17 2.3.1 Unitary Features, Features of Context ,
22 2.4.1 Pipeline Models, 23 Trigger Detection . . . . . . . . . . . . . . . . . . . . . . . . 23 ,
31 BIND theme Fusion, p.32 ,
32 REG-theme Pair Extraction, p.33 ,
36 SVM Scores Combination 36 Logistic Regression, Decision Thresholds, p.37 ,
40 Longest Sentence, p.40 ,
41 Encoding Paths, Statistics of Path Lengths, p.41 ,
Overview of BioNLP'09 shared task on event extraction, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, pp.1-9, 2009. ,
DOI : 10.3115/1572340.1572342
Overview of genia event task in bionlp shared task 2011, Proceedings of BioNLP Shared Task 2011 Workshop, pp.7-15, 2011. ,
The genia event extraction shared task, 2013 edition -overview, Proceedings of the BioNLP Shared Task, 2013. ,
DOI : 10.1186/1471-2105-13-s11-s1
URL : http://doi.org/10.1186/1471-2105-13-s11-s1
Gro task: Populating the gene regulation ontology with events and relations, Proceedings of the BioNLP Shared Task 2013 Workshop, pp.50-57, 2013. ,
Overview of the cancer genetics (cg) task of bionlp shared task 2013, Proceedings of the BioNLP Shared Task 2013 Workshop, pp.58-66, 2013. ,
Overview of the pathway curation (pc) task of bionlp shared task 2013, Proceedings of the BioNLP Shared Task 2013 Workshop, pp.67-75, 2013. ,
Overview of bionlp shared task 2013, Proceedings of the BioNLP Shared Task 2013 Workshop, pp.1-7, 2013. ,
Overview of the entity relations (rel) supporting task of bionlp shared task 2011, Proceedings of BioNLP Shared Task 2011 Workshop, pp.83-88, 2011. ,
Overview of bionlp 2011 protein coreference shared task, Proceedings of BioNLP Shared Task 2011 Workshop, pp.74-82, 2011. ,
Bionlp shared task 2011 -bacteria biotope, Proceedings of BioNLP Shared Task 2011 Workshop, pp.56-64, 2011. ,
DOI : 10.1186/1471-2105-13-s11-s3
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S11-S3?site=bmcbioinformatics.biomedcentral.com
Overview of the infectious diseases (id) task of bionlp shared task 2011, Proceedings of BioNLP Shared Task 2011 Workshop, pp.26-35, 2011. ,
Overview of the epigenetics and post-translational modifications (epi) task of bionlp shared task 2011, Proceedings of BioNLP Shared Task 2011 Workshop, pp.16-25, 2011. ,
Overview of bionlp shared task 2011, Proceedings of BioNLP Shared Task 2011 Workshop, pp.1-6, 2011. ,
Static relations, Proceedings of the Workshop on BioNLP, BioNLP '09, pp.1-9, 2009. ,
DOI : 10.3115/1572364.1572366
Bioinfer: a corpus for information extraction in the biomedical domain, BMC Bioinformatics, vol.8, issue.1, p.50, 2007. ,
DOI : 10.1186/1471-2105-8-50
Corpus annotation for mining biomedical events from literature, BMC Bioinformatics, vol.9, issue.1, p.10, 2008. ,
DOI : 10.1186/1471-2105-9-10
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-9-10?site=bmcbioinformatics.biomedcentral.com
Event extraction as dependency parsing for bionlp 2011, Proceedings of BioNLP Shared Task 2011 Workshop, pp.41-45, 2011. ,
A Markov logic approach to bio-molecular event extraction, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, 2009. ,
DOI : 10.3115/1572340.1572347
URL : http://aclweb.org/anthology-new/W/W09/W09-1406.pdf
Fast and robust joint models for biomedical event extraction, Proceedings of the 2011 Conference on Empirical Methods in Natural Language Processing, pp.1-12, 2011. ,
Robust biomedical event extraction with dual decomposition and minimal domain adaptation, Proceedings of BioNLP Shared Task 2011 Workshop, pp.46-50, 2011. ,
DOI : 10.1111/j.1467-8640.2011.00400.x
URL : http://maroo.cs.umass.edu/pub/web/getpdf.php?id=928
Model combination for event extraction in bionlp, 2011. ,
Combining joint models for biomedical event extraction, BMC Bioinformatics, vol.13, issue.Suppl 11 ,
DOI : 10.1186/1471-2105-13-S11-S9
Extracting complex biological events with rich graph-based feature sets, Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pp.10-18, 2009. ,
Generalizing biomedical event extraction, Proceedings of BioNLP Shared Task 2011 Workshop, pp.183-191, 2011. ,
TEES 2.1: Automated annotation scheme learning in the BioNLP 2013 shared task, Proceedings of BioNLP Shared Task, 2013. ,
The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011, BMC Bioinformatics, vol.13, issue.Suppl 11, pp.11471-2105, 2012. ,
DOI : 10.1186/1471-2105-13-S11-S1
Feature Forest Models for Probabilistic HPSG Parsing, Computational Linguistics, vol.15, issue.1, pp.35-80, 2008. ,
DOI : 10.2307/2006193
URL : http://doi.org/10.1162/coli.2008.34.1.35
Dependency parsing and domain adaptation with lr models and parser ensembles, EMNLP-CoNLL, pp.1044-1050, 2007. ,
DOI : 10.1007/978-90-481-9352-3_4
A comparative study of syntactic parsers for event extraction, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp.37-45, 2010. ,
Msrnlp entry in bionlp shared task 2011, Proceedings of BioNLP Shared Task, 2011. ,
The taming of reconcile as a biomedical coreference resolver, Proceedings of BioNLP Shared Task 2011 Workshop, pp.89-93, 2011. ,
Event extraction from trimmed dependency graphs, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, pp.19-27, 2009. ,
DOI : 10.3115/1572340.1572344
URL : http://aclweb.org/anthology-new/W/W09/W09-1403.pdf
A multi-phase approach to biomedical event extraction, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, pp.107-110, 2009. ,
DOI : 10.3115/1572340.1572357
URL : http://dl.acm.org/ft_gateway.cfm?id=1572357&type=pdf
Syntactic dependency based heuristics for biological event extraction, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, pp.119-127, 2009. ,
DOI : 10.3115/1572340.1572361
URL : http://aclweb.org/anthology-new/W/W09/W09-1418.pdf
Biomedical event extraction from abstracts and full papers using search-based structured prediction, Proceedings of BioNLP Shared Task 2011 Workshop, pp.36-40, 2011. ,
DOI : 10.1186/1471-2105-13-S11-S5
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S11-S5?site=bmcbioinformatics.biomedcentral.com
Complex biological event extraction from full text using signatures of linguistic and semantic features, Proceedings of BioNLP Shared Task 2011 Workshop, pp.130-137, 2011. ,
Double layered learning for biological event extraction from text, Proceedings of BioNLP Shared Task 2011 Workshop, pp.153-154, 2011. ,
Semantically linking molecular entities in literature through entity relationships, BMC Bioinformatics, vol.13, issue.Suppl 11, p.6, 2012. ,
DOI : 10.1002/(SICI)1097-4571(199401)45:1<12::AID-ASI2>3.0.CO;2-L
Improving feature-based biomedical event extraction system by integrating argument information, Proceedings of the BioNLP Shared Task 2013 Workshop, pp.109-115, 2013. ,
A memory-based learning approach to event extraction in biomedical texts, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, pp.59-67, 2009. ,
DOI : 10.3115/1572340.1572349
Biomedical event annotation with CRFs and precision grammars, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, 2009. ,
DOI : 10.3115/1572340.1572351
From proteinprotein interaction to molecular event extraction, Proceedings of the BioNLP, 2009. ,
A pattern approach for biomedical event annotation, Proceedings of BioNLP Shared Task 2011 Workshop, pp.149-150, 2011. ,
UZurich in the BioNLP 2009 shared task, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, pp.28-36, 2009. ,
DOI : 10.3115/1572340.1572345
Biomedical event extraction without training data, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, 2009. ,
DOI : 10.3115/1572340.1572346
URL : http://aclweb.org/anthology-new/W/W09/W09-1405.pdf
Extracting biological events from text using simple syntactic patterns, Proceedings of BioNLP Shared Task 2011 Workshop, pp.143-146, 2011. ,
A fast rule-based approach for biomedical event extraction, Proceedings of the BioNLP Shared Task 2013 Workshop, pp.104-108, 2013. ,
Bioeve: Bio-molecular event extraction from text using semantic classification and dependency parsing, Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pp.99-102, 2009. ,
Tees 2.1: Automated annotation scheme learning in the bionlp 2013 shared task, Proceedings of the BioNLP Shared Task, 2013. ,
EVENT EXTRACTION WITH COMPLEX EVENT CLASSIFICATION USING RICH FEATURES, Journal of Bioinformatics and Computational Biology, vol.9, issue.01, pp.131-146, 2010. ,
DOI : 10.1093/bioinformatics/btp289
Molecular event extraction from link grammar parse trees, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, pp.86-94, 2009. ,
DOI : 10.3115/1572340.1572353
URL : http://aclweb.org/anthology-new/W/W09/W09-1411.pdf
Extracting biomedical events and modifications using subgraph matching with noisy training data, Proceedings of the BioNLP Shared Task 2013 Workshop, pp.35-44, 2013. ,
From graphs to events: A subgraph matching approach for information extraction from biomedical text ,
Analyzing text in search of bio-molecular events, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, pp.128-136, 2009. ,
DOI : 10.3115/1572340.1572362
Exploring ways beyond the simple supervised learning approach for biological event extraction, Proceedings of the Workshop on BioNLP Shared Task, BioNLP '09, pp.137-140, 2009. ,
DOI : 10.3115/1572340.1572363
Supervised classification for extracting biomedical events, Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pp.111-114, 2009. ,
Medical entity recognition: A comparison of semantic and statistical methods, Proceedings of BioNLP 2011 Workshop, pp.56-64, 2011. ,
Shirish Krishnaj Shevade, and Aun Neow Poo. Multi-category classification by soft-max combination of binary classifiers, 4th International Workshop on Multiple Classifier Systems, 2003. ,
Probabilistic outputs for support vector machines and comparisons to regularized likelihood methods, Advances in Large Margin Classifiers, pp.61-74, 1999. ,
Using two-class classifiers for multiclass classification, Object recognition supported by user interaction for service robots, pp.124-127, 2002. ,
DOI : 10.1109/ICPR.2002.1048253
Yves Van de Peer, and Filip Ginter. EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction, Proceedings of BioNLP Shared Task, 2013. ,
Combining statistical learning with a knowledge-based approach -a case study in intensive care monitoring, Proceedings of the Sixteenth International Conference on Machine Learning (ICML 1999), 1999. ,
Controlling the sensitivity of support vector machines, Proceedings of the International Joint Conference on Artificial Intelligence, pp.55-60, 1999. ,
Algorithms for minimization without derivatives, 1973. ,
Biomedical event extraction from abstracts and full papers using search-based structured prediction, BMC Bioinformatics, vol.13, issue.Suppl 11, p.5, 2012. ,
DOI : 10.1186/1471-2105-13-S11-S5
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S11-S5?site=bmcbioinformatics.biomedcentral.com
A unified architecture for natural language processing, Proceedings of the 25th international conference on Machine learning, ICML '08, 2008. ,
DOI : 10.1145/1390156.1390177
Improving word representations via global context and multiple word prototypes, Proceedings of the 50th Annual Meeting of the Association for Computational Linguistics: Long Papers, pp.873-882, 2012. ,
Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization, ACM Transactions on Mathematical Software, vol.23, issue.4, pp.550-560, 1997. ,
DOI : 10.1145/279232.279236
A simplex method for function minimization, Computer journal, vol.7, issue.4, pp.308-313, 1965. ,
Direct search methods: Once scorned, now respectable, Pitman Research Notes in Mathematics Series, pp.191-208, 1996. ,
An efficient method for finding the minimum of a function of several variables without calculating derivatives. The computer journal, pp.155-162, 1964. ,
Numerical recipes 3rd edition: The art of scientific computing, 2007. ,
Numerical optimization, 1999. ,
Search-based structured prediction, Machine Learning, vol.6, issue.1???2, pp.297-325, 2009. ,
DOI : 10.1007/s10994-009-5106-x
Joint learning of words and meaning representations for open-text semantic parsing, International Conference on Artificial Intelligence and Statistics, pp.127-135, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00752499
Linguistic regularities in continuous space word representations, Proceedings of NAACL-HLT, pp.746-751, 2013. ,
Nouns are vectors, adjectives are matrices: Representing adjective-noun constructions in semantic space, Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing, pp.1183-1193, 2010. ,
On the limited memory bfgs method for large scale optimization, Mathematical programming, vol.45, issue.1-3, pp.503-528, 1989. ,
A comparison of vector-based representations for semantic composition, Proceedings of the 2012 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning, pp.546-556, 2012. ,
Semantic compositionality through recursive matrix-vector spaces, Proceedings of the 2012 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning, pp.1201-1211, 2012. ,
Semi-supervised recursive autoencoders for predicting sentiment distributions, Proceedings of the Conference on Empirical Methods in Natural Language Processing, pp.151-161, 2011. ,
Parsing with compositional vector grammars, Proceedings of the ACL conference. Citeseer, 2013. ,
Coreference based event-argument relation extraction on biomedical text, Journal of Biomedical Semantics, vol.2, issue.Suppl 5, p.6, 2011. ,
DOI : 10.1162/089120101753342653
URL : https://doi.org/10.1186/2041-1480-2-s5-s6
General estimation and evaluation of compositional distributional semantic models, Proceedings of the Workshop on Continuous Vector Space Models and their Compositionality, pp.50-58, 2013. ,
Chinese word segmentation: A decade review, Journal of Chinese Information Processing, vol.21, issue.3, pp.8-20, 2007. ,
Recurrent continuous translation models, EMNLP, pp.1700-1709, 2013. ,