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Multiclass cancer classification by using fuzzy support vector machine and binary decision tree with gene selection.

ABSTRACT: We investigate the problems of multiclass cancer classification with gene selection from gene expression data. Two different constructed multiclass classifiers with gene selection are proposed, which are fuzzy support vector machine (FSVM) with gene selection and binary classification tree based on SVM with gene selection. Using F test and recursive feature elimination based on SVM as gene selection methods, binary classification tree based on SVM with F test, binary classification tree based on SVM with recursive feature elimination based on SVM, and FSVM with recursive feature elimination based on SVM are tested in our experiments. To accelerate computation, preselecting the strongest genes is also used. The proposed techniques are applied to analyze breast cancer data, small round blue-cell tumors, and acute leukemia data. Compared to existing multiclass cancer classifiers and binary classification tree based on SVM with F test or binary classification tree based on SVM with recursive feature elimination based on SVM mentioned in this paper, FSVM based on recursive feature elimination based on SVM can find most important genes that affect certain types of cancer with high recognition accuracy.

SUBMITTER: Mao Y

PROVIDER: S-EPMC1184049 | biostudies-literature | 2005 Jun

REPOSITORIES: biostudies-literature

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Multiclass cancer classification by using fuzzy support vector machine and binary decision tree with gene selection.

Mao Yong Y Zhou Xiaobo X Pi Daoying D Sun Youxian Y Wong Stephen T C ST

Journal of biomedicine & biotechnology 20050601 2

We investigate the problems of multiclass cancer classification with gene selection from gene expression data. Two different constructed multiclass classifiers with gene selection are proposed, which are fuzzy support vector machine (FSVM) with gene selection and binary classification tree based on SVM with gene selection. Using F test and recursive feature elimination based on SVM as gene selection methods, binary classification tree based on SVM with F test, binary classification tree based on ...[more]

PMID: 16046822

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Project description:BackgroundPlasminogen (Pg), the precursor of the proteolytic and fibrinolytic enzyme of blood, is converted to the active enzyme plasmin (Pm) by different plasminogen activators (tissue plasminogen activators and urokinase), including the bacterial activators streptokinase and staphylokinase, which activate Pg to Pm and thus are used clinically for thrombolysis. The identification of Pg-activators is therefore an important step in understanding their functional mechanism and derives new therapies.MethodsIn this study, different computational methods for predicting plasminogen activator peptide sequences with high accuracy were investigated, including support vector machines (SVM) based on amino acid (AC), dipeptide composition (DC), PSSM profile and Hybrid methods used to predict different Pg-activators from both prokaryotic and eukaryotic origins.ResultsOverall maximum accuracy, evaluated using the five-fold cross validation technique, was 88.37%, 84.32%, 87.61%, 85.63% in 0.87, 0.83,0.86 and 0.85 MCC with amino (AC) or dipeptide composition (DC), PSSM profile and Hybrid methods respectively. Through this study, we have found that the different subfamilies of Pg-activators are quite closely correlated in terms of amino, dipeptide, PSSM and Hybrid compositions. Therefore, our prediction results show that plasminogen activators are predictable with a high accuracy from their primary sequence. Prediction performance was also cross-checked by confusion matrix and ROC (Receiver operating characteristics) analysis. A web server to facilitate the prediction of Pg-activators from primary sequence data was implemented.ConclusionThe results show that dipeptide, PSSM profile, and Hybrid based methods perform better than single amino acid composition (AC). Furthermore, we also have developed a web server, which predicts the Pg-activators and their classification (available online at http://mamsap.it.deakin.edu.au/plas_pred/home.html). Our experimental results show that our approaches are faster and achieve generally a good prediction performance.

Project description:PurposeThe aim of this study was to investigate if ischemic stroke final infarction volume and location can be used to predict the associated functional outcome using a multi-class support vector machine (SVM).Material and methodsSixty-eight follow-up MR FLAIR datasets of ischemic stroke patients with known modified Rankin Scale (mRS) functional outcome after 30 days were used. The infarct regions were segmented and used to calculate the percentage of lesioned voxels in the predefined MNI, Harvard-Oxford cortical and subcortical atlas regions as well as using four problem-specific VOIs, which were identified from the database using voxel-based lesion symptom mapping. An overall of 12 SVM classification models for predicting the corresponding mRS score were generated using the lesion overlap values from the different brain region definitions, stroke laterality information, and the optional parameters infarct volume, admission NIHSS, and patient age.ResultsLeave-one-out cross validations revealed that including information about the stroke location in terms of lesion overlap measurements led to improved mRS prediction results compared to classification models not utilizing the stroke location information. Furthermore, integration of the optional features led to improved mRS prediction results in all cases tested. The problem-specific brain regions and additional integration of the optional features led to the best mRS predictions with a precise multi-value mRS prediction accuracy of 56%, sliding window multi-value mRS prediction accuracy (mRS±1) of 82%, and binary mRS (0-2 vs. 3-5) prediction accuracy of 85%.ConclusionTherefore, a graded SVM-based functional stroke outcome prediction using the problem-specific brain regions for lesion overlap quantification leads to promising results but needs to be further validated using an independent database to rule out a potential methodical bias and overfitting effects. The prediction of the graded mRS functional outcome could be a valuable tool if combined with voxel-wise tissue outcome predictions based on multi-parametric datasets acquired at the acute phase.

Dataset Information

Multiclass cancer classification by using fuzzy support vector machine and binary decision tree with gene selection.

Publications

Multiclass cancer classification by using fuzzy support vector machine and binary decision tree with gene selection.

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