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Performance and efficiency of machine learning algorithms for analyzing rectangular biomedical data


Most biomedical datasets, including those of ‘omics, population studies, and surveys, are rectangular in shape and have few missing data. Recently, their sample sizes have grown significantly. Rigorous analyses on these large datasets demand considerably more efficient and more accurate algorithms. Machine learning (ML) algorithms have been used to classify outcomes in biomedical datasets, including random forests (RF), decision tree (DT), artificial neural networks (ANN), and support vector machine (SVM). However, their performance and efficiency in classifying multi-category outcomes of rectangular data are poorly understood. Therefore, we compared these metrics among the 4 ML algorithms. As an example, we created a large rectangular dataset using the female breast cancers in the surveillance, epidemiology, and end results-18 database, which were diagnosed in 2004 and followed up until December 2016. The outcome was the five-category cause of death, namely alive, non-breast cancer, breast cancer, cardiovascular disease, and other cause. We analyzed the 54 dichotomized features from ~45,000 patients using MatLab (version 2018a) and the tenfold cross-validation approach. The accuracy in classifying five-category cause of death with DT, RF, ANN, and SVM was 69.21%, 70.23%, 70.16%, and 69.06%, respectively, which was higher than the accuracy of 68.12% with multinomial logistic regression. Based on the features' information entropy, we optimized dimension reduction (i.e., reduce the number of features in models). We found 32 or more features were required to maintain similar accuracy, while the running time decreased from 55.57 s for 54 features to 25.99 s for 32 features in RF, from 12.92 s to 10.48 s in ANN, and from 175.50 s to 67.81 s in SVM. In summary, we here show that RF, DT, ANN, and SVM had similar accuracy for classifying multi-category outcomes in this large rectangular dataset. Dimension reduction based on information gain will increase the model’s efficiency while maintaining classification accuracy.

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Fig. 1: Confusion matrices of the 4 tuned machine learning models.
Fig. 2: The receiver operator curve of the tuned random forests (RF) and artificial neural networks (ANN) models by 5 causes of death.


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We thank Lingling Han at Shenzhen Horb Technology Corporate, Ltd. for invaluable discussions and comments.

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FD, CC, and LZ designed the study, FD and JH conducted the study and drafted the manuscript, all authors discussed, revised, and edited the manuscript, and LZ supervised the work.

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Correspondence to Lanjing Zhang.

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Deng, F., Huang, J., Yuan, X. et al. Performance and efficiency of machine learning algorithms for analyzing rectangular biomedical data. Lab Invest (2021).

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