Towards Machine Learning in Molecular Biology.

Countless women and men worldwide have lost their lives to breast cancer (BC). Although researchers from around the world have proposed various diagnostic methods for detecting this disease, there is still room for improvement in the accuracy and efficiency with which they can be used. A novel approach has been proposed for the early detection of BC by applying data mining techniques to the levels of prolactin (P), testosterone (T), cortisol (C), and human chorionic gonadotropin (HCG) in the blood and saliva of 20 women with histologically confirmed BC, 20 benign subjects, and 20 age-matched control women. In the proposed method, blood and saliva were used to categorize the severity of the BC into normal, benign, and malignant cases. Ten statistical features were collected to identify the severity of the BC using three different classification schemes—a decision tree (DT), a support vector machine (SVM), and k-nearest neighbors (KNN) were evaluated. Moreover, dimensionality reduction techniques using factor analysis (FA) and t-stochastic neighbor embedding (t-SNE) have been computed to obtain the best hyperparameters. The model has been validated using the k-fold cross-validation method in the proposed approach. Metrics for gauging a model’s effectiveness were applied. Dimensionality reduction approaches for salivary biomarkers enhanced the results, particularly with the DT, thereby increasing the classification accuracy from 66.67% to 93.3% and 90%, respectively, by utilizing t-SNE and FA. Furthermore, dimensionality reduction strategies for blood biomarkers enhanced the results, particularly with the DT, thereby increasing the classification accuracy from 60% to 80% and 93.3%, respectively, by utilizing FA and t-SNE. These findings point to t-SNE as a potentially useful feature selection for aiding in the identification of patients with BC, as it consistently improves the discrimination of benign, malignant, and control healthy subjects, thereby promising to aid in the improvement of breast tumour early detection. 

Comparison of the Effectiveness of Various Classifiers for Breast Cancer Detection Using Data Mining Methods

Protein Markers in the Detection of Cancer

The classification and prediction of T-cell receptors (TCRs) protein sequences are of significant interest in understanding the immune system and developing personalized immunotherapies. In this study, we propose a novel approach using Pseudo Amino Acid Composition (PseAAC) protein encoding for accurate TCR protein sequence classification. The PseAAC2Vec encoding method captures the physicochemical properties of amino acids and their local sequence information, enabling the representation of protein sequences as fixed-length feature vectors. By incorporating physicochemical properties such as hydrophobicity, polarity, charge, molecular weight, and solvent accessibility, PseAAC2Vec provides a comprehensive and informative characterization of TCR protein sequences. To evaluate the effectiveness of the proposed PseAAC2Vec encoding approach, we assembled a large dataset of TCR protein sequences with annotated classes. We applied the PseAAC2Vec encoding scheme to each sequence and generated feature vectors based on a specified window size. Subsequently, we employed state-of-the-art machine learning algorithms, such as support vector machines (SVM) and random forests (RF), to classify the TCR protein sequences. Experimental results on the benchmark dataset demonstrated the superior performance of the PseAAC2Vec-based approach compared to existing methods. The PseAAC2Vec encoding effectively captures the discriminative patterns in TCR protein sequences, leading to improved classification accuracy and robustness. Furthermore, the encoding scheme showed promising results across different window sizes, indicating its adaptability to varying sequence contexts. 

PseAAC2Vec protein encoding for TCR protein sequence classification.

In recent years, many studies have supported that cancer tissues can make disease-specific changes in some salivary proteins through some mediators in the pathogenesis of systemic diseases. These salivary proteins have the potential to become cancer-specific biomarkers in the early diagnosis stage. How to effectively identify these potential markers is one of the challenging issues. In this paper, we propose novel machine learning methods for recognition cancer biomarkers in saliva by two stages. In the first stage, salivary secreted proteins are recognized which are considered as candidate biomarkers of cancers. We picked up 557 salivary secretory proteins from 20379 human proteins by public databases and published literatures. Then, we present a training set construction strategy to solve the imbalance problem in order to make the classification methods get better accuracy. From all human protein set, the proteins belonging to the same families as salivary secretory proteins are removed. After that, we use SVC-KM method to cluster the remaining proteins, and select negative samples from each cluster in proportion. Next, the features of proteins are calculated by tools. We collect 24 protein properties such as sequence, structure and physicochemical properties, a total of 1087 features. An innovative procedure based on the local samples is proposed for selecting the appropriate features, in order to further improve the performance of SVM classifier. Experimental results show that the average sensitivity, specificity and accuracy of salivary secretory protein recognition using selected 32 features in training set are 97.09%, 98.10%, 97.61%, respectively. The use of these methods can improve the accuracy of recognition by solving the problems of unbalanced sample size and uneven distribution in training set. In the second stage, we apply the best model to dig out the salivary secreted proteins from 58 reported cancer markers, and get a total of 42 proteins which are considered to be used for salivary diagnosis. We analyze the gene expression data of three types of cancer, and predict that 33 genes will appear in saliva after they are translated into proteins. This study provides an important computational tool to help biologists and researchers reduce the number of candidate proteins and the cost of research. So as to further accelerate the discovery of cancer biomarkers in saliva and promote the development of saliva diagnosis.

Computational methods for recognition of cancer protein markers in saliva.

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Computational methods for recognition of cancer protein markers in saliva.