Proteomics enables understanding the composition, structure, function and interactions of the entire protein complement of a cell, a tissue, or an organism under exactly defined conditions. Some factors such as stress or drug effects will change the protein pattern and cause the present or absence of a protein or gradual variation in abundances. Changes in the proteome provide a snapshot of the...

Devising fast and scalable algorithms, able to crunch huge amount of data, was for many years one of the main goals of data mining research. But then we realized that this was not enough. It does not matter how efficient such algorithms can be, the results we obtain are often of limited use in practice. Typically, the knowledge we seek is in a small pool of local patterns hidden within an ocean...

In this thesis we have developed novel methods for analyzing biological data, the primary sequences of the DNA and proteins, the microarray based gene expression data, and other functional genomics data. The main contribution is the development of the pattern discovery algorithm SPEXS, accompanied by several practical applications for analyzing real biological problems. For performing these bio...

y Abstract Future research directions in Knowledge Discovery in Databases (KDD) include the ability to extract an overlying concept relating useful data. Current limitations involve the search complexity to nd that concept and what it means to be \useful." The Pattern Theory research crosses over in a natural way to the aforementioned domain. The goal of this paper is threefold. First, we prese...

Finding a good pattern which discriminates one set of strings from the other set is a critical task in knowledge discovery. In this paper, we review a series of our works concerning with the string pattern discovery. It includes theoretical analyses of learnabilities of some pattern classes, as well as development of practical data structures which support efficient string processing.