1. Global Discriminative Training for Higher-Accuracy Computational Gene Prediction
    A. Bernal, K. Crammer, A. Hatzigeorgiou, and F. Pereira
    PLoS Computational Biology  3(3):e54  (2007)
    compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0030054
  2. Analysis of Representations for Domain Adaptation
    S. Ben-David, J. Blitzer, K. Crammer, and F. Pereira
    Advances in Neural Information Processing Systems 20    (2007)
    PDF/nips06.pdf
  3. "Sorry I forgot the attachment": Email Attachment Prediction
    M. Dredze, J. Blitzer, and F. Pereira
    3rd Conference on Email and Anti-Spam    (2006)
    PDF/ceas06.pdf
  4. Automated recognition of malignancy mentions in biomedical literature.
    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
    BMC Bioinformatics  7  492  (2006)
    http://www.biomedcentral.com/1471-2105/7/492
  5. An automated procedure to identify biomedical articles that contain cancer-associated gene variants
    R. McDonald, R. Scott Winters, C. K. Ankuda, J. A. Murphy, A. E. Rogers, F. Pereira, M. S. Greenblatt, and P. S. White
    Human Mutation  27  957-64  (2006)
    http://www3.interscience.wiley.com/cgi-bin/abstract/112729153/ABSTRACT
  6. A Context Pattern Induction Method for Named Entity Extraction
    P. P. Talukdar, T. Brants, M. Liberman, and F. Pereira
    Tenth Conference on Computational Natural Language Learning (CoNLL-X)    (2006)
    PDF/cpi_conll2006_camera.pdf
  7. Multilingual Dependency Parsing with a Two-Stage Discriminative Parser
    R. McDonald, K. Lerman, and F. Pereira
    Tenth Conference on Computational Natural Language Learning (CoNLL-X)    (2006)
    PDF/conll2006.pdf
  8. Domain Adaptation with Structural Correspondence Learning
    J. Blitzer, R. McDonald, and F. Pereira
    EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing  120-128  (2006)
    PDF/transferEMNLP06.pdf
  9. Online Learning of Approximate Dependency Parsing Algorithms
    R. McDonald and F. Pereira
    11th Conference of the European Chapter of the Association for Computational Linguistics: EACL 2006  81-88  (2006)
    PDF/approxDepEACL2006.pdf
  10. Flexible Text Segmentation with Structured Multilabel Classification
    R. McDonald, K. Crammer, and F. Pereira
    Proceedings of HLT/EMNLP 2005    (2005)
    PDF/segmentationHLT-EMNLP2005.pdf
  11. Non-projective Dependency Parsing using Spanning Tree Algorithms
    R. McDonald, F. Pereira, K. Ribarov, and J. Haji\v{c}
    Proceedings of HLT/EMNLP 2005    (2005)
    PDF/nonprojectiveHLT-EMNLP2005.pdf
  12. A Conditional Random Field for Discriminatively-trained Finite-state String Edit Distance
    A. McCallum, K. Bellare, and F. Pereira
    Proceedings of the 21st Conference on Uncertainty in Artificial Intelligence (UAI 2005)    (2005)
    PDF/crfstredit.pdf
  13. Simple Algorithms for Complex Relation Extraction with Applications to Biomedical IE
    R. McDonald, F. Pereira, S. Kulick, S. Winters, Y. Jin, and P. White
    43rd Annual Meeting of the Association for Computational Linguistics (ACL 2005)    (2005)
    PDF/relationACL2005.pdf
  14. Online Large-Margin Training of Dependency Parsers
    R. McDonald, K. Crammer, and F. Pereira
    43rd Annual Meeting of the Association for Computational Linguistics (ACL 2005)    (2005)
    PDF/dependencyACL2005.pdf
  15. Automatically annotating documents with normalized gene lists
    J. Crim, R. McDonald, and F. Pereira
    {BMC} Bioinformatics  6  S13  (2005)
    http://www.biomedcentral.com/1471-2105/6/S1/S13
  16. Identifying Gene and Protein Mentions in Text Using Conditional Random Fields
    R. McDonald and F. Pereira
    {BMC} Bioinformatics  6  S6  (2005)
    http://www.biomedcentral.com/1471-2105/6/S1/S6
  17. Reply Expectation Prediction for Email Management
    M. Dredze, J. Blitzer, and F. Pereira
    2nd Conference on Email and Anti-Spam    (2005)
    PDF/ceas05.pdf
  18. Distributed Latent Variable Models of Lexical Co-occurrences
    J. Blitzer, A. Globerson, and F. Pereira
    Tenth International Workshop on Artificial Intelligence and Statistics    (2005)
    PDF/aistats.pdf
  19. Hierarchical Distributed Representations for Statistical Language Modeling
    J. Blitzer, K. Weinberger, L. Saul, and F. Pereira
    Advances in Neural Information Processing Systems 17    (2004)
    PDF/nips04.pdf
  20. Euclidean Embedding of Co-occurrence Data
    A. Globerson, G. Chechik, F. Pereira, and N. Tishby
    Advances in Neural Information Processing Systems 17    (2004)
    PDF/CODE_final.pdf
  21. Case-Factor Diagrams for Structured Probabilistic Modeling
    D. McAllester, M. Collins, and F. Pereira
    Proceedings of the 20th Conference on Uncertainty in Artificial Intelligence    (2004)
    PDF/casefactor.pdf
  22. An entity tagger for recognizing acquired genomic variations in cancer literature
    R. T. McDonald, R. S. Winters, M. Mandel, Y. Jin, P. S. White, and F. Pereira
    Bioinformatics  20  3249 - 3251  (2004)
    http://bioinformatics.oupjournals.org/cgi/reprint/20/17/3249
  23. Shallow Parsing with Conditional Random Fields
    F. Sha and F. Pereira
    Proceedings of HLT-NAACL 2003  213-220  (2003)
    PDF/shallow.pdf
  24. Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data
    J. Lafferty, A. McCallum, and F. Pereira
    Proceedings of ICML-01  282-289  (2001)
    PDF/crf.pdf
  25. Maximum Entropy Markov Models for Information Extraction and Segmentation
    A. McCallum, D. Freitag, and F. Pereira
    Machine Learning: Proceedings of the Seventeenth International Conference (ICML 2000)  591-598  (2000)
    PDF/memm-icml2000.pdf