Recursive gene selection based on maximum margin criterion: a comparison with SVM-RFE

BACKGROUND: In class prediction problems using microarray data, gene selection is essential to improve the prediction accuracy and to identify potential marker genes for a disease. Among numerous existing methods for gene selection, support vector machine-based recursive feature elimination (SVM-RFE) has become one of the leading methods and is being widely used. The SVM-based approach performs gene selection using the weight vector of the hyperplane constructed by the samples on the margin. However, the performance can be easily affected by noise and outliers, when it is applied to noisy, small sample size microarray data. RESULTS: In this paper, we propose a recursive gene selection method using the discriminant vector of the maximum margin criterion (MMC), which is a variant of classical linear discriminant analysis (LDA). To overcome the computational drawback of classical LDA and the problem of high dimensionality, we present efficient and stable algorithms for MMC-based RFE (MMC-RFE). The MMC-RFE algorithms naturally extend to multi-class cases. The performance of MMC-RFE was extensively compared with that of SVM-RFE using nine cancer microarray datasets, including four multi-class datasets. CONCLUSION: Our extensive comparison has demonstrated that for binary-class datasets MMC-RFE tends to show intermediate performance between hard-margin SVM-RFE and SVM-RFE with a properly chosen soft-margin parameter. Notably, MMC-RFE achieves significantly better performance with a smaller number of genes than SVM-RFE for multi-class datasets. The results suggest that MMC-RFE is less sensitive to noise and outliers due to the use of average margin, and thus may be useful for biomarker discovery from noisy data

MultiMiTar: A Novel Multi Objective Optimization based miRNA-Target Prediction Method

BACKGROUND: Machine learning based miRNA-target prediction algorithms often fail to obtain a balanced prediction accuracy in terms of both sensitivity and specificity due to lack of the gold standard of negative examples, miRNA-targeting site context specific relevant features and efficient feature selection process. Moreover, all the sequence, structure and machine learning based algorithms are unable to distribute the true positive predictions preferentially at the top of the ranked list; hence the algorithms become unreliable to the biologists. In addition, these algorithms fail to obtain considerable combination of precision and recall for the target transcripts that are translationally repressed at protein level. METHODOLOGY/PRINCIPAL FINDING: In the proposed article, we introduce an efficient miRNA-target prediction system MultiMiTar, a Support Vector Machine (SVM) based classifier integrated with a multiobjective metaheuristic based feature selection technique. The robust performance of the proposed method is mainly the result of using high quality negative examples and selection of biologically relevant miRNA-targeting site context specific features. The features are selected by using a novel feature selection technique AMOSA-SVM, that integrates the multi objective optimization technique Archived Multi-Objective Simulated Annealing (AMOSA) and SVM. CONCLUSIONS/SIGNIFICANCE: MultiMiTar is found to achieve much higher Matthew's correlation coefficient (MCC) of 0.583 and average class-wise accuracy (ACA) of 0.8 compared to the others target prediction methods for a completely independent test data set. The obtained MCC and ACA values of these algorithms range from -0.269 to 0.155 and 0.321 to 0.582, respectively. Moreover, it shows a more balanced result in terms of precision and sensitivity (recall) for the translationally repressed data set as compared to all the other existing methods. An important aspect is that the true positive predictions are distributed preferentially at the top of the ranked list that makes MultiMiTar reliable for the biologists. MultiMiTar is now available as an online tool at www.isical.ac.in/~bioinfo_miu/multimitar.htm. MultiMiTar software can be downloaded from www.isical.ac.in/~bioinfo_miu/multimitar-download.htm

Identification of User Behavioural Biometrics for Authentication using Keystroke Dynamics and Machine Learning

This thesis focuses on the effective classification of the behavior of users accessing computing devices to authenticate them. The authentication is based on keystroke dynamics, which captures the users behavioral biometric and applies machine learning concepts to classify them. The users type a strong passcode ”.tie5Roanl” to record their typing pattern. In order to confirm identity, anonymous data from 94 users were collected to carry out the research. Given the raw data, features were extracted from the attributes based on the button pressed and action timestamp events. The support vector machine classifier uses multi-class classification with one vs. one decision shape function to classify different users. To reduce the classification error, it is essential to identify the important features from the raw data. In an effort to confront the generation of features from attributes an efficient feature extraction algorithm has been developed, obtaining high classification performance are now being sought. To handle the multi-class problem, the random forest classifier is used to identify the users effectively. In addition, mRMR feature selection has been applied to increase the classification performance metrics and to confirm the identity of the users based on the way they access computing devices. From the results, we conclude that device information and touch pressure effectively contribute to identifying each user. Out of them, features that contain device information are responsible for increasing the performance metrics of the system by adding a token-based authentication layer. Based upon the results, random forest yields better classification results for this dataset. The research will contribute significantly to the field of cyber-security by forming a robust authentication system using machine learning algorithms

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Thirty Years of Machine Learning: The Road to Pareto-Optimal Wireless Networks

Future wireless networks have a substantial potential in terms of supporting a broad range of complex compelling applications both in military and civilian fields, where the users are able to enjoy high-rate, low-latency, low-cost and reliable information services. Achieving this ambitious goal requires new radio techniques for adaptive learning and intelligent decision making because of the complex heterogeneous nature of the network structures and wireless services. Machine learning (ML) algorithms have great success in supporting big data analytics, efficient parameter estimation and interactive decision making. Hence, in this article, we review the thirty-year history of ML by elaborating on supervised learning, unsupervised learning, reinforcement learning and deep learning. Furthermore, we investigate their employment in the compelling applications of wireless networks, including heterogeneous networks (HetNets), cognitive radios (CR), Internet of things (IoT), machine to machine networks (M2M), and so on. This article aims for assisting the readers in clarifying the motivation and methodology of the various ML algorithms, so as to invoke them for hitherto unexplored services as well as scenarios of future wireless networks.Comment: 46 pages, 22 fig

An Efficient Primal-Dual Prox Method for Non-Smooth Optimization

We study the non-smooth optimization problems in machine learning, where both the loss function and the regularizer are non-smooth functions. Previous studies on efficient empirical loss minimization assume either a smooth loss function or a strongly convex regularizer, making them unsuitable for non-smooth optimization. We develop a simple yet efficient method for a family of non-smooth optimization problems where the dual form of the loss function is bilinear in primal and dual variables. We cast a non-smooth optimization problem into a minimax optimization problem, and develop a primal dual prox method that solves the minimax optimization problem at a rate of $O(1/T)$ {assuming that the proximal step can be efficiently solved}, significantly faster than a standard subgradient descent method that has an $O(1/\sqrt{T})$ convergence rate. Our empirical study verifies the efficiency of the proposed method for various non-smooth optimization problems that arise ubiquitously in machine learning by comparing it to the state-of-the-art first order methods