title: Transfer learning of classification rules for biomarker discovery and verification from molecular profiling studies.
abstract: We present a novel framework for integrative biomarker discovery from related but separate data sets created in biomarker profiling studies. The framework takes prior knowledge in the form of interpretable, modular rules, and uses them during the learning of rules on a new data set. The framework consists of two methods of transfer of knowledge from source to target data: transfer of whole rules and transfer of rule structures. We evaluated the methods on three pairs of data sets: one genomic and two proteomic. We used standard measures of classification performance and three novel measures of amount of transfer. Preliminary evaluation shows that whole-rule transfer improves classification performance over using the target data alone, especially when there is more source data than target data. It also improves performance over using the union of the data sets.
authors.affiliation: Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, United States. Electronic address: phil.ganchev@gmail.com.
authors.forename: Philip
authors.initials: P
authors.lastname: Ganchev
authors.affiliation: Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States.
authors.forename: David
authors.initials: D
authors.lastname: Malehorn
authors.affiliation: Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States.
authors.forename: William L
authors.initials: WL
authors.lastname: Bigbee
authors.affiliation: Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, United States; Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, United States. Electronic address: vanathi@pitt.edu.
authors.forename: Vanathi
authors.initials: V
authors.lastname: Gopalakrishnan
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D015415:Biomarkers; D020869:Gene Expression Profiling / Q000379:methods*; D040901:Proteomics
chemical_list: D015415:Biomarkers