Inference of switching networks by using a piecewise linear formulation

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Tezin Türü: Yüksek Lisans

Tezin Yürütüldüğü Kurum: Orta Doğu Teknik Üniversitesi, Fen Edebiyat Fakültesi, Biyolojik Bilimler Bölümü, Türkiye

Tezin Onay Tarihi: 2005

Öğrenci: DİDEM AKÇAY

Danışman: SEMRA KOCABIYIK

Özet:

Inference of regulatory networks has received attention of researchers from many fields. The challenge offered by this problem is its being a typical modeling problem under insufficient information about the process. Hence, we need to derive the apriori unavailable information from the empirical observations. Modeling by inference consists of selecting or defining the most appropriate model structure and inferring the parameters. An appropriate model structure should have the following properties. The model parameters should be inferable. Given the observation and the model class, all parameters used in the model should have a unique solution restriction of the solution space). The forward model should be accurately computable (restriction of the solution space). The model should be capable of exhibiting the essential qualitative features of the system (limit of the restriction). The model should be relevant with the process (limit of the restriction). A piecewise linear formulation, described by a switching state transition matrix and a switching state transition vector with a Boolean function indicating the switching conditions is proposed for the inference of gene regulatory networks. This thesis mainly concerns using a formulation of switching networks obeying all the above mentioned requirements and developing an inference algorithm for estimating the parameters of the formulation. The methodologies used or developed during this study are applicable to various fields of science and engineering.