Comparing deep belief networks with support vector machines for classifying gene expression data from complex disorders

Johannes Smolander, Matthias Dehmer, Frank Emmert-Streib

Research output: Contribution to journalArticlepeer-review

25 Citations (Scopus)


Genomics data provide great opportunities for translational research and the clinical practice, for example, for predicting disease stages. However, the classification of such data is a challenging task due to their high dimensionality, noise, and heterogeneity. In recent years, deep learning classifiers generated much interest, but due to their complexity, so far, little is known about the utility of this method for genomics. In this paper, we address this problem by studying a computational diagnostics task by classification of breast cancer and inflammatory bowel disease patients based on high-dimensional gene expression data. We provide a comprehensive analysis of the classification performance of deep belief networks (DBNs) in dependence on its multiple model parameters and in comparison with support vector machines (SVMs). Furthermore, we investigate combined classifiers that integrate DBNs with SVMs. Such a classifier utilizes a DBN as representation learner forming the input for a SVM. Overall, our results provide guidelines for the complex usage of DBN for classifying gene expression data from complex diseases.

Original languageEnglish
Pages (from-to)1232-1248
Number of pages17
JournalFEBS Open Bio
Issue number7
Publication statusPublished - Jul 2019


  • artificial intelligence
  • deep belief network
  • deep learning
  • genomics
  • neural networks
  • support vector machine
  • Gene Expression Profiling/methods
  • Neural Networks, Computer
  • Gene Expression
  • Artificial Intelligence
  • Genomics
  • Humans
  • Male
  • Support Vector Machine
  • Computational Biology/methods
  • Machine Learning
  • Deep Learning
  • Sequence Analysis, DNA/methods
  • Breast Neoplasms/classification
  • Female
  • Inflammatory Bowel Diseases/classification


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