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Improving accuracy for cancer classification with a new algorithm for genes selection.

ABSTRACT: BACKGROUND: Even though the classification of cancer tissue samples based on gene expression data has advanced considerably in recent years, it faces great challenges to improve accuracy. One of the challenges is to establish an effective method that can select a parsimonious set of relevant genes. So far, most methods for gene selection in literature focus on screening individual or pairs of genes without considering the possible interactions among genes. Here we introduce a new computational method named the Binary Matrix Shuffling Filter (BMSF). It not only overcomes the difficulty associated with the search schemes of traditional wrapper methods and overfitting problem in large dimensional search space but also takes potential gene interactions into account during gene selection. This method, coupled with Support Vector Machine (SVM) for implementation, often selects very small number of genes for easy model interpretability. RESULTS: We applied our method to 9 two-class gene expression datasets involving human cancers. During the gene selection process, the set of genes to be kept in the model was recursively refined and repeatedly updated according to the effect of a given gene on the contributions of other genes in reference to their usefulness in cancer classification. The small number of informative genes selected from each dataset leads to significantly improved leave-one-out (LOOCV) classification accuracy across all 9 datasets for multiple classifiers. Our method also exhibits broad generalization in the genes selected since multiple commonly used classifiers achieved either equivalent or much higher LOOCV accuracy than those reported in literature. CONCLUSIONS: Evaluation of a gene's contribution to binary cancer classification is better to be considered after adjusting for the joint effect of a large number of other genes. A computationally efficient search scheme was provided to perform effective search in the extensive feature space that includes possible interactions of many genes. Performance of the algorithm applied to 9 datasets suggests that it is possible to improve the accuracy of cancer classification by a big margin when joint effects of many genes are considered.

SUBMITTER: Zhang H

PROVIDER: S-EPMC3562261 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Improving accuracy for cancer classification with a new algorithm for genes selection.

Zhang Hongyan H Wang Haiyan H Dai Zhijun Z Chen Ming-shun MS Yuan Zheming Z

BMC bioinformatics 20121113

<h4>Background</h4>Even though the classification of cancer tissue samples based on gene expression data has advanced considerably in recent years, it faces great challenges to improve accuracy. One of the challenges is to establish an effective method that can select a parsimonious set of relevant genes. So far, most methods for gene selection in literature focus on screening individual or pairs of genes without considering the possible interactions among genes. Here we introduce a new computat ...[more]

PMID: 23148517

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Project description:BackgroundIn the typical setting of gene-selection problems from high-dimensional data, e.g., gene expression data from microarray or next-generation sequencing-based technologies, an enormous volume of high-throughput data is generated, and there is often a need for a simple, computationally-inexpensive, non-parametric screening procedure than can quickly and accurately find a low-dimensional variable subset that preserves biological information from the original very high-dimensional data (dimension p > 40,000). This is in contrast to the very sophisticated variable selection methods that are computationally expensive, need pre-processing routines, and often require calibration of priors.ResultsWe present a tree-based sequential CART (S-CART) approach to variable selection in the binary classification setting and compare it against the more sophisticated procedures using simulated and real biological data. In simulated data, we analyze S-CART performance versus (i) a random forest (RF), (ii) a fully-parametric Bayesian stochastic search variable selection (SSVS), and (iii) the moderated t-test statistic from the LIMMA package in R. The simulation study is based on a hierarchical Bayesian model, where dataset dimensionality, percentage of significant variables, and substructure via dependency vary. Selection efficacy is measured through false-discovery and missed-discovery rates. In all scenarios, the S-CART method is seen to consistently outperform SSVS and RF in both speed and detection accuracy. We demonstrate the utility of the S-CART technique both on simulated data and in a control-treatment mouse study. We show that the network analysis based on the S-CART-selected gene subset in essence recapitulates the biological findings of the study using only a fraction of the original set of genes considered in the study's analysis.ConclusionsThe relatively simple-minded gene selection algorithms like S-CART may often in practical circumstances be preferred over much more sophisticated ones. The advantage of the "greedy" selection methods utilized by S-CART and the likes is that they scale well with the problem size and require virtually no tuning or training while remaining efficient in extracting the relevant information from microarray-like datasets containing large number of redundant or irrelevant variables.AvailabilityThe MATLAB 7.4b code for the S-CART implementation is available for download from https://neyman.mcg.edu/posts/scart.zip.

Project description:BackgroundDiffusion magnetic resonance imaging (MRI) is integral to detection of prostate cancer (PCa), but conventional apparent diffusion coefficient (ADC) cannot capture the complexity of prostate tissues and tends to yield noisy images that do not distinctly highlight cancer. A four-compartment restriction spectrum imaging (RSI4 ) model was recently found to optimally characterize pelvic diffusion signals, and the model coefficient for the slowest diffusion compartment, RSI4 -C1 , yielded greatest tumor conspicuity.PurposeTo evaluate the slowest diffusion compartment of a four-compartment spectrum imaging model (RSI4 -C1 ) as a quantitative voxel-level classifier of PCa.Study typeRetrospective.SubjectsForty-six men who underwent an extended MRI acquisition protocol for suspected PCa. Twenty-three men had benign prostates, and the other 23 men had PCa.Field strength/sequenceA 3 T, multishell diffusion-weighted and axial T2-weighted sequences.AssessmentHigh-confidence cancer voxels were delineated by expert consensus, using imaging data and biopsy results. The entire prostate was considered benign in patients with no detectable cancer. Diffusion images were used to calculate RSI4 -C1 and conventional ADC. Classifier images were also generated.Statistical testsVoxel-level discrimination of PCa from benign prostate tissue was assessed via receiver operating characteristic (ROC) curves generated by bootstrapping with patient-level case resampling. RSI4 -C1 was compared to conventional ADC for two metrics: area under the ROC curve (AUC) and false-positive rate for a sensitivity of 90% (FPR90 ). Statistical significance was assessed using bootstrap difference with two-sided α = 0.05.ResultsRSI4 -C1 outperformed conventional ADC, with greater AUC (mean 0.977 [95% CI: 0.951-0.991] vs. 0.922 [0.878-0.948]) and lower FPR90 (0.032 [0.009-0.082] vs. 0.201 [0.132-0.290]). These improvements were statistically significant (P < 0.05).Data conclusionRSI4 -C1 yielded a quantitative, voxel-level classifier of PCa that was superior to conventional ADC. RSI classifier images with a low false-positive rate might improve PCa detection and facilitate clinical applications like targeted biopsy and treatment planning.Evidence level3 TECHNICAL EFFICACY: Stage 2.

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Improving accuracy for cancer classification with a new algorithm for genes selection.

Publications

Improving accuracy for cancer classification with a new algorithm for genes selection.

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