Gene Ontology-based Similarity Measures for Gene Clustering and Knowledge Discovery

Computing with words and perceptions, or CWP for short, is a mode of computing in which the objects of computation are words, propositions and perceptions described in a natural language. Perceptions play a key role in human cognition. Humans-but not machines-have a remarkable capability to perform a wide variety of physical and mental tasks without any measurements and any computations. Everyday examples of such tasks are driving a car in city traffic, playing tennis and summarizing a book. One of the major aims of CWP is to serve as a basis for equipping machines with a capability to operate on perception-based information. A key idea in CWP is that of dealing with perceptions through their descriptions in a natural language. In this way, computing and reasoning with perceptions is reduced to operating on propositions drawn from a natural language. In CWP, what is employed for this purpose is PNL (Precisiated Natural Language.) In PNL, a proposition, p, drawn from a natural language, NL, is represented as a generalized constraint, with the language of generalized constraints, GCL, serving as a precisiation language for computation and reasoning, PNL is equipped with two dictionaries and a modular multiagent deduction database. The rules of deduction are expressed in what is referred to as the Protoform Language (PFL). Any measurement-based theory, T, may be generalized to a perception-based theory, Tp, by adding to T the capability to operate on perception-based information. Two generalizations that are of particular importance involve probability theory, PT, and decision analysis, DA. Conceptually, computationally and mathematically, PTp and DAp are significantly more complex than their measurement-based versions. In this instance, as in many others, complexity is the price that has to be paid to reduce the gap between theory and reality. Knowledge Base-Clustering of Multi-Class SVM for Genes Expression Analysis Theodore B. Trafalis , Budi Santosa and Tyrrell Conway School of Industrial Engineering, University of Oklahoma Department of Botany and Microbiology, University of Oklahoma