An evolutionary kernel-based reasoning system using reconfigurable VLSIs: its hardware prototyping and application to the splicing boundary problem

Author

Yasunaga, Moritoshi ; Ushiyama, Kentaro ; Aibe, Noriyuki ; Fujiwara, Hidetoshi ; Yoshiyara, Ikuo ; Kim, Jung H.

Author_Institution

Inst. of Inf. Sci. & Electron., Univ. of Tsukuba, Japan

Volume

1

fYear

2002

Firstpage

285

Lastpage

290

Abstract

We propose a novel reasoning algorithm SKBR (symbolical kernel-bases reasoning) that is an extension of the conventional pattern recognition algorithm KB (kernel based method) to the symbolical recognition, or reasoning. We apply SKMR to the splicing boundary prediction problem in human and other species DNA data, and show a new rule extracted from the splice site boundary. We also develop a SKBR hardware system using FPGA and memory LSIs. Performance evaluation of the system shows its very short reasoning time of less than 100 micro-second/query

Keywords

VLSI; field programmable gate arrays; inference mechanisms; logic CAD; pattern recognition; reconfigurable architectures; FPGA; evolutionary kernel-based reasoning system; hardware prototyping; pattern recognition algorithm; performance evaluation; reasoning algorithm; reconfigurable VLSIs; splicing boundary problem; symbolical kernel-bases reasoning; symbolical recognition; Bioinformatics; DNA; Genomics; Hardware; Informatics; Kernel; Pattern recognition; Prototypes; Splicing; Very large scale integration;

fLanguage

English

Publisher

ieee

Conference_Titel

Evolutionary Computation, 2002. CEC '02. Proceedings of the 2002 Congress on

Print_ISBN

0-7803-7282-4

Type

conf

DOI

10.1109/CEC.2002.1006248

Filename

1006248