Turkiye Klinikleri Journal of Biostatistics

.: ORIGINAL RESEARCH
Comparison of the Effect of Dimension Reduction Methods on Classification Performance in Gene Expression Data Sets: Observational Study
Gen İfadesi Veri Setlerinde Boyut Azaltma Yöntemlerinin Sınıflandırma Performansına Etkisinin Karşılaştırılması: Gözlemsel Çalışma
Fatma Hilal YAĞINa , Harika Gözde GÖZÜKARA BAĞa
aİnönü University Faculty of Medicine, Department of Biostatistics and Medical Informatics, Malatya, Türkiye
Turkiye Klinikleri J Biostat. 2025;17(2):81-91
doi: 10.5336/biostatic.2025-111609
Article Language: EN
Full Text
ABSTRACT
Objective: The aim of this study is to compare the effects of dimensionality reduction methods [least absolute shrinkage and selection operator (LASSO), principal component analysis (PCA), and independent component analysis (ICA)] on various support vector machine (SVM) classification methods in high-dimensional acute myeloid leukemia (AML) gene expression data. Material and Methods: In this study, gene expression omnibus database was used to analyze gene expression profiles in AML patients. Data included expression levels for 64 individuals and 22,283 genes. SVM with different kernel functions were used in dimensionality reduction analyses LASSO, PCA, and ICA classification analyses. 10-fold cross-validation with 10 iterations and random search were used for resampling and hyperparameter optimization. The performance of the model was evaluated using the average accuracy, sensitivity, specificity, precision, and F criterion of 500 iterations. Results: AML data were filtered to reveal 6,201 genes. After PCA/ICA, 10 components were extracted, and 21 genes were selected as biomarkers for AML disease. While the polynomial kernel function model with PCA achieved the highest accuracy, the SVM models with polynomial kernel function showed the best performance for all analyses. The models were then selected for their potential biomarkers. Conclusion: In order to build classification models using gene expression data, high dimensionality should be eliminated using dimensionality reduction methods. This reduces the analysis time and improves the prediction performance. In the AML gene expression dataset, SVM models with polynomial kernel function give better results than linear and radial basis models.

Keywords: Dimension reduction; gene expression; feature extraction; feature selection; biomarker discovery
ÖZET
Amaç: Bu çalışmanın amacı, yüksek boyutlu akut miyeloid lösemi (AML) hastalığı gen ifadesi verilerinde boyut azaltma yöntemlerinin [en az mutlak küçülme ve seçim operatörü (least absolute shrinkage and selection operator ''LASSO''), temel bileşen analizi (principal component analysis ''PCA'') ve bağımsız bileşen analizi (independent component analysis ''ICA'')], çeşitli destek vektör makinesi [support vector machine (SVM)] sınıflandırma yöntemleri üzerindeki etkilerini karşılaştırmaktır. Gereç ve Yöntemler: Bu çalışmada, AML hastalarında gen ekspresyon profillerini analiz etmek için gen ekspresyon omnibus veri tabanı kullanılmıştır. Veriler, 64 kişi ve 22.283 gen için ifade düzeylerini içermektedir. Boyut azaltma analizleri LASSO, PCA ve ICA sınıflandırma analizlerinde, farklı çekirdek fonksiyonlardaki SVM kullanıldı. Yeniden örnekleme için 10 tekrarlı 10 kat çapraz doğrulama ve hiperparametre optimizasyonu için rastgele arama kullanılmıştır. Modelin performansı, 500 tekrarlı örneğin ortalama doğruluk, duyarlılık, seçicilik, kesinlik ve F kriteri kullanılarak değerlendirilmiştir. Bulgular: AML verileri filtrelenerek 6.201 gen ortaya çıkarılmıştır. PCA/ICA sonrasında 10 bileşen çıkarılmış ve 21 gen, AML hastalığı için biyobelirteç olarak seçilmiştir. PCA ile polinom çekirdek fonksiyonu modeli en yüksek doğruluk elde ederken, polinom çekirdek fonksiyonlu SVM modelleri tüm analizler için en iyi performansı göstermiştir. Modeller, daha sonra potansiyel biyobelirteçleri için seçilmiştir. Sonuç: Gen ifadesi verilerini kullanarak sınıflandırma modelleri oluşturmak için boyut azaltma yöntemleri kullanılarak yüksek boyutluluk ortadan kaldırılmalıdır. Bu durum, analiz süresini kısaltır ve tahmin performansını artırır. AML gen ifadesi veri setinde polinomial çekirdek fonksiyonuna sahip SVM modelleri, doğrusal ve radyal tabanlı modellerden daha iyi sonuçlar vermektedir.

Anahtar Kelimeler: Boyut indirgeme; gen ifadesi; özellik çıkarımı; özellik seçimi; biyobelirteç keşfi
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