synced: about 2 months ago - Pushed: 4 months ago

JoaoLMPereira/acx-acronym-expander

==1.3.7 Pipfile
==1.3.6 Pipfile.lock

Size: 24.2 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

acul3/nusa-crowd Fork of IndoNLP/nusa-crowd

A collaborative project to collect datasets in Indonesian languages.

==1.3.7 requirements.txt

Size: 1.5 MB - Last synced: 10 months ago - Pushed: over 1 year ago

jakelever/biotext

Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!

* requirements.txt
* setup.py

Size: 210 KB - Last synced: 13 days ago - Pushed: 13 days ago

jopilipina/thesis

Literature mining for cancer-marker databasing

==1.2.3 kindred/requirements.readthedocs.txt
==1.2.3 kindred/requirements.txt
==1.2.3 requirements.txt

Size: 5.28 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

Stephanie-Shen324/ifcc

An IFCC repo supporting IU-XRAY dataset (based on https://github.com/ysmiura/ifcc)

==1.3.4 setup.py

Size: 38.8 MB - Last synced: 11 months ago - Pushed: almost 3 years ago

jakelever/pubrunner

A framework for keeping biomedical text mining result up-to-date

* examples/SummaryData/requirements.txt
>=1.3.1 requirements.txt

Size: 565 KB - Last synced: about 2 months ago - Pushed: almost 4 years ago

esizikova/medsynth_public

Code Repository for Computed Tomography (CT) Reconstruction

==1.3.7 requirements.txt

Size: 580 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

IvanHalimP/nusa-crowd Fork of IndoNLP/nusa-crowd

A collaborative project to collect datasets in Indonesian languages.

==1.3.7 requirements.txt

Size: 2.46 MB - Last synced: 7 months ago - Pushed: 7 months ago

bionlplab/radtext

Python Radiology Text Analysis System

>=2.0 requirements.txt

Size: 14.3 MB - Last synced: about 1 month ago - Pushed: 10 months ago

zzxslp/WCL

Code for Weakly Supervised Contrastive Learning for Chest X-Ray Report Generation (EMNLP-21)

==1.1.dev3 chexpert-labeler/environment.yml

Size: 44.9 KB - Last synced: 9 months ago - Pushed: over 1 year ago

MIT-LCP/mimic-cxr 📦

Code, documentation, and discussion around the MIMIC-CXR database

==1.1.dev3 txt/chexpert/environment.yml
==1.3.1 txt/negbio/environment.yml

Size: 1.08 MB - Last synced: about 2 months ago - Pushed: almost 4 years ago

ncbi-nlp/COVID-19-CT-CXR

COVID-19-CT-CXR, a public database of COVID-19 CXR and CT images

* requirements.txt

Size: 950 KB - Last synced: 10 days ago - Pushed: about 1 year ago

ZooPhy/geoboost2

==1.3.1 requirements.txt

Size: 40.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

fhudi/nusa-crowd Fork of IndoNLP/nusa-crowd

A collaborative project to collect datasets in Indonesian languages.

==1.3.7 requirements.txt

Size: 1.94 MB - Last synced: 4 months ago - Pushed: over 1 year ago

nxwi/illacceptanything Fork of illacceptanything/illacceptanything

The project where literally anything* goes.

* data/requirements.txt

Size: 1.33 GB - Last synced: 8 months ago - Pushed: over 1 year ago

pulmo/chexpert-labeler

CheXpert NLP tool to extract observations from radiology reports.

==1.1.dev3 environment.yml

Last synced: over 1 year ago

ncbi/AIONER

AIONER

==2.0.post4 requirements.txt

Size: 20.8 MB - Last synced: 12 months ago - Pushed: 12 months ago

illacceptanything/illacceptanything

The project where literally anything* goes.

* data/requirements.txt

Size: 1.47 GB - Last synced: 19 days ago - Pushed: 19 days ago

classicvalues/cervello.v2 Fork of shiva16/cervello.v2

An open sourced query engine for brainarchitecture.org project to extract functional relation between two brain regions from a corpus of scientific articles in neuroscience.

==1.1.dev3 requirements.txt

Size: 12.6 MB - Last synced: about 1 month ago - Pushed: about 1 year ago

SuperSupermoon/MedViLL

MedViLL official code. (Published IEEE JBHI 2021)

==1.1.dev3 requirements.txt

Size: 12.6 MB - Last synced: 10 days ago - Pushed: over 1 year ago

giovp/SingleCellOpenProblems Fork of openproblems-bio/openproblems

Formalizing and benchmarking open problems in single-cell genomics

* docker/openproblems-r-base/r_requirements.txt
* docker/openproblems-r-extras/r_requirements.txt

Size: 90.1 MB - Last synced: about 1 month ago - Pushed: 9 months ago

faridlazuarda/nusa-crowd Fork of IndoNLP/nusa-crowd

A collaborative project to collect datasets in Indonesian languages.

==1.3.7 requirements.txt

Size: 2.14 MB - Last synced: almost 1 year ago - Pushed: over 1 year ago

dbdimitrov/openproblems Fork of openproblems-bio/openproblems

Formalizing and benchmarking open problems in single-cell genomics

* docker/openproblems-r-base/r_requirements.txt
* docker/openproblems-r-extras/r_requirements.txt

Size: 78.1 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

muhsatrio/nusa-crowd Fork of IndoNLP/nusa-crowd

A collaborative project to collect datasets in Indonesian languages.

==1.3.7 requirements.txt

Size: 2.42 MB - Last synced: 7 months ago - Pushed: 7 months ago

davidkartchner/biomedical Fork of bigscience-workshop/biomedical

Tools for curating biomedical training data for large-scale language modeling

==2.0.post4 dev-requirements.txt
==2.0.post1 requirements.txt

Size: 25.5 MB - Last synced: 4 months ago - Pushed: 4 months ago

wes-lewis/SingleCellOpenProblems Fork of openproblems-bio/openproblems

Formalizing and benchmarking open problems in single-cell genomics

* docker/openproblems-r-base/r_requirements.txt
* docker/openproblems-r-extras/r_requirements.txt

Size: 90.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

schu/mimic-code Fork of MIT-LCP/mimic-code

MIMIC Code Repository: Code shared by the research community for the MIMIC-III database

==1.1.dev3 mimic-iv-cxr/txt/chexpert/environment.yml
==1.3.1 mimic-iv-cxr/txt/negbio/environment.yml

Size: 18.8 MB - Last synced: 22 days ago - Pushed: over 1 year ago

LuckyMD/SingleCellOpenProblems Fork of openproblems-bio/openproblems

Formalizing and benchmarking open problems in single-cell genomics

* docker/openproblems-r-base/r_requirements.txt
* docker/openproblems-r-extras/r_requirements.txt

Size: 76.3 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

sg-wbi/biomedical Fork of bigscience-workshop/biomedical

Tools for curating biomedical training data for large-scale language modeling

==2.0.post4 dev-requirements.txt
==2.0.post4 requirements.txt

Size: 25.6 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

vitkl/openproblems Fork of openproblems-bio/openproblems

Formalizing and benchmarking open problems in single-cell genomics

* docker/openproblems-r-base/r_requirements.txt
* docker/openproblems-r-extras/r_requirements.txt

Size: 72.6 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

mxposed/SingleCellOpenProblems Fork of openproblems-bio/openproblems

Formalizing and benchmarking open problems in single-cell genomics

* docker/openproblems-r-base/r_requirements.txt
* docker/openproblems-r-extras/r_requirements.txt

Size: 90.5 MB - Last synced: about 1 month ago - Pushed: about 1 year ago

scottgigante-immunai/openproblems Fork of openproblems-bio/openproblems

Formalizing and benchmarking open problems in single-cell genomics

* docker/openproblems-r-base/r_requirements.txt
* docker/openproblems-r-extras/r_requirements.txt

Size: 73 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

suinleelab/Useful_Datasets_CSE_527

==1.1.dev3 mimic-code/mimic-iv-cxr/txt/chexpert/environment.yml
==1.3.1 mimic-code/mimic-iv-cxr/txt/negbio/environment.yml
==1.1.dev3 mimic-cxr/txt/chexpert/environment.yml
==1.3.1 mimic-cxr/txt/negbio/environment.yml

Size: 19.8 MB - Last synced: 10 days ago - Pushed: over 1 year ago

bmewing/requirements

R package for managing requirements

* tests/testthat/testdata/requirements_3.txt

Size: 246 KB - Last synced: 2 months ago - Pushed: over 2 years ago

ncbi/SpeciesAssignment

SpeciesAssignment

==2.0.post4 requirements.txt

Size: 891 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

BLannoo/medical-named-entity-recognition

==1.3.4 docs/reference-materials/pubtator/ExampleCode.Python/requirements.txt

Size: 284 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

cbaziotis/hierarchical-rnn-biocreative-4

Repository containing the winning submission for the BioCreative VI Task A (2017). The model is a Hierarchical Bidirectional Attention-Based RNN, implemented in Keras.