Cancer Classification with Data-dependent Kernels.ppt

DIMACS Workshop on Machine Learning Techniques in Bioinformatics Cancer Classification with Data-dependent Kernels Anne Ya Zhang (with Xue-wen Chen Huilin Xiong) EECS ITTC University of Kansas Outline Introduction Data-dependent Kernel Results Conclusion Cancer facts Cancer is a group of many related diseases Cells continue to grow and divide and do not die when they should. Changes in the genes that control normal cell growth and death. Cancer is the second leading cause of death in the United States Cancer causes 1 of every 4 deaths NIH estimate overall costs for cancer in 2004 at $189.8 billion ($64.9 billion for direct medical cost) Cancer types Breast cancer, Lung cancer, Colon cancer, … Death rates vary greatly by cancer type and stage at diagnosis Motivation Why do we need to classify cancers? The general way of treating cancer is to: Categorize the cancers in different classes Use specific treatment for each of the classes Traditional way to classify cancers Morphological appearance Not accurate! Enzyme-based histochemical analyses. Immunophenotyping. Cytogenetic analysis. Complicated needs highly specialized laboratories Motivation Why traditional ways are not enough ? There exists some tumors in the same class with completely different clinical courses May be more accurate classification is needed Assigning new tumors to known cancer classes is not easy e.g. assigning an acute leukemia tumor to one of the AML (acute myeloid leukemia) ALL (acute lymphoblastic leukemia) DNA Microarray-based Cancer Diagnosis Cancer is caused by changes in the genes that control normal cell growth and death. Molecular diagnostics offer the promise of precise, objective, and systematic cancer classification These tests are not widely applied because characteristic molecular markers for most solid tumors have to be identified. Recently, microarray tumor gene expression profiles have been used for cancer diagnosis. Microarray A microarray experiment monitors the express