Learning to construct knowledge bases from the World Wide Web
Artificial Intelligence - Special issue on Intelligent internet systems
Predicting Structured Data (Neural Information Processing)
Predicting Structured Data (Neural Information Processing)
Introduction to Statistical Relational Learning (Adaptive Computation and Machine Learning)
Introduction to Statistical Relational Learning (Adaptive Computation and Machine Learning)
Efficient Weight Learning for Markov Logic Networks
PKDD 2007 Proceedings of the 11th European conference on Principles and Practice of Knowledge Discovery in Databases
Overview of BioNLP'09 shared task on event extraction
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Extracting complex biological events with rich graph-based feature sets
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
A Markov logic approach to bio-molecular event extraction
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
From protein-protein interaction to molecular event extraction
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
The CoNLL-2009 shared task: syntactic and semantic dependencies in multiple languages
CoNLL '09 Proceedings of the Thirteenth Conference on Computational Natural Language Learning: Shared Task
Sound and efficient inference with probabilistic and deterministic dependencies
AAAI'06 Proceedings of the 21st national conference on Artificial intelligence - Volume 1
Joint inference in information extraction
AAAI'07 Proceedings of the 22nd national conference on Artificial intelligence - Volume 1
Unsupervised morphological segmentation with log-linear models
NAACL '09 Proceedings of Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics
Markov Logic: An Interface Layer for Artificial Intelligence
Markov Logic: An Interface Layer for Artificial Intelligence
Two strong baselines for the BioNLP 2009 event extraction task
BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
Automatic construction and multi-level visualization of semantic trajectories
Proceedings of the 18th SIGSPATIAL International Conference on Advances in Geographic Information Systems
Event extraction as dependency parsing
HLT '11 Proceedings of the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies - Volume 1
Search-based structured prediction applied to biomedical event extraction
CoNLL '11 Proceedings of the Fifteenth Conference on Computational Natural Language Learning
Customizing an information extraction system to a new domain
RELMS '11 Proceedings of the ACL 2011 Workshop on Relational Models of Semantics
Biomedical events extraction using the hidden vector state model
Artificial Intelligence in Medicine
Joint inference for cross-document information extraction
Proceedings of the 20th ACM international conference on Information and knowledge management
Overview of BioNLP Shared Task 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Overview of Genia event task in BioNLP Shared Task 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Biomedical event extraction from abstracts and full papers using search-based structured prediction
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Robust biomedical event extraction with dual decomposition and minimal domain adaptation
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
BioNLP Shared Task 2011: supporting resources
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
MSR-NLP entry in BioNLP Shared Task 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Fast and robust joint models for biomedical event extraction
EMNLP '11 Proceedings of the Conference on Empirical Methods in Natural Language Processing
Joint inference of entities, relations, and coreference
Proceedings of the 2013 workshop on Automated knowledge base construction
IJCAI'13 Proceedings of the Twenty-Third international joint conference on Artificial Intelligence
Using compositional semantics and discourse consistency to improve Chinese trigger identification
Information Processing and Management: an International Journal
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Knowledge extraction from online repositories such as PubMed holds the promise of dramatically speeding up biomedical research and drug design. After initially focusing on recognizing proteins and binary interactions, the community has recently shifted their attention to the more ambitious task of recognizing complex, nested event structures. State-of-the-art systems use a pipeline architecture in which the candidate events are identified first, and subsequently the arguments. This fails to leverage joint inference among events and arguments for mutual disambiguation. Some joint approaches have been proposed, but they still lag much behind in accuracy. In this paper, we present the first joint approach for bio-event extraction that obtains state-of-the-art results. Our system is based on Markov logic and adopts a novel formulation by jointly predicting events and arguments, as well as individual dependency edges that compose the argument paths. On the BioNLP'09 Shared Task dataset, it reduced F1 errors by more than 10% compared to the previous best joint approach.