Semantics-Preserving Dimensionality Reduction: Rough and Fuzzy-Rough-Based Approaches

Abstract—Semantics-preserving dimensionality reduction refers to the problem of selecting those input features that are most predictive of a given outcome; a problem encountered in many areas such as machine learning, pattern recognition, and signal processing. This has found successful application in tasks that involve data sets containing huge numbers of features (in the order of tens of thousands), which would be impossible to process further. Recent examples include text processing and Web content classification. One of the many successful applications of rough set theory has been to this feature selection area. This paper reviews those techniques that preserve the underlying semantics of the data, using crisp and fuzzy rough set-based methodologies. Several approaches to feature selection based on rough set theory are experimentally compared. Additionally, a new area in feature selection, feature grouping, is highlighted and a rough set-based feature grouping technique is detailed. Index Terms—Dimensionality reduction, feature selection, feature transformation, rough selection, fuzzy-rough selection.

Feature Selection with Harmony Search for Classification: A Review

In the area of data mining, feature selection is an important task for classification and dimensionality reduction. Feature selection is the process of choosing the most relevant features in a datasets. If the datasets contains irrelevant features, it will not only affect the training of the classification process but also the accuracy of the model. A good classification accuracy can be achieved when the model correctly predicted the class labels. This paper gives a general review of feature selection with Harmony Search (HS) algorithm for classification in various application. From the review, feature selection with HS algorithm shows a good performance as compared to other metaheuristics algorithm such as Genetic Algorithm (GA) and Particle Swarm Optimization (PSO)

A Novel Two-Stage Spectrum-Based Approach for Dimensionality Reduction: A Case Study on the Recognition of Handwritten Numerals

Dimensionality reduction (feature selection) is an important step in pattern recognition systems. Although there are different conventional approaches for feature selection, such as Principal Component Analysis, Random Projection, and Linear Discriminant Analysis, selecting optimal, effective, and robust features is usually a difficult task. In this paper, a new two-stage approach for dimensionality reduction is proposed. This method is based on one-dimensional and two-dimensional spectrum diagrams of standard deviation and minimum to maximum distributions for initial feature vector elements. The proposed algorithm is validated in an OCR application, by using two big standard benchmark handwritten OCR datasets, MNIST and Hoda. In the beginning, a 133-element feature vector was selected from the most used features, proposed in the literature. Finally, the size of initial feature vector was reduced from 100% to 59.40% (79 elements) for the MNIST dataset, and to 43.61% (58 elements) for the Hoda dataset, in order. Meanwhile, the accuracies of OCR systems are enhanced 2.95% for the MNIST dataset, and 4.71% for the Hoda dataset. The achieved results show an improvement in the precision of the system in comparison to the rival approaches, Principal Component Analysis and Random Projection. The proposed technique can also be useful for generating decision rules in a pattern recognition system using rule-based classifiers

Applying Machine Learning Algorithms for the Analysis of Biological Sequences and Medical Records

The modern sequencing technology revolutionizes the genomic research and triggers explosive growth of DNA, RNA, and protein sequences. How to infer the structure and function from biological sequences is a fundamentally important task in genomics and proteomics fields. With the development of statistical and machine learning methods, an integrated and user-friendly tool containing the state-of-the-art data mining methods are needed. Here, we propose SeqFea-Learn, a comprehensive Python pipeline that integrating multiple steps: feature extraction, dimensionality reduction, feature selection, predicting model constructions based on machine learning and deep learning approaches to analyze sequences. We used enhancers, RNA N6- methyladenosine sites and protein-protein interactions datasets to evaluate the validation of the tool. The results show that the tool can effectively perform biological sequence analysis and classification tasks. Applying machine learning algorithms for Electronic medical record (EMR) data analysis is also included in this dissertation. Chronic kidney disease (CKD) is prevalent across the world and well defined by an estimated glomerular filtration rate (eGFR). The progression of kidney disease can be predicted if future eGFR can be accurately estimated using predictive analytics. Thus, I present a prediction model of eGFR that was built using Random Forest regression. The dataset includes demographic, clinical and laboratory information from a regional primary health care clinic. The final model included eGFR, age, gender, body mass index (BMI), obesity, hypertension, and diabetes, which achieved a mean coefficient of determination of 0.95. The estimated eGFRs were used to classify patients into CKD stages with high macro-averaged and micro-averaged metrics

Feature subset selection and ranking for data dimensionality reduction

A new unsupervised forward orthogonal search (FOS) algorithm is introduced for feature selection and ranking. In the new algorithm, features are selected in a stepwise way, one at a time, by estimating the capability of each specified candidate feature subset to represent the overall features in the measurement space. A squared correlation function is employed as the criterion to measure the dependency between features and this makes the new algorithm easy to implement. The forward orthogonalization strategy, which combines good effectiveness with high efficiency, enables the new algorithm to produce efficient feature subsets with a clear physical interpretation

Feature subset selection and ranking for data dimensionality reduction

A new unsupervised forward orthogonal search (FOS) algorithm is introduced for feature selection and ranking. In the new algorithm, features are selected in a stepwise way, one at a time, by estimating the capability of each specified candidate feature subset to represent the overall features in the measurement space. A squared correlation function is employed as the criterion to measure the dependency between features and this makes the new algorithm easy to implement. The forward orthogonalization strategy, which combines good effectiveness with high efficiency, enables the new algorithm to produce efficient feature subsets with a clear physical interpretation

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A number of scRNA-seq protocols have been developed, and these methods possess their unique features with distinct advantages and disadvantages. Due to technical limitations and biological factors, scRNA-seq data are noisier and more complex than bulk RNA-seq data. The high variability of scRNA-seq data raises computational challenges in data analysis. Although an increasing number of bioinformatics methods are proposed for analyzing and interpreting scRNA-seq data, novel algorithms are required to ensure the accuracy and reproducibility of results. In this review, we provide an overview of currently available single-cell isolation protocols and scRNA-seq technologies, and discuss the methods for diverse scRNA-seq data analyses including quality control, read mapping, gene expression quantification, batch effect correction, normalization, imputation, dimensionality reduction, feature selection, cell clustering, trajectory inference, differential expression calling, alternative splicing, allelic expression, and gene regulatory network reconstruction. Further, we outline the prospective development and applications of scRNA-seq technologies