Information Retrieval
Introduction to the CoNLL-2003 shared task: language-independent named entity recognition
CONLL '03 Proceedings of the seventh conference on Natural language learning at HLT-NAACL 2003 - Volume 4
Annotating multiple types of biomedical entities: a single word classification approach
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Named entity recognition in biomedical texts using an HMM model
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Exploiting context for biomedical entity recognition: from syntax to the web
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Adapting an NER-system for German to the biomedical domain
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Exploring deep knowledge resources in biomedical name recognition
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
POSBIOTM-NER in the shared task of BioNLP/NLPBA 2004
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Biomedical named entity recognition using conditional random fields and rich feature sets
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Instance Filtering for entity recognition
ACM SIGKDD Explorations Newsletter - Natural language processing and text mining
A search result clustering method using informatively named entities
Proceedings of the 7th annual ACM international workshop on Web information and data management
ME-based biomedical named entity recognition using lexical knowledge
ACM Transactions on Asian Language Information Processing (TALIP)
Boosting performance of bio-entity recognition by combining results from multiple systems
Proceedings of the 5th international workshop on Bioinformatics
Accelerated training of conditional random fields with stochastic gradient methods
ICML '06 Proceedings of the 23rd international conference on Machine learning
Text mining without document context
Information Processing and Management: an International Journal - Special issue: Informetrics
Improving the scalability of semi-Markov conditional random fields for named entity recognition
ACL-44 Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the Association for Computational Linguistics
Rich features based Conditional Random Fields for biological named entities recognition
Computers in Biology and Medicine
Computational Biology and Chemistry
Exploiting the contextual cues for bio-entity name recognition in biomedical literature
Journal of Biomedical Informatics
Evaluating and Comparing Biomedical Term Identification Systems
ICIC '08 Proceedings of the 4th international conference on Intelligent Computing: Advanced Intelligent Computing Theories and Applications - with Aspects of Theoretical and Methodological Issues
Semantic Classification of Bio-Entities Incorporating Predicate-Argument Features
IEICE - Transactions on Information and Systems
The development of a schema for semantic annotation: Gain brought by a formal ontological method
Applied Ontology - Biomedical Ontology in Action
Data Mining and Knowledge Discovery
BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
Recognizing nested named entities in GENIA corpus
BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
Biomedical term recognition with the perceptron HMM algorithm
BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
Accelerating the annotation of sparse named entities by dynamic sentence selection
BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
How to make the most of NE dictionaries in statistical NER
BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
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
Annotation of chemical named entities
BioNLP '07 Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing
Recognising nested named entities in biomedical text
BioNLP '07 Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing
Reranking for biomedical named-entity recognition
BioNLP '07 Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing
Brief Communication: Two-phase biomedical named entity recognition using CRFs
Computational Biology and Chemistry
EACL '09 Proceedings of the 12th Conference of the European Chapter of the Association for Computational Linguistics
An analysis of active learning strategies for sequence labeling tasks
EMNLP '08 Proceedings of the Conference on Empirical Methods in Natural Language Processing
MMR-based active machine learning for bio named entity recognition
NAACL-Short '06 Proceedings of the Human Language Technology Conference of the NAACL, Companion Volume: Short Papers
A comparison of tagging strategies for statistical information extraction
NAACL-Short '06 Proceedings of the Human Language Technology Conference of the NAACL, Companion Volume: Short Papers
Tools to address the interdependence between tokenisation and standoff annotation
NLPXML '06 Proceedings of the 5th Workshop on NLP and XML: Multi-Dimensional Markup in Natural Language Processing
SETQA-NLP '09 Proceedings of the Workshop on Software Engineering, Testing, and Quality Assurance for Natural Language Processing
Feature selection techniques for maximum entropy based biomedical named entity recognition
Journal of Biomedical Informatics
Corpus design for biomedical natural language processing
ISMB '05 Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics
LNLBioNLP '06 Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Recognizing nested named entities in GENIA corpus
LNLBioNLP '06 Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Biomedical term recognition with the perceptron HMM algorithm
LNLBioNLP '06 Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Latent variable perceptron algorithm for structured classification
IJCAI'09 Proceedings of the 21st international jont conference on Artifical intelligence
Using conditional random fields for result identification in biomedical abstracts
Integrated Computer-Aided Engineering
Classifier subset selection for biomedical named entity recognition
Applied Intelligence
Stochastic gradient descent training for L1-regularized log-linear models with cumulative penalty
ACL '09 Proceedings of the Joint Conference of the 47th Annual Meeting of the ACL and the 4th International Joint Conference on Natural Language Processing of the AFNLP: Volume 1 - Volume 1
Towards a methodology for named entities annotation
ACL-IJCNLP '09 Proceedings of the Third Linguistic Annotation Workshop
Investigating the effects of selective sampling on the annotation task
CONLL '05 Proceedings of the Ninth Conference on Computational Natural Language Learning
Scalable biomedical Named Entity Recognition: investigation of a database-supported SVM approach
International Journal of Bioinformatics Research and Applications
PAKDD'07 Proceedings of the 2007 international conference on Emerging technologies in knowledge discovery and data mining
Recognizing biomedical named entities in Chinese research abstracts
Canadian AI'08 Proceedings of the Canadian Society for computational studies of intelligence, 21st conference on Advances in artificial intelligence
DAS '10 Proceedings of the 9th IAPR International Workshop on Document Analysis Systems
A composite kernel for named entity recognition
Pattern Recognition Letters
Efficient Extraction of Protein-Protein Interactions from Full-Text Articles
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast and simple semantic class assignment for biomedical text
BioNLP '11 Proceedings of BioNLP 2011 Workshop
SimSem: fast approximate string matching in relation to semantic category disambiguation
BioNLP '11 Proceedings of BioNLP 2011 Workshop
Learning with lookahead: can history-based models rival globally optimized models?
CoNLL '11 Proceedings of the Fifteenth Conference on Computational Natural Language Learning
DS'06 Proceedings of the 9th international conference on Discovery Science
Biomedical named entities recognition using conditional random fields model
FSKD'06 Proceedings of the Third international conference on Fuzzy Systems and Knowledge Discovery
Overview of the infectious diseases (ID) task of BioNLP Shared Task 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Instance pruning by filtering uninformative words: an information extraction case study
CICLing'05 Proceedings of the 6th international conference on Computational Linguistics and Intelligent Text Processing
Boosting performance of gene mention tagging system by hybrid methods
Journal of Biomedical Informatics
Exploring predicate-argument relations for named entity recognition in the molecular biology domain
DS'05 Proceedings of the 8th international conference on Discovery Science
Incremental maintenance of biological databases using association rule mining
PRIB'06 Proceedings of the 2006 international conference on Pattern Recognition in Bioinformatics
Grammatical inference in practice: a case study in the biomedical domain
ICGI'06 Proceedings of the 8th international conference on Grammatical Inference: algorithms and applications
A generic classifier-ensemble approach for biomedical named entity recognition
PAKDD'12 Proceedings of the 16th Pacific-Asia conference on Advances in Knowledge Discovery and Data Mining - Volume Part I
Active learning technique for biomedical named entity extraction
Proceedings of the International Conference on Advances in Computing, Communications and Informatics
Domain adaptation of a dependency parser with a class-class selectional preference model
ACL '12 Proceedings of ACL 2012 Student Research Workshop
Building trainable taggers in a web-based, UIMA-supported NLP workbench
ACL '12 Proceedings of the ACL 2012 System Demonstrations
Classifying gene sentences in biomedical literature by combining high-precision gene identifiers
BioNLP '12 Proceedings of the 2012 Workshop on Biomedical Natural Language Processing
Open-domain anatomical entity mention detection
ACL '12 Proceedings of the Workshop on Detecting Structure in Scholarly Discourse
Biomedical named entity recognition: a poor knowledge HMM-based approach
NLDB'07 Proceedings of the 12th international conference on Applications of Natural Language to Information Systems
Topic-Oriented words as features for named entity recognition
CICLing'13 Proceedings of the 14th international conference on Computational Linguistics and Intelligent Text Processing - Volume Part I
Introducing baselines for russian named entity recognition
CICLing'13 Proceedings of the 14th international conference on Computational Linguistics and Intelligent Text Processing - Volume Part I
Stacked ensemble coupled with feature selection for biomedical entity extraction
Knowledge-Based Systems
Unsupervised biomedical named entity recognition: Experiments with clinical and biological texts
Journal of Biomedical Informatics
Towards a Protein-Protein Interaction information extraction system: Recognizing named entities
Knowledge-Based Systems
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We describe here the JNLPBA shared task of bio-entity recognition using an extended version of the GENIA version 3 named entity corpus of MEDLINE abstracts. We provide background information on the task and present a general discussion of the approaches taken by participating systems.