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Measuring Over-Generalization in the Minimal Multiple Generalizations of Biosequences

  • Yen Kaow Ng
  • Hirotaka Ono
  • Takeshi Shinohara
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3735)

Abstract

We consider the problem of finding a set of patterns that best characterizes a set of strings. To this end, Arimura et. al. [3] considered the use of minimal multiple generalizations (mmg) for such characterizations. Given any sample set, the mmgs are, roughly speaking, the most (syntactically) specific set of languages containing the sample within a given class of languages. Takae et. al. [17] found the mmgs of the class of pattern languages [1] which includes so-called sort symbols to be fairly accurate as predictors for signal peptides. We first reproduce their results using updated data. Then, by using a measure for estimating the level of over-generalizations made by the mmgs, we show results that explain the high level of accuracies resulting from the use of sort symbols, and discuss how better results can be obtained. The measure that we suggests here can also be applied to other types of patterns, e.g. the PROSITE patterns [4].

Keywords

Positive Accuracy Regular Pattern Pattern Language Coverage 2x10 Kyushu Institute 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Yen Kaow Ng
    • 1
  • Hirotaka Ono
    • 2
  • Takeshi Shinohara
    • 3
  1. 1.Graduate School of Computer Science and SystemsKyushu Institute of TechnologyIizukaJapan
  2. 2.Department of Computer Science and Communication EngineeringKyushu UniversityFukuokaJapan
  3. 3.Department of Artificial IntelligenceKyushu Institute of TechnologyIizukaJapan

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