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This paper discusses the problem of detecting cancer using such biomarkers as blood protein markers. The purpose of this research is to propose an approach for making decisions in the diagnosis of cancer through the creation of cost-sensitive SVM classifiers on the basis of datasets with a variety of features of different nature. Such datasets may include compositions of known features corresponding to blood protein markers and new features constructed using methods for calculating entropy and fractal dimensions, as well as using the UMAP algorithm. Based on these datasets, multiclass SVM classifiers were developed. They use cost-sensitive learning principles to overcome the class imbalance problem, which is typical for medical datasets. When implementing the UMAP algorithm, various variants of the loss function were considered. This was performed in order to select those that provide the formation of such new features that ultimately allow us to develop the best cost-sensitive SVM classifiers in terms of maximizing the mean value of the metric M a c r o F 1 − s c o r e . The experimental results proved the possibility of applying the UMAP algorithm, approximate entropy and, in addition, Higuchi and Katz fractal dimensions to construct new features using blood protein markers. It turned out that when working with the UMAP algorithm, the most promising is the application of a loss function on the basis of fuzzy cross-entropy, and the least promising is the application of a loss function on the basis of intuitionistic fuzzy cross-entropy. Augmentation of the original dataset with either features on the basis of the UMAP algorithm, features on the basis of the UMAP algorithm and approximate entropy, or features on the basis of approximate entropy provided the creation of the three best cost-sensitive SVM classifiers with mean values of the metric M a c r o F 1 − s c o r e increased by 5.359%, 5.245% and 4.675%, respectively, compared to the mean values of this metric in the case when only the original dataset was utilized for creating the base SVM classifier (without performing any manipulations to overcome the class imbalance problem, and also without introducing new features). [ABSTRACT FROM AUTHOR]

This paper deals with the problem of diagnosing oncological diseases based on blood protein markers. The goal of the study is to develop a novel approach in decision-making on diagnosing oncological diseases based on blood protein markers by generating datasets that include various combinations of features: both known features corresponding to blood protein markers and new features generated with the help of mathematical tools, particularly with the involvement of the non-linear dimensionality reduction algorithm UMAP, formulas for various entropies and fractal dimensions. These datasets were used to develop a group of multiclass kNN and SVM classifiers using oversampling algorithms to solve the problem of class imbalance in the dataset, which is typical for medical diagnostics problems. The results of the experimental studies confirmed the feasibility of using the UMAP algorithm and approximation entropy, as well as Katz and Higuchi fractal dimensions to generate new features based on blood protein markers. Various combinations of these features can be used to expand the set of features from the original dataset in order to improve the quality of the received classification solutions for diagnosing oncological diseases. The best kNN and SVM classifiers were developed based on the original dataset augmented respectively with a feature based on the approximation entropy and features based on the UMAP algorithm and the approximation entropy. At the same time, the average values of the metric MacroF 1 - score used to assess the quality of classifiers during cross-validation increased by 16.138% and 7.910%, respectively, compared to the average values of this metric in the case when the original dataset was used in the development of classifiers of the same name. [ABSTRACT FROM AUTHOR]

Dimensionality reduction techniques are often used by researchers in order to make high dimensional data easier to interpret visually, as data visualization is only possible in low dimensional spaces. Recent research in nonlinear dimensionality reduction introduced many effective algorithms, including t-distributed stochastic neighbor embedding (t-SNE), uniform manifold approximation and projection (UMAP), dimensionality reduction technique based on triplet constraints (TriMAP), and pairwise controlled manifold approximation (PaCMAP), aimed to preserve both the local and global structure of high dimensional data while reducing the dimensionality. The UMAP algorithm has found its application in bioinformatics, genetics, genomics, and has been widely used to improve the accuracy of other machine learning algorithms. In this research, we compare the performance of different fuzzy information discrimination measures used as loss functions in the UMAP algorithm while constructing low dimensional embeddings. In order to achieve this, we derive the gradients of the considered losses analytically and employ the Adam algorithm during the loss function optimization process. From the conducted experimental studies we conclude that the use of either the logarithmic fuzzy cross entropy loss without reduced repulsion or the symmetric logarithmic fuzzy cross entropy loss with sufficiently large neighbor count leads to better global structure preservation of the original multidimensional data when compared to the loss function used in the original UMAP algorithm implementation. [ABSTRACT FROM AUTHOR]