Multiple antigen miniarrays can provide accurate tools for cancer detection and diagnosis. These miniarrays can be validated by examining their operating characteristics in classifying individuals as either cancer patients or normal (non-cancer) subjects. We describe the use of restricted Boltzmann machines for this classification problem, relative to diagnosis of hepatocellular carcinoma. In this setting, we find that its operating characteristics are similar to a logistic regression standard and suggest that restricted Boltzmann machines merit further consideration for classification problems. 1. Introduction We have previously investigated the utility of antibody profiles to seven tumor-associated antigens (TAAs) for discriminating between cancer patients and controls [1]. We found that these multiple antigen miniarrays could provide accurate tools for cancer detection and diagnosis and suggested that performance of the miniarrays might be enhanced by other combinations of TAAs appropriately selected for different cancer cohorts. We return to this theme in the present paper, where we examine the utility of an expanded panel of 12 antibody profiles for cancer diagnosis of hepatocellular carcinoma (HCC), based on serum samples from newly diagnosed HCC patients and normal controls. To this end, we apply a fairly recent approach, restricted Boltzmann machines [2–5], to the classification problem at hand. For comparative purposes, we also utilize logistic regression, to provide a baseline of discriminative performance. Our aim here is to determine whether restricted Boltzmann machines provide a viable technique for classification of HCC, compared to the logistic regression standard. 2. Materials and Methods 2.1. Sera Samples In all, sera samples from 175 HCC patients and 90 normal controls were amassed, as follows. Sera from 76 patients with HCC from Xiamen in China were obtained from the serum bank of the Cancer Autoimmunity Research Laboratory at the University of Texas (El Paso, Texas, USA), which were originally provided by a collaborator in Sun Yat-sen University (Guangzhou, China). 84 HCC patients’ sera were collected from Korea and 15 from Japan. Ninety normal human sera (NHS) were originally obtained from the serum bank of the Autoimmune Disease Center at the Scripps Research Institute (La Jolla, CA, USA). All cancer patients were diagnosed according to established criteria; their serum samples were collected at the time of initial cancer diagnosis, when the patients had not received treatment with any chemotherapy or radiation therapy. Normal
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