Early cancer detection from genome-wide cell-free DNA fragmentation via shuffled frog leaping algorithm and support vector machine.

ABSTRACT

MOTIVATION Early cancer detection is significant for patient mortality rate reduction. Although machine learning has been widely employed in that context, there are still deficiencies. In this work, we studied different machine learning algorithms for early cancer detection and proposed an Adaptive Support Vector Machine (ASVM) method by synergizing Shuffled Frog Leaping Algorithm and Support Vector Machine (SVM) in this study. RESULTS: Since ASVM regulates SVM for parameter adaption based on data characteristics, the experimental results reflected the robust generalization capability of ASVM on different datasets under different settings; for instance, ASVM can enhance the sensitivity by over 10% for early cancer detection compared with SVM. Besides, our proposed ASVM outperformed Grid Search + SVM and Random Search + SVM by significant margins in terms of the area under the ROC curve (AUC) (0.938 versus 0.922 versus 0.921). AVAILABILITY AND IMPLEMENTATION The proposed algorithm and dataset are available at https//github.com/ElaineLIU-920/ASVM-for-Early-Cancer-Detection. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.