ALVIS BRAZMA

Scientific interests:

bioinformatics and computational biology,
machine learning, data mining, and algorithmic learning theory,
string algorithms,
graph drawing and scientific visualization,
program synthesis and logic programming.

Currently working on data mining in biosequence data bases (see Transcription Factor Combintaion Discoverer), and applications of minimum description length (MDL) principle to automatic discovery of patterns in biosequences (see significant publications ).

Academic degrees and employment history:

Ph.D. - Moscow State University, 1988 (Computer Science)
M.Sc. - University of Latvia, 1982 (Mathematics and Physics)

Currently Associate Professor at University of Latvia
and visiting researcher at the European Bioinformatics Institute, Cambridge, UK; Has worked at New Mexico State University, USA, 1991-1992; University of Helsinki, Finland, 1995-1996; and University of Latvia;

Address:

Institute of Mathematics and Computer Science
University of Latvia
29 Rainis Blvd., Riga, LV-1459, Latvia
Phone: +371-7213 716
Fax: +371-7820 153
Email: abra@cclu.lv

List of Important Publications


A. Brazma, J. Vilo, E. Ukkonen, K. Valtonen. Data mining for regulatory elements in yeast genome. In Proc. of 5th International Conference Intelligent Systems for Molecular Biology ISMB'97, AAAI Press, 1997, p.65-74.
A. Brazma, K. Cerans. Noise-tolerant inductive synthesis of regular expressions from good examples. New Generation Computing, Vol. 15, Januray 1997, p. 105-140.
A. Brazma. Efficient learning of regular expressions from approximate examples. In Computational Learning Theory and Natural Learning Systems, Vol 4, MIT Press, 1997, p.351--366.
A. Brazma, E. Ukkonen, J. Vilo. Discovering unbounded unions of regular pattern languages from positive examples. In Proc. of the 7th Annual International Symposium on Algorithms and Computation (ISAAC-96), Lect. Notes in Coputer Science, vol. 1178, 1996, p.95-104.
A. Brazma, I. Jonassen, E. Ukkonen, J. Vilo. Discovering patterns and subfamilies in biosequences, In Proc. of 4th International Conference Intelligent Systems for Molecular Biology ISMB'96, AAAI Press, 1996, p.34-43.
A. Brazma, I. Jonassen, I.Eidhammer, D. Gilbert. Approaches to Automatic Discovery of Patterns in Biosequences, Technical Report (accepted for publication in the Journal of Computational Biology), Department of Informatics, University of Bergen, TR-113, 1995, Bergen, Norway, 42 pp. (available ftp://ftp.ii.uib.no/pub/bio/papers/, file name survey.ps).
A. Brazma, E. Ukkonen, J. Vilo. Finding a Good Collection of Patterns Covering a set of Sequences, Technical Report C-1995-60, Department of Computer Science, University of Helsinki, P. O. Bo 26, FIN-00014, University of Helsinki, December 1995 (available ftp://ftp.cs.helsinki.fi/pub/Reports/).
A. Brazma. Learning of regular expressions by pattern matching. In Proc. of 2nd European Conf. on Computational Learning - EuroColt'95 Lect. Notes in AI, Springer, 904, 1995, p.392-403.
K. Kaugars, J. Reinfelds, A. Brazma. A simple algorithm for drawing large graphs on small screens. In Proc. of Graph Drawing 94, Lect. Notes in Comp. Sci., 894, Springer, 1995, p.278-281.
A. Brazma. Efficient algorithm for learning simple regular expressions from noisy examples. In Proc. of Int. Annual. Workshop on Algorithmic Learning Theory ALT'94, Lect. Notes in AI, 872, Springer, 1994, p.260-271.
A. Brazma, K.Cerans. Efficient learning of regular expressions from good examples. In Proc. of Int. Workshop on Analogical and Inductive Inference AII'94, Lect. Notes in AI, 872, Springer, 1994, p.76-90.
A. Brazma. Efficient identification of regular expressions from representative examples. In Proc. of the 6th Annual Workshop on Computational Learning Theory COLT'93, ACM press, 1993, p.236-242.
A. Brazma. Learning a subclass of regular expressions by recognizing periodic repetitions. In Proc. of the 4th Scandinavian Conference on Artificial Intelligence, IOS Press, the Netherlands, 1993, p.137-146.
A. Brazma. Inductive synthesis of dot expressions. Lect. Notes in Computer Science, Vol 502, Springer, 1991, p.156-212.
J. Barzdin, A. Brazma, J. Kinber. Models of inductive syntactical synthesis. Machine Intelligence, Vol 12, Oxford University Press, 1990, p.139-148.
J. Kinber, A. Brazma. Models of inductive synthesis. Journal of Logic Programming, 9, (Sept./Oct.), 1990, p.221-233.
A. Brazma, J. Kinber. Generalized regular expressions - a language for synthesis of programs with branching in loops. Theoretical Computer Science, 46, 1986, p.175-195, North Holland.