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- Publications
- Influence
Universal Dependencies v1: A Multilingual Treebank Collection
- Joakim Nivre, Marie-Catherine de Marneffe, +9 authors D. Zeman
- Computer Science
- LREC
- 2016
Cross-linguistically consistent annotation is necessary for sound comparative evaluation and cross-lingual learning experiments. It is also useful for multilingual system development and comparative… Expand
Overview of BioNLP'09 Shared Task on Event Extraction
- Jin-Dong Kim, T. Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii
- Computer Science
- BioNLP@HLT-NAACL
- 5 June 2009
The paper presents the design and implementation of the BioNLP'09 Shared Task, and reports the final results with analysis. The shared task consists of three sub-tasks, each of which addresses… Expand
brat: a Web-based Tool for NLP-Assisted Text Annotation
- Pontus Stenetorp, Sampo Pyysalo, Goran Topic, T. Ohta, S. Ananiadou, Jun'ichi Tsujii
- Computer Science
- EACL
- 23 April 2012
We introduce the brat rapid annotation tool (BRAT), an intuitive web-based tool for text annotation supported by Natural Language Processing (NLP) technology. BRAT has been developed for rich… Expand
BioInfer: a corpus for information extraction in the biomedical domain
- Sampo Pyysalo, F. Ginter, +4 authors T. Salakoski
- Computer Science, Medicine
- BMC Bioinformatics
- 9 February 2007
BackgroundLately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins,… Expand
All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning
- Antti Airola, Sampo Pyysalo, Jari Björne, T. Pahikkala, F. Ginter, T. Salakoski
- Computer Science, Medicine
- BMC Bioinformatics
- 19 November 2008
BackgroundAutomated extraction of protein-protein interactions (PPI) is an important and widely studied task in biomedical text mining. We propose a graph kernel based approach for this task. In… Expand
Distributional Semantics Resources for Biomedical Text Processing
- Sampo Pyysalo, F. Ginter, Hans Moen, T. Salakoski, S. Ananiadou
- Computer Science
- 2013
The openly available biomedical literature contains over 5 billion words in publication abstracts and full texts. Recent advances in unsupervised language processing methods have made it possible to… Expand
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How to Train good Word Embeddings for Biomedical NLP
- Billy Chiu, Gamal K. O. Crichton, A. Korhonen, Sampo Pyysalo
- Computer Science
- BioNLP@ACL
- 2016
The quality of word embeddings depends on the input corpora, model architectures, and hyper-parameter settings. Using the state-of-the-art neural embedding tool word2vec and both intrinsic and… Expand
CoNLL 2017 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies
The Conference on Computational Natural Language Learning (CoNLL) features a shared task, in which participants train and test their learning systems on the same data sets. In 2017, one of two tasks… Expand
Comparative analysis of five protein-protein interaction corpora
- Sampo Pyysalo, Antti Airola, J. Heimonen, Jari Björne, F. Ginter, T. Salakoski
- Computer Science, Medicine
- BMC Bioinformatics
- 11 April 2008
BackgroundGrowing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction… Expand
Overview of BioNLP Shared Task 2013
- C. Nedellec, R. Bossy, +4 authors Pierre Zweigenbaum
- Computer Science
- BioNLP@ACL
- 1 August 2013
The BioNLP Shared Task 2013 is the third edition of the BioNLP Shared Task series that is a community-wide effort to address fine-grained, structural information extraction from biomedical… Expand