Research

My current research work is focused on probabilistic methods for comparative string analysis with applications in computational biology and text mining.

In particular, I work with Marti Hearst on algorithms and infrastructure for text mining in the biosciences domain as part of the BioText project,
and with Lior Pachter on comparative genomics algorithms for improved sequence alignment accuracy, and comparative gene finding.
See my PhD qualifying exam draft research proposal and publications for more details.

Data and Software

• 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.
• ENCODE Alignment agreement custom tracks for the UCSC Genome Browser.
• Layered Query Language (LQL) - Infrastructure and query language for layers of annotated text (Demo and information).
• Abbreviation recognition software.
• Software to parse and load MEDLINE into an RDBMS.

Publications

• A. S. Schwartz and L. Pachter, Multiple Alignment by Sequence Annealing, in the Proceedings of the European Conference on Computation Biology (ECCB), Eilat, Israel, September 2006, to appear.
• A. S. Schwartz, E. W. Myers and L. Pachter, Alignment Metric Accuracy, submitted.
• 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).