Ariel Schwartz's Home Page

Ariel Schwartz

Postdoctoral Scholar
Ideker Lab
Department of Bioengineering
University of California, San Diego

CV

AMAP - fast and accurate amino acid multiple sequence alignment program, which utilizes posterior decoding, and a novel sequence annealing alignment method.
It is the only alignment program that allows to control the sensitivity / specificity tradeoff.
In its default configuration, AMAP is tuned to maximize the expected Alignment Metric Accuracy (AMA) score - a new alignment accuracy measure, based on a metric for the multiple-alignment space, which integrates sensitivity and specificity into a single balanced measure.

Layered Query Language (LQL) - Infrastructure and query language for layers of annotated text (Demo and information).

A. S. Schwartz, Posterior Decoding Methods for Optimization and Accuracy Control of Multiple Alignments, PhD dissertation, EECS Department, University of California, Berkeley, Technical Report No. UCB/EECS-2007-39, March 28, 2007.

A. S. Schwartz, A. Divoli and M. Hearst, Multiple Alignment of Citation Sentences with Conditional Random Fields and Posterior Decoding, Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning (EMNLP-CoNLL), Prague, Czech Republic, June 2007, p 847--857.

A. S. Schwartz and L. Pachter, Multiple Alignment by Sequence Annealing, Bioinformatics 23 (2007), e24–e29. (Best paper award ECCB 2006).

A. S. Schwartz, E. W. Myers and L. Pachter, Alignment Metric Accuracy, submitted.

E.H. Margulies et al., Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome , Genome Research 2007 17: 760--774.

P. Nakov, A. Schwartz, B. Wolf and M. Hearst, Scaling Up BioNLP: Application of a Text Annotation Architecture to Noun Compound Bracketing, in ACL/ISMB BioLINK SIG: Linking Literature, Information and Knowledge for Biology, Detroit, MI, June 2005.

P. Nakov, A. Schwartz, B. Wolf and M. Hearst, Supporting Annotation Layers for Natural Language Processing, in Proceedings of the ACL Interactive Poster and Demonstration Sessions, Ann Arbor, MI, June 2005, p 65--68.

P. I. Nakov, A. S. Schwartz, E. Stoica and M. A. Hearst, BioText Team Experiments for the TREC 2004 Genomics Track, in Proceedings of TREC 2004 Gaithersburg, MD, 2005.

P. I. Nakov, A. Schwartz and M. A. Hearst, Citances: Citation Sentences for Semantic Analysis of Bioscience Text, in the SIGIR'04 Workshop on Search and Discovery in Bioinformatics.

D. E. Oliver, G. Bhalotia, A. S. Schwartz, R. B. Altman and M. A. Hearst, Tools for Loading MEDLINE into a Local Relational Database, BMC Bioinformatics, 5 (146), Oct 2004.

G. Bhalotia, P. I. Nakov, A. S. Schwartz and M. A. Hearst, BioText Team Report for the TREC 2003 Genomics Track, in Proceedings of TREC 2003, Gaithersburg, MD, 2004.

A. S. Schwartz and M. A. Hearst, A Simple Algorithm for Identifying Abbreviation Definitions in Biomedical Text, in the Proceedings of the Pacific Symposium on Biocomputing, 8:451-462(2003).