\contentsline {section}{\numberline {1}Introduction}{4}{section.1}
\contentsline {section}{\numberline {2}Getting Started: FABIA}{4}{section.2}
\contentsline {subsection}{\numberline {2.1}Quick start : without outputs and plots}{4}{subsection.2.1}
\contentsline {subsection}{\numberline {2.2}Test on Toy Data Set}{6}{subsection.2.2}
\contentsline {subsection}{\numberline {2.3}Demos}{7}{subsection.2.3}
\contentsline {section}{\numberline {3}The FABIA Model}{8}{section.3}
\contentsline {subsection}{\numberline {3.1}Model Assumptions}{8}{subsection.3.1}
\contentsline {subsection}{\numberline {3.2}Sparse Coding and Laplace Prior}{10}{subsection.3.2}
\contentsline {subsection}{\numberline {3.3}Model Selection}{11}{subsection.3.3}
\contentsline {subsubsection}{\numberline {3.3.1}Variational Approach for Sparse Factors}{11}{subsubsection.3.3.1}
\contentsline {subsubsection}{\numberline {3.3.2}New Update Rules for Sparse Loadings}{11}{subsubsection.3.3.2}
\contentsline {subsubsection}{\numberline {3.3.3}Extremely Sparse Priors}{12}{subsubsection.3.3.3}
\contentsline {subsection}{\numberline {3.4}Data Preprocessing and Initialization}{12}{subsection.3.4}
\contentsline {subsection}{\numberline {3.5}Information Content of Biclusters}{13}{subsection.3.5}
\contentsline {subsection}{\numberline {3.6}Extracting Members of Biclusters}{14}{subsection.3.6}
\contentsline {subsection}{\numberline {3.7}C implementation of FABIA}{14}{subsection.3.7}
\contentsline {section}{\numberline {A}Class Factorization}{14}{appendix.A}
\contentsline {section}{\numberline {B}Biclustering and Matrix Factorization Methods}{16}{appendix.B}
\contentsline {subsection}{\numberline {B.1}fabi}{16}{subsection.B.1}
\contentsline {subsection}{\numberline {B.2}fabia}{20}{subsection.B.2}
\contentsline {subsection}{\numberline {B.3}fabiap}{26}{subsection.B.3}
\contentsline {subsection}{\numberline {B.4}fabias}{32}{subsection.B.4}
\contentsline {subsection}{\numberline {B.5}fabiasp}{38}{subsection.B.5}
\contentsline {subsection}{\numberline {B.6}mfsc}{43}{subsection.B.6}
\contentsline {subsection}{\numberline {B.7}nmfdiv}{48}{subsection.B.7}
\contentsline {subsection}{\numberline {B.8}nmfeu}{50}{subsection.B.8}
\contentsline {subsection}{\numberline {B.9}nmfsc}{52}{subsection.B.9}
\contentsline {section}{\numberline {C}Analyzing the Results of Biclustering / Matrix Factorization}{54}{appendix.C}
\contentsline {subsection}{\numberline {C.1}plot}{54}{subsection.C.1}
\contentsline {subsection}{\numberline {C.2}show}{58}{subsection.C.2}
\contentsline {subsection}{\numberline {C.3}showSelected}{59}{subsection.C.3}
\contentsline {subsection}{\numberline {C.4}summary}{60}{subsection.C.4}
\contentsline {subsection}{\numberline {C.5}extract\_bic}{61}{subsection.C.5}
\contentsline {subsection}{\numberline {C.6}extract\_plot}{64}{subsection.C.6}
\contentsline {subsection}{\numberline {C.7}plotBicluster}{66}{subsection.C.7}
\contentsline {section}{\numberline {D}Data Generation Methods}{68}{appendix.D}
\contentsline {subsection}{\numberline {D.1}make\_fabi\_data}{68}{subsection.D.1}
\contentsline {subsection}{\numberline {D.2}make\_fabi\_data\_pos}{70}{subsection.D.2}
\contentsline {subsection}{\numberline {D.3}make\_fabi\_data\_blocks}{72}{subsection.D.3}
\contentsline {subsection}{\numberline {D.4}make\_fabi\_data\_blocks\_pos}{73}{subsection.D.4}
\contentsline {section}{\numberline {E}Utilities}{75}{appendix.E}
\contentsline {subsection}{\numberline {E.1}fabiaVersion}{75}{subsection.E.1}
\contentsline {subsection}{\numberline {E.2}myImagePlot}{76}{subsection.E.2}
\contentsline {subsection}{\numberline {E.3}nprojfunc}{76}{subsection.E.3}
\contentsline {subsection}{\numberline {E.4}projfunc}{77}{subsection.E.4}
\contentsline {subsection}{\numberline {E.5}estimateMode}{78}{subsection.E.5}
\contentsline {subsection}{\numberline {E.6}eqscplotLoc}{79}{subsection.E.6}
\contentsline {section}{\numberline {F}Data Sets}{80}{appendix.F}
\contentsline {subsection}{\numberline {F.1}Breast\_A}{80}{subsection.F.1}
\contentsline {subsection}{\numberline {F.2}DLBCL\_B}{81}{subsection.F.2}
\contentsline {subsection}{\numberline {F.3}Multi\_A}{81}{subsection.F.3}
