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Laura Zanella's Projects

bern icon bern

A neural named entity recognition and multi-type normalization tool for biomedical text mining

bert-ner icon bert-ner

Pytorch-Named-Entity-Recognition-with-BERT

biobert icon biobert

BioBERT: a pre-trained biomedical language representation model

biobert-pretrained icon biobert-pretrained

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

biomedical_corpora icon biomedical_corpora

Table compiling the list of biomedically-related corpora available for named entity recognition (and some also suitable for association detection). This has been published as part of the paper: Dieter Galea, Ivan Laponogov, Kirill Veselkov; Exploiting and assessing multi-source data for supervised biomedical named entity recognition, Bioinformatics, bty152, https://doi.org/10.1093/bioinformatics/bty152 . If you would like to add other (or your) corpora, please submit a pull request and I'll happily approve it.

brat icon brat

brat rapid annotation tool (brat) - for all your textual annotation needs

clinicalbert icon clinicalbert

repository for Publicly Available Clinical BERT Embeddings

deepeventmine icon deepeventmine

DeepEventMine: End-to-end Neural Nested Event Extraction from Biomedical Texts

kgen icon kgen

Knowledge graphs generation from unstructured text.

kindred icon kindred

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

lrp_toolbox icon lrp_toolbox

The LRP Toolbox provides simple and accessible stand-alone implementations of LRP for artificial neural networks supporting Matlab and Python. The Toolbox realizes LRP functionality for the Caffe Deep Learning Framework as an extension of Caffe source code published in 10/2015.

lsgn icon lsgn

Labeled Span Graph Networks

mateplus icon mateplus

Extension of the mate-tools NLP pipeline

mer icon mer

Minimal Named-Entity Recognizer (MER)

ncbo_annotator icon ncbo_annotator

To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations.

nlp-progress icon nlp-progress

Repository to track the progress in Natural Language Processing (NLP), including the datasets and the current state-of-the-art for the most common NLP tasks.

open-sesame icon open-sesame

A frame-semantic parsing system based on a softmax-margin SegRNN.

propbank-frames icon propbank-frames

Lexicon of frame files used by Propbank annotation. A searchable, readable version of these files is stored at http://verbs.colorado.edu/propbank/framesets-english-aliases/

propbank-release icon propbank-release

The official released annotations, both in .prop pointer format and as conll files. Does not contain the source texts

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