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bionlp

Here are 27 public repositories matching this topic...

ncbi-nlp / BioSentVec

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BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences

natural-language-processing word-embeddings pubmed fasttext mimic-iii bionlp sentence-similarity sentence-embeddings sent2vec

Updated Feb 26, 2020
Jupyter Notebook

ncbi-nlp / BLUE_Benchmark

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BLUE benchmark consists of five different biomedicine text-mining tasks with ten corpora.

benchmark natural-language-understanding bionlp

Updated Apr 14, 2020
Python

jakelever / kindred

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

python text-mining relation-extraction bionlp

Updated Jul 9, 2020
Python

Rostlab / nalaf

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Open

Delete Output Formats wiki page ?

2

juanmirocks commented Dec 9, 2015

Wiki page: https://github.com/Rostlab/nalaf/wiki/Output-Formats
Confirm if you still use the simple JSON export
- if yes:
  - fix documentation of format (I guess it's wrong because I guess each document should be an array of parts
  - Link wiki page link to Home wiki
  - Support output format in example & nala scripts
- else:
  - delete that wiki page since

Read more

Open

Change the way features are saved

4

hu-ner / huner

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Named Entity Recognition for biomedical entities

named-entity-recognition neural-networks corpora ner bionlp

Updated May 20, 2020
Python

jakelever / pubrunner

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

python infrastructure text-mining snakemake pubmed pubmed-central bionlp

Updated May 6, 2020
Python

abachaa / MEDIQA2019

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Challenge on Textual Inference and Question Entailment in the Medical Domain https://sites.google.com/view/mediqa2019

nlp inference question-answering bionlp entailment medical-natural-language-processing

Updated Jan 31, 2020
Python

datquocnguyen / BioPosDep

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Tokenization, sentence segmentation, POS tagging and dependency parsing for biomedical texts (BMC Bioinformatics 2019)

bioinformatics tokenizer pos-tagging dependency-parsing bionlp segmenter biomedical-text-mining

Updated Apr 6, 2019
Python

Bohdan-Khomtchouk / biosemble

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AI assembly of bioNLP wordnets

python nlp machine-learning bioinformatics cython computational-biology artificial-intelligence wordnet bionlp

Updated Oct 31, 2017
Python

jakelever / VERSE

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Vancouver Event and Relation System for Extraction

text-mining relation-extraction bionlp

Updated Nov 9, 2017
Python

jakelever / civicmine

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Text mining cancer biomarkers for the CIVIC database

text-mining cancer biomarkers precision-medicine bionlp

Updated Mar 10, 2020
R

leebird / bionlp17

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Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction

text-mining relation-extraction bionlp distant-supervision

Updated Oct 25, 2017
Python

yfpeng / bioc

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Data structures and code to read/write BioC XML and Json.

json xml writer reader bioc bionlp

Updated Jun 6, 2020
Python

jakelever / biowordlists

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Biomedical wordlists (of drugs, genes, etc) for several text mining projects

text-mining nomenclature bionlp

Updated Feb 6, 2019
Python

ncbi-nlp / PubTator-Covid19

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natural-language-processing text-mining pubmed bionlp covid-19 covid19

Updated May 6, 2020

jakelever / tumorantigens

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Text mining tumor antigens for cancer immunotherapy research

text-mining cancer immunology bionlp

Updated Dec 20, 2018
Python

bionlp-hzau / BioNLP-Corpus

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Repository used to collect biomedical corpus on the Internet!

corpus biomedical bionlp

Updated May 29, 2019

pdsujnow / Multi-BioNER

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Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)

motivation to-do ner bionlp

Updated Dec 4, 2018
Python

pdsujnow / crnn-relation-classification

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Tensorflow implementation of the Convolutional Recurrent Neural Network model with max pooling and attentive pooling, for relation classification on biomedical text.

motivation idea to-do bionlp inspired

Updated Dec 1, 2017
Python

pdsujnow / Transfer-Learning-BNER-Bioinformatics-2018

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This repository contains supplementary data, and links to the model and corpora used for the paper: Transfer learning for biomedical named entity recognition with neural networks.

ner bionlp corppus

Updated Sep 21, 2018
Python

pdsujnow / DDI-extraction-through-LSTM

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DDI Extraction from Biomedical text using LSTM network

motivation idea to-do bionlp inspired

Updated Nov 17, 2018
Python

miladnouriezade / HUNER-evaluation

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This repository stands for applying and evaluating HUNER pre-trained model ("disease_all") on "BC5CDR-Disease" data set .

python nlp named-entity-recognition disease ner biomedical bionlp huner

Updated Jun 21, 2020
Python

pdsujnow / Resources

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motivation idea to-do bionlp inspired

Updated May 17, 2018
Batchfile

pdsujnow / MTL-Bioinformatics-2016

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datasets ner bionlp

Updated Aug 15, 2017
Python

pdsujnow / NeuroNER

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Named-entity recognition using neural networks. Easy-to-use and state-of-the-art results.

Updated Jun 27, 2018
Python

pdsujnow / HSCRF-pytorch

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ACL 2018: Hybrid semi-Markov CRF for Neural Sequence Labeling (http://aclweb.org/anthology/P18-2038)

Updated Jul 22, 2018
Python

miladnouriezade / Ktrain-BioBert_NER

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This repository contains data and BioBert based NER model monologg/biobert_v1.1_pubmed from community-uploaded Hugging Face models for detecting entities such as chemical and disease.

python nlp spacy named-entity-recognition disease name fasttext ner biomedical bionlp biobert huggingface ktrain

Updated Jun 26, 2020
Python

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