Publications

General and Miscellaneous

2006 | 2005 | 2004 | 2003

Entity and Relation Extraction

2007 | 2006 | 2005 | 2004

Normalization

2006 | 2005

Parsing

2006 | 2005

General and Miscellaneous

2006

J. Blitzer, R. McDonald, and F. Pereira. Domain Adaptation with Structural Correspondence Learning. In EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, pp. 120-128. Association for Computational Linguistics, 2006. [.pdf]

R. McDonald. Discriminative Sentence Compression with Soft Syntactic Constraints.  In 11th Conference of the European Chapter of the Association for Computational Linguistics: EACL 2006, pp. 297-304. Association for Computational Linguistics, 2006.

Mark A. Mandel. Integrated Annotation of Biomedical Text: Creating the PennBioIE Corpus. March 2006. Text Mining, Ontologies and Natural Language Processing in Biomedicine. [abstract, slides as .pdf]

2005

A. Bies, S. Kulick, and M. Mandel. Parallel Entity and Treebank Annotation. ACL 2005 workshop on "Frontiers in Corpus Annotation II: Pie in the Sky". [.pdf]

2004

S. Kulick, A. Bies, M. Liberman, M. Mandel, R. McDonald, M. Palmer, A. Schein, and L. Ungar. Integrated Annotation for Biomedical Information Extraction. HLT/NAACL, 2004. [.pdf, slides as .ppt]

2003

S. Kulick, M. Liberman, M. Palmer, and A. Schein. Shallow Semantic Annotation of Biomedical Corpora for Information Extraction. To appear in the 2003 ISMB Special Interest Group Meeting on Text Mining (a.k.a. BioLink). June 2003. Brisbane, Australia. [.pdf, .ppt]

Entity and Relation Extraction

2007

K. Ganchev, K. Crammer, F. Pereira, G. Mann, K. Bellare, A. McCallum, S. Carroll, Y. Jin, P. White. Penn/UMass/CHOP Biocreative II Systems. Proceedings of Biocreative 2. [In Press]

K. Ganchev, F. Pereira, M. Mandel, S. Carroll, P. White. Semi-automated Named Entity Annotation. Proceedings of the Linguistic Annotation Workshop 2007. [In Press]

2006

Y. Jin, R. T. McDonald, K. Lerman, M. A. Mandel, S. Carroll, M. Y. Liberman, F. C. Pereira, R. S. Winters, and P. S. White. Automated Recognition of Malignancy Mentions in Biomedical Literature. BMC Bioinformatics 2006, 7:492. [.pdf]

R. McDonald, R.S. Winters, C.K. Ankuda, C.A. Murphy, A.E. Rogers, F. Pereira, M.S. Greenblatt, P.S. White. An Automated Procedure to Identify Biomedical Articles that Contain Cancer-Associated Gene Variants. Human Mutation 2006, Sep;27(9):957-64. [.pdf]

H. Fang, K. Murphy, Y. Jin, J. Kim, and P. White. Human Gene Name Normalization Using Text Matching with Automatically Extracted Synonym Dictionaries. BioNLP, 2006. [.pdf]

P. Talukdar, T. Brants, M. Liberman, and F. Pereira. A Context Pattern Induction Method for Named Entity Extraction. Computational Natural Language Learning (CoNLL-X), 2006. [.pdf]

2005

R. McDonald, F. Pereira, S. Kulick, S. Winters, Y. Jin, and P. White. Simple Algorithms for Complex Relation Extraction with Applications to Biomedical IE. 43rd Annual Meeting of the Association for Computational Linguistics, 2005. [.pdf]

Y. Jin, K. Lerman, M. Liberman, M. Mandel, R. McDonald, F. Pereira, P. White, and S. Winters. Identifying and Extracting Malignancy Types in Cancer Literature. Proceedings of BioLINK 2005. [In Press] [.doc]

R. McDonald and F. Pereira. Identifying Gene and Protein Mentions in Text Using Conditional Random Fields. BMC Bioinformatics 2005, 6(Suppl 1):S6. [.pdf]

2004

R. McDonald, S. Winters, M. Mandel, Y. Jin, P. White, and F. Pereira. An Entity Tagger for Recognizing Acquired Genomic Variations in Cancer Literature. Bioinformatics 2004, 20:3249-3251. [.pdf]

Normalization

2006

T. Sandler, A. I. Schein, and L. H. Ungar. Automatic Term List Generation for Entity Tagging. Bioinformatics 2006, 22(6): 651. [.pdf]

2005

J. Crim, R. McDonald, and F. Pereira. Automatically Annotating Documents with Normalized Gene Lists. BMC Bioinformatics 2005, 6(Suppl 1):S13. [.pdf]

Parsing

2006

R. McDonald, K. Lerman, and F. Pereira. Multilingual Dependency Parsing with a Two-Stage Discriminative Parser. Computational Natural Language Learning (CoNLL-X), 2006.

R. McDonald and F. Pereira. Online Learning of Approximate Dependency Parsing Algorithms. In 11th Conference of the European Chapter of the Association for Computational Linguistics: EACL 2006, pp. 81-88. Association for Computational Linguistics, 2006.  [.pdf]

R. Gabbard, S. Kulick, and M. Marcus. Fully Parsing the Penn Treebank. HLT-NAACL, 2006.

2005

R. McDonald, K. Crammer, and F. Pereira. Flexible Text Segmentation with Structured Multilabel Classification. HLT-EMNLP, 2005. [.pdf]

R. McDonald, F. Pereira, K. Ribarov, and J. Hajic. Non-Projective Dependency Parsing Using Spanning Tree Algorithms. HLT-EMNLP, 2005. (Best Student Paper Award) [.pdf]

R. McDonald, K. Crammer, and F. Pereira. Online Large-Margin Training of Dependency Parsers. 43rd Annual Meeting of the Association for Computational Linguistics, 2005. [.pdf]