Classifying Dry Eye Disease Patients from Healthy Controls Using Machine Learning and Metabolomics Data

Dry eye disease is a common disorder of the ocular surface, leading patients to seek eye care. Clinical signs and symptoms are currently used to diagnose dry eye disease. Metabolomics, a method for analyzing biological systems, has been found helpful in identifying distinct metabolites in patients and in detecting metabolic profiles that may indicate dry eye disease at early stages. In this study, we explored using machine learning and metabolomics information to identify which cataract patients suffered from dry eye disease. As there is no one-size-fits-all machine learning model for metabolomics data, choosing the most suitable model can significantly affect the quality of predictions and subsequent metabolomics analyses. To address this challenge, we conducted a comparative analysis of nine machine learning models on three metabolomics data sets from cataract patients with and without dry eye disease. The models were evaluated and optimized using nested k-fold cross-validation. To assess the performance of these models, we selected a set of suitable evaluation metrics tailored to the data set's challenges. The logistic regression model overall performed the best, achieving the highest area under the curve score of 0.8378, balanced accuracy of 0.735, Matthew's correlation coefficient of 0.5147, an F1-score of 0.8513, and a specificity of 0.5667. Additionally, following the logistic regression, the XGBoost and Random Forest models also demonstrated good performance.

Principle Components Analysis based frameworks for efficient missing data imputation algorithms

Missing data is a commonly occurring problem in practice, and imputation, i.e., filling the missing entries of the data, is a popular way to deal with this problem. This motivates multiple works on imputation to deal with missing data of various types and dimensions. However, for high-dimensional datasets, these imputation methods can be computationally expensive. Therefore, in this work, we propose Principle Component Analysis Imputation (PCAI), a simple framework based on Principle Component Analysis (PCA) to speed up the imputation process of many available imputation techniques. Next, based on PCAI, we propose PCA Imputation - Classification (PIC), an imputation-dimension reduction-classification framework to deal with missing data classification problems where it is desirable to reduce the dimensions before training a classification model. Our experiments show that the proposed frameworks can be utilized with various imputation algorithms and improve the imputation speed significantly. Interestingly, the frameworks aid imputation methods that rely on many parameters by reducing the dimension of the data and hence, reducing the number of parameters needed to be estimated. Moreover, they not only can achieve compatible mean square error/higher classification accuracy compared to the traditional imputation style on the original missing dataset but many times deliver even better results. In addition, the frameworks also help to tackle the memory issue that many imputation approaches have by reducing the number of features.