Review Article

Intelligent Techniques Using Molecular Data Analysis in Leukaemia: An Opportunity for Personalized Medicine Support System

Table 2

Review of the studies, data sources, their purpose, and machine-learning algorithms reported from 2001 to 2015.

StudyYearTasksData sourceLeukaemia types involved in the studyPurposeMethods

1Cho [82]2002Feature selection and classificationDNA microarrayAML, ALLClassifying leukaemia typesPearson’s and Spearman’s correlation coefficients, Euclidean distance, cosine coefficient, information gain, mutual information and signal-to-noise ratio being used for feature selection

2Inza et al. [83]2002Feature selection and classificationDNA microarrayAML, ALLClassifying cancer, select genes related to cancerFeature subset selection, case-based, and nearest neighbor classifier

3Farag [84]2003Feature selection and classificationBlood cells imageAML, ALLClassifying leukaemia typesA three-layer backpropagation neural network

4Futschik et al. [85]2003Knowledge discoveryGene expressionAML, ALLClassifying leukaemia types and select gene expressionKnowledge-based neural networks and evolving fuzzy neural networks and adaptive learning and rule extraction

5Cho and Won [86]2003Feature selection, classification, and ensemble classifiersDNA microarrayAML, ALLClassifying leukaemia types and select genes related to cancerCorrelation coefficient, Euclidean distance, cosine coefficient, information gain, mutual information, a feed-forward multilayer perceptron, -nearest neighbor, self-organizing map, and support vector machine. Majority voting, weighted voting, and Bayesian approach

6Marx et al. [44]2003Feature selection and classificationDNA microarrayAML, ALLClassifying leukaemia from nonleukaemiaPrincipal component analysis and clustering

7Marohnic et al. [87]2004Feature selection and classificationDNA microarrayAML, ALLClassifying leukaemia typesMutual information and support vector machine

8McCarthy et al. [88]2004Knowledge extraction, classification, feature selection, visualizationProteomic mass spectroscopy data, and gene expressionMelanoma, leukaemiaCancer detection, diagnosis, and managementNaïve Bayes, support vector machines, instance-based learning (-nearest neighbor), logistic regression, and neural networks

9Rowland [89]2004ClassificationGene expressionAML, ALLClassifying leukaemia typesGenetic Programming

10Markiewicz et al. [90]2005Feature selection and classificationImages of different blast cellMyelogenous leukaemiaClassifying patientsSupport vector machine

11Tung and Quek [91]2005ClassificationDNA microarraysALLClassifying leukaemia typesA neural fuzzy system, NN, SVM and the -nearest neighbor (-NN) classifier

12Nguyen et al. [92]2005ClassificationDNA microarraysAML, ALLClassifying leukaemia typesSupport vector machine (SVM)

13Plagianakos et al. [93]2005Feature selection and classificationDNA microarraysAML, ALLClassifying leukaemia typesartificial neural networks

14Li and Yang [94]2005Feature selection and classificationDNA microarraysAML, ALLClassifying leukaemia typesSVM, ridge regression and Rocchio,
feature selection in recursive and nonrecursive settings

15Jinlian et al. [95]2005Knowledge extractionDNA microarrayAML, ALLLeukaemia gene association structureClusters

16Diaz et al. [96]2006Feature selection and classificationDNA microarrays Acute Promyelocytic LeukaemiaClassifying Acute Promyelocytic Leukaemia (APL) from the non-APL leukaemiaDiscriminant fuzzy pattern

17Feng and Lipo [97]2006Feature selection and classificationDNA microarraysAML, ALLAcute leukaemia types-statistics to rank the gene and support vector machines

18Nguyen and Ohn [98]2006Feature selection and classificationDNA microarraysAML, ALLClassifying leukaemia typesDynamic recursive feature elimination and random forest

19Shulin et al. [99]2006Feature selection and classificationDNA microarraysAML, ALLClassifying leukaemia typesIndependent component analysis and SVM

20Chen et al. [100]2007Feature selection, rule extraction, and classificationDNA microarraysAML, ALLClassifying leukaemia typesA multiple kernel support vector machine

21Ujwal et al. [43]2007Feature selection and classificationDNA microarrayALLIdentifying functional cancer cell line classes, classifying leukaemia from nonleukaemia value and clustering

22Perez et al. [101]2008ClassificationGene expressionAML, ALLClassify leukaemia typesHybrid fuzzy-SVM

23Yoo and Gernaey [42]2008Feature selection and classificationDNA microarrays dataALLClassifying ALL origin cell lines from non-ALL leukaemia origin cell linesDiscriminant partial least squares, principal component and Fisher’s linear discriminant analysis,
linear discriminant function and SVM, and
hierarchical clustering method

24Avogadri et al. [102]2009Knowledge extractionGene expressionMyeloid leukaemiaDiscovering significant clustersStability-based methods

25Eisele et al. [49]2009Knowledge extractionGene expressionCLLPrognostic markersMultivariate model

26Chaiboonchoe et al. [103]2009ClassificationDNA microarrays dataALLIdentification of differentially expressed genes Self-organizing maps (neural networks), emergent self-organizing maps (extension of neural networks), the short-time series expression miner (STEM), and fuzzy clustering by local approximation of membership (FLAME)

27Oehler et al. [46]2009Knowledge extractionGene expressionCMLIdentifying molecular markersBayesian model averaging

28Corchado et al. [45]2009Decision
support system preprocessing, filtering, classification, and extraction of knowledge
Exon arraysALL, AML, CLL, CMLClassifying patients who suffer from different forms of leukaemia at various stagesPrincipal components, clustering, CART

29Glez-Peña et al. [104]2009Feature selection and classificationDNA microarray AMLClassifying gene expressionFuzzy pattern algorithm

30He and Hui [105]2009ClassificationDNA microarrayALL, AMLClassifying leukaemia typesAnt-based clustering (Ant-C) and an ant-based association rule mining (Ant-ARM) algorithms

31Mukhopadhyay et al. [106]2009Feature selection and classificationDNA microarrayALL, AMLClassifying leukaemia typesGA-based fuzzy clustering, neural network, and support vector machine

32Torkaman et al. [107]2009ClassificationHuman leukaemia tissueALL, AMLDetermining different CD markersCooperative game

33Zheng et al. [108]2009Feature selectionDNA microarrayALLGene rankingKnowledge-oriented gene selection

34Mehdi et al. [109]2009Knowledge acquisitionGene expressionALL, AMLPattern clustering-nearest neighbor technique

35Porzelius et al. [110]2011Feature selection, classificationMicroarray and clinical dataALLRisk predictionFeature selection approach for support vector machines as well as a boosting approach for regression models

36Chen et al. [111]2011Feature selection, data fusion, class prediction, decision rule extraction, associated rule extraction, and subclass discoveryDNA microarrayALL, AMLSelect gene, classify leukaemia types, rule extractionMultiple kernel SVM

37Gonzalez et al. [112]2011ClassificationBone marrow cells imagesALL, AMLClassifying leukaemia subtypesSegmentation method to obtain leukaemia cells and extract from them descriptive characteristics (geometrical, texture, statistical) and eigenvalues

38Tong and Schierz [113]2011Feature selection and classificationDNA microarrayALL, AMLClassifying two-class oligonucleotide microarray data for acute leukaemiaHybrid genetic algorithm-neural network

39Chauhan et al. [114]2012ClassificationGenotypeALL, AMLIdentifying gene-gene interactionClassification and regression tree

40Escalante et al. [115]2012Feature selection and classificationThe morphological properties of bone marrow imagesALL, AMLClassifying leukaemia subtypesEnsemble particle swarm model selection

41 Yeung et al. [116]2012Feature selection and classificationGene expressionCMLselect gene, and predicted functional relationshipsIntegrating gene expression data with expert knowledge and predicted functional relationships using iterative Bayesian model averaging

42Manninen et al. [117]2013ClassificationFlow cytometry dataAMLPrediction method for diagnosis of AMLSparse logistic regression

43El-Nasser et al. [118]2014ClassificationDNA microarraysALL, AMLClassifying leukaemia typesImplement enhanced classification (ECA) algorithm, SMIG module, and ranking procedure.

44Singhal and Singh [119]2015Feature selection and classificationImage based analysis of bone marrow samplesALLClassifying leukaemia subtypesMultilayer perceptron (MLP), linear vector quantization (LVQ), -nearest neighbor (-NN), and SVM

45Yao et al. [120]2015Feature selection and classificationDNA microarraysALL, AML, the mixed-lineage leukaemia (MLL) dataClassifying leukaemia subtypesRandom forests and ranking features

46Rawat et al. [121]2015Computer-aided diagnostic system, feature selection, and classificationBone marrow cells in microscopic imagesALLDiagnosis lymphoblast cells from healthy lymphocytesSupport vector machine

47Kar et al. [122]2015Feature selection and classificationDNA microarraysALL, AML, the mixed-lineage leukaemia (MLL) dataClassifying leukaemia subtypesParticle swarm optimization (PSO) method along with adaptive -nearest neighborhood (KNN)

48Li et al. [123]2016ClassificationGene expressionAMLIdentifying feature genesSupport vector machine (SVM) and random forest (RF)

49Dwivedi et al. [124]2016ClassificationMicroarray gene expressionALL, AMLClassifying leukaemia subtypesArtificial neural network (ANN)

50Krappe et al. [125]2016ClassificationImage based analysis of bone marrow samplesLeukaemiaDiagnosis of leukaemia and classifying 16 different classes for bone marrowKnowledge-based hierarchical tree classifier

51Li et al. [123]2016ClassificationDNA microarraysAML, ALLClassifying leukaemia subtypesA weighted doubly regularized support vector machine

52Ocampo-Vega et al. [126]2016Feature selection and classificationDNA microarraysAML, ALLClassifying leukaemia subtypesPrincipal component analysis and logistic regression

53Rajwa et al. [127]2016ClassificationFlow cytometry dataAMLDetermining progression of the diseaseNonparametric Bayesian framework

54Ni et al. [128]2016ClassificationFlow cytometry dataAMLAnalyzing minimal residual diseaseSupport vector machines (SVM)

55Savvopoulos et al. [48]2016Knowledge extractionCLL cells in peripheral bloodCLLCapturing disease pathophysiology across patient typesTemporally and spatially distributed model