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attention_model_clinical_text

This code implements attention network on top of the CNN used in the paper titled "Relation extraction from clinical texts using domain invariant convolutional neural network" which was accepted in BioNLP at ACL-2016, Berlin, Germany

bacteria_biotope_event_extraction_corpus

bionlp

Biomedical Text Mining (BioNLP) Library

bionlp-1

bioNLP

bionlp-2

BioNLP: mutation, Gene, disease Entity Recognition, and their relation extraction

bionlp-2016

bionlp-2017

bionlp-3

Deep learning model to extract entity relation

bionlp-bb3

BioNLP 2016 BB3 Contest Submission

bionlp-clasificacion-final

Códigos para preprocesamiento y divisiónd e data sets de interacciones reguladoras de E coli.

bionlp-classifier

Códigos para la clasificación de TF - genes de la red de E. coli

bionlp-genia-ee

Event extraction for Genia corpus

bionlp-lcg

bionlp-literature-tool

Please see Webdev-for-BioNLP-literature-tool for the most up-to-date code. I'll up date this repo later (its 5 months out of date!!!!!). Code here scrapes pubmed XML for basic info, NER, document clustering, visualization

bionlp-st-2016_bb3-event

bionlp17

Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction

bionlp2016

University of Melbourne's SeeDev binary event extraction system for BioNLP-Shared Task 2016.

bionlp_analysis

NLP preprocessing pipeline: sentence split, term detection, part-of-speech tagging , lemmatization, biological name entity recognition and transformation to internal representation

bionlp_st_2011_supporting

Supporting resources and a replicable pipeline for the BioNLP Shared Task 2011 data

bionlpextract

Event Extraction for BioNLP

bionlpst2016

Code for BioNLP 2016. Seedev Binary Task.

bioposdep

Pre-trained models for biomedical POS tagging and dependency parsing

biosemble

AI assembly of bioNLP wordnets

biowordlists

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

birnn-bionlp

Bidirectional Recurrent Neural Network based sequence labeling for Medical Text.

dcnn_mlee

Dependency-tree based convolutional neural network for event extraction in MLEE dataset.

geniajsonreader

a json reader for the BioNLP '13 ST Genia RE task

kindred

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

lstm_mlee

Using lstm to detect mlee event trigger.

mlee-nce

Biological Event Trigger Identification with Noise Contrastive Estimation