title: Multi-class BCGA-ELM based classifier that identifies biomarkers associated with hallmarks of cancer.
abstract: BACKGROUND
  Traditional cancer treatments have centered on cytotoxic drugs and general purpose chemotherapy that may not be tailored to treat specific cancers. Identification of molecular markers that are related to different types of cancers might lead to discovery of drugs that are patient and disease specific. This study aims to use microarray gene expression cancer data to identify biomarkers that are indicative of different types of cancers. Our aim is to provide a multi-class cancer classifier that can simultaneously differentiate between cancers and identify type-specific biomarkers, through the application of the Binary Coded Genetic Algorithm (BCGA) and a neural network based Extreme Learning Machine (ELM) algorithm.
  
  
  RESULTS
  BCGA and ELM are combined and used to select a subset of genes that are present in the Global Cancer Mapping (GCM) data set. This set of candidate genes contains over 52 biomarkers that are related to multiple cancers, according to the literature. They include APOA1, VEGFC, YWHAZ, B2M, EIF2S1, CCR9 and many other genes that have been associated with the hallmarks of cancer. BCGA-ELM is tested on several cancer data sets and the results are compared to other classification methods. BCGA-ELM compares or exceeds other algorithms in terms of accuracy. We were also able to show that over 50% of genes selected by BCGA-ELM on GCM data are cancer related biomarkers.
  
  
  CONCLUSIONS
  We were able to simultaneously differentiate between 14 different types of cancers, using only 92 genes, to achieve a multi-class classification accuracy of 95.4% which is between 21.6% and 38% higher than other results in the literature for multi-class cancer classification. Our findings suggest that computational algorithms such as BCGA-ELM can facilitate biomarker-driven integrated cancer research that can lead to a detailed understanding of the complexities of cancer.
authors.affiliation: Department of Information, Communication and Electronics Engineering, Catholic University of Korea, Bucheon, Republic of Korea. bassvasys@hotmail.com.
authors.forename: Vasily
authors.initials: V
authors.lastname: Sachnev
authors.affiliation: Battelle Center for Mathematical Medicine at The Research Institute at Nationwide Children's Hospital; currently at Sidra, Medical and Research Center, Doha, Qatar. ssundararajan@sidra.org.
authors.forename: Saras
authors.initials: S
authors.lastname: Saraswathi
authors.affiliation: Department of Medical Informatics, Sidra Medical and Research Center, Doha, Qatar. rniaz@sidra.org.
authors.forename: Rashid
authors.initials: R
authors.lastname: Niaz
authors.affiliation: Battelle Center for Mathematical Medicine at The Research Institute at Nationwide Children's Hospital; Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, USA. andrzej.kloczkowski@nationwidechildrens.org.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kloczkowski
authors.affiliation: School of Computer Science, Nanyang Technological University, Nanyang, Singapore. ssundaram@ntu.edu.sg.
authors.forename: Sundaram
authors.initials: S
authors.lastname: Suresh
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D014408:Biomarkers, Tumor / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009369:Neoplasms / Q000145:classification* / Q000175:diagnosis* / Q000235:genetics; D016571:Neural Networks, Computer; D020411:Oligonucleotide Array Sequence Analysis; D010363:Pattern Recognition, Automated
chemical_list: D014408:Biomarkers, Tumor