Learning Local Languages and Their Application to DNA Sequence Analysis

—This paper concerns an efficient algorithm for learning in the limit a special type of regular languages called strictly locally testable languages from positive data, and its application to identifying the protein a-chain region in amino acid sequences. First, we present a linear time algorithm that, given a strictly locally testable language, learns (identifies) its deterministic finite state automaton in the limit from only positive data. This provides us with a practical and efficient method for learning a specific concept domain of sequence analysis. We then describe several experimental results using the learning algorithm developed above. Following a theoretical observation which strongly suggests that a certain type of amino acid sequences can be expressed by a locally testable language, we apply the learning algorithm to identifying the protein a-chain region in amino acid sequences for hemoglobin. Experimental scores show an overall success rate of 95 percent correct ident...

• Type: Journal
• Year: 1998
• Where: PAMI
• Authors: Takashi Yokomori, Satoshi Kobayashi
• Keywords: Acid Sequences, Amino Acid, PAMI 1998, Testable Language