A Survey of Feature Selection Strategies for DNA Microarray Classification

Classification tasks are difficult and challenging in the bioinformatics field, that used to predict or diagnose patients at an early stage of disease by utilizing DNA microarray technology. However, crucial characteristics of DNA microarray technology are a large number of features and small sample sizes, which means the technology confronts a "dimensional curse" in its classification tasks because of the high computational execution needed and the discovery of biomarkers difficult. To reduce the dimensionality of features to find the significant features that can employ feature selection algorithms and not affect the performance of classification tasks. Feature selection helps decrease computational time by removing irrelevant and redundant features from the data. The study aims to briefly survey popular feature selection methods for classifying DNA microarray technology, such as filters, wrappers, embedded, and hybrid approaches. Furthermore, this study describes the steps of the feature selection process used to accomplish classification tasks and their relationships to other components such as datasets, cross-validation, and classifier algorithms. In the case study, we chose four different methods of feature selection on two-DNA microarray datasets to evaluate and discuss their performances, namely classification accuracy, stability, and the subset size of selected features. Keywords: Brief survey; DNA microarray data; feature selection; filter methods; wrapper methods; embedded methods; and hybrid methods. DOI: 10.7176/CEIS/14-2-01 Publication date:March 31st 202

Strongly Constrained Discrete Hashing

Learning to hash is a fundamental technique widely used in large-scale image retrieval. Most existing methods for learning to hash address the involved discrete optimization problem by the continuous relaxation of the binary constraint, which usually leads to large quantization errors and consequently suboptimal binary codes. A few discrete hashing methods have emerged recently. However, they either completely ignore some useful constraints (specifically the balance and decorrelation of hash bits) or just turn those constraints into regularizers that would make the optimization easier but less accurate. In this paper, we propose a novel supervised hashing method named Strongly Constrained Discrete Hashing (SCDH) which overcomes such limitations. It can learn the binary codes for all examples in the training set, and meanwhile obtain a hash function for unseen samples with the above-mentioned constraints preserved. Although the model of SCDH is fairly sophisticated, we are able to find closed-form solutions to all of its optimization subproblems and thus design an efficient algorithm that converges quickly. In addition, we extend SCDH to a kernelized version SCDH_K. Our experiments on three large benchmark datasets have demonstrated that not only can SCDH and SCDH_K achieve substantially higher MAP scores than state-of-the-art baselines, but they run much faster than those that are also supervised

Automated Species Classification Methods for Passive Acoustic Monitoring of Beaked Whales

The Littoral Acoustic Demonstration Center has collected passive acoustic monitoring data in the northern Gulf of Mexico since 2001. Recordings were made in 2007 near the Deepwater Horizon oil spill that provide a baseline for an extensive study of regional marine mammal populations in response to the disaster. Animal density estimates can be derived from detections of echolocation signals in the acoustic data. Beaked whales are of particular interest as they remain one of the least understood groups of marine mammals, and relatively few abundance estimates exist. Efficient methods for classifying detected echolocation transients are essential for mining long-term passive acoustic data. In this study, three data clustering routines using k-means, self-organizing maps, and spectral clustering were tested with various features of detected echolocation transients. Several methods effectively isolated the echolocation signals of regional beaked whales at the species level. Feedforward neural network classifiers were also evaluated, and performed with high accuracy under various noise conditions. The waveform fractal dimension was tested as a feature for marine biosonar classification and improved the accuracy of the classifiers. [This research was made possible by a grant from The Gulf of Mexico Research Initiative. Data are publicly available through the Gulf of Mexico Research Initiative Information & Data Cooperative (GRIIDC) at https://data.gulfresearchinitiative.org.] [DOIs: 10.7266/N7W094CG, 10.7266/N7QF8R9K