Hidden Markov Models for Gene Sequence Classification: Classifying the VSG genes in the Trypanosoma brucei Genome

The article presents an application of Hidden Markov Models (HMMs) for pattern recognition on genome sequences. We apply HMM for identifying genes encoding the Variant Surface Glycoprotein (VSG) in the genomes of Trypanosoma brucei (T. brucei) and other African trypanosomes. These are parasitic protozoa causative agents of sleeping sickness and several diseases in domestic and wild animals. These parasites have a peculiar strategy to evade the host's immune system that consists in periodically changing their predominant cellular surface protein (VSG). The motivation for using patterns recognition methods to identify these genes, instead of traditional homology based ones, is that the levels of sequence identity (amino acid and DNA sequence) amongst these genes is often below of what is considered reliable in these methods. Among pattern recognition approaches, HMM are particularly suitable to tackle this problem because they can handle more naturally the determination of gene edges. We evaluate the performance of the model using different number of states in the Markov model, as well as several performance metrics. The model is applied using public genomic data. Our empirical results show that the VSG genes on T. brucei can be safely identified (high sensitivity and low rate of false positives) using HMM.Comment: Accepted article in July, 2015 in Pattern Analysis and Applications, Springer. The article contains 23 pages, 4 figures, 8 tables and 51 reference

Multilayer Feedforward Neural Network for Internet Traffic Classification

Recently, the efficient internet traffic classification has gained attention in order to improve service quality in IP networks. But the problem with the existing solutions is to handle the imbalanced dataset which has high uneven distribution of flows between the classes. In this paper, we propose a multilayer feedforward neural network architecture to handle the high imbalanced dataset. In the proposed model, we used a variation of multilayer perceptron with 4 hidden layers (called as mountain mirror networks) which does the feature transformation effectively. To check the efficacy of the proposed model, we used Cambridge dataset which consists of 248 features spread across 10 classes. Experimentation is carried out for two variants of the same dataset which is a standard one and a derived subset. The proposed model achieved an accuracy of 99.08% for highly imbalanced dataset (standard)

Handling minority class problem in threats detection based on heterogeneous ensemble learning approach.

Multiclass problem, such as detecting multi-steps behaviour of Advanced Persistent Threats (APTs) have been a major global challenge, due to their capability to navigates around defenses and to evade detection for a prolonged period of time. Targeted APT attacks present an increasing concern for both cyber security and business continuity. Detecting the rare attack is a classification problem with data imbalance. This paper explores the applications of data resampling techniques, together with heterogeneous ensemble approach for dealing with data imbalance caused by unevenly distributed data elements among classes with our focus on capturing the rare attack. It has been shown that the suggested algorithms provide not only detection capability, but can also classify malicious data traffic corresponding to rare APT attacks

Data classification using the Dempster-Shafer method

In this paper, the Dempster-Shafer method is employed as the theoretical basis for creating data classification systems. Testing is carried out using three popular (multiple attribute) benchmark datasets that have two, three and four classes. In each case, a subset of the available data is used for training to establish thresholds, limits or likelihoods of class membership for each attribute, and hence create mass functions that establish probability of class membership for each attribute of the test data. Classification of each data item is achieved by combination of these probabilities via Dempster’s Rule of Combination. Results for the first two datasets show extremely high classification accuracy that is competitive with other popular methods. The third dataset is non-numerical and difficult to classify, but good results can be achieved provided the system and mass functions are designed carefully and the right attributes are chosen for combination. In all cases the Dempster-Shafer method provides comparable performance to other more popular algorithms, but the overhead of generating accurate mass functions increases the complexity with the addition of new attributes. Overall, the results suggest that the D-S approach provides a suitable framework for the design of classification systems and that automating the mass function design and calculation would increase the viability of the algorithm for complex classification problems

An Empirical Study of AML Approach for Credit Card Fraud Detection—Financial Transactions

Credit card fraud is one of the flip sides of the digital world, where transactions are made without the knowledge of the genuine user. Based on the study of various papers published between 1994 and 2018 on credit card fraud, the following objectives are achieved: the various types of credit card frauds has identified and to detect automatically these frauds, an adaptive machine learning techniques (AMLTs) has studied and also their pros and cons has summarized. The various dataset are used in the literature has studied and categorized into the real and synthesized datasets.The performance matrices and evaluation criteria have summarized which has used to evaluate the fraud detection system.This study has also covered the deep analysis and comparison of the performance (i.e sensitivity, specificity, and accuracy) of existing machine learning techniques in the credit card fraud detection area.The findings of this study clearly show that supervised learning, card-not-present fraud, skimming fraud, and website cloning method has been used more frequently.This Study helps to new researchers by discussing the limitation of existing fraud detection techniques and providing helpful directions of research in the credit card fraud detection field

DMP_MI: an effective diabetes mellitus classification algorithm on imbalanced data with missing values

© 2019 Institute of Electrical and Electronics Engineers Inc.. All rights reserved. As a widely known chronic disease, diabetes mellitus is called a silent killer. It makes the body produce less insulin and causes increased blood sugar, which leads to many complications and affects the normal functioning of various organs, such as eyes, kidneys, and nerves. Although diabetes has attracted high attention in research, due to the existence of missing values and class imbalance in the data, the overall performance of diabetes classification using machine learning is relatively low. In this paper, we propose an effective Prediction algorithm for Diabetes Mellitus classification on Imbalanced data with Missing values (DMP_MI). First, the missing values are compensated by the Naïve Bayes (NB) method for data normalization. Then, an adaptive synthetic sampling method (ADASYN) is adopted to reduce the influence of class imbalance on the prediction performance. Finally, a random forest (RF) classifier is used to generate predictions and evaluated using comprehensive set of evaluation indicators. Experiments performed on Pima Indians diabetes dataset from the University of California at Irvine, Irvine (UCI) Repository, have demonstrated the effectiveness and superiority of our proposed DMP_MI

Machine learning for network based intrusion detection: an investigation into discrepancies in findings with the KDD cup '99 data set and multi-objective evolution of neural network classifier ensembles from imbalanced data.

For the last decade it has become commonplace to evaluate machine learning techniques for network based intrusion detection on the KDD Cup '99 data set. This data set has served well to demonstrate that machine learning can be useful in intrusion detection. However, it has undergone some criticism in the literature, and it is out of date. Therefore, some researchers question the validity of the findings reported based on this data set. Furthermore, as identified in this thesis, there are also discrepancies in the findings reported in the literature. In some cases the results are contradictory. Consequently, it is difficult to analyse the current body of research to determine the value in the findings. This thesis reports on an empirical investigation to determine the underlying causes of the discrepancies. Several methodological factors, such as choice of data subset, validation method and data preprocessing, are identified and are found to affect the results significantly. These findings have also enabled a better interpretation of the current body of research. Furthermore, the criticisms in the literature are addressed and future use of the data set is discussed, which is important since researchers continue to use it due to a lack of better publicly available alternatives. Due to the nature of the intrusion detection domain, there is an extreme imbalance among the classes in the KDD Cup '99 data set, which poses a significant challenge to machine learning. In other domains, researchers have demonstrated that well known techniques such as Artificial Neural Networks (ANNs) and Decision Trees (DTs) often fail to learn the minor class(es) due to class imbalance. However, this has not been recognized as an issue in intrusion detection previously. This thesis reports on an empirical investigation that demonstrates that it is the class imbalance that causes the poor detection of some classes of intrusion reported in the literature. An alternative approach to training ANNs is proposed in this thesis, using Genetic Algorithms (GAs) to evolve the weights of the ANNs, referred to as an Evolutionary Neural Network (ENN). When employing evaluation functions that calculate the fitness proportionally to the instances of each class, thereby avoiding a bias towards the major class(es) in the data set, significantly improved true positive rates are obtained whilst maintaining a low false positive rate. These findings demonstrate that the issues of learning from imbalanced data are not due to limitations of the ANNs; rather the training algorithm. Moreover, the ENN is capable of detecting a class of intrusion that has been reported in the literature to be undetectable by ANNs. One limitation of the ENN is a lack of control of the classification trade-off the ANNs obtain. This is identified as a general issue with current approaches to creating classifiers. Striving to create a single best classifier that obtains the highest accuracy may give an unfruitful classification trade-off, which is demonstrated clearly in this thesis. Therefore, an extension of the ENN is proposed, using a Multi-Objective GA (MOGA), which treats the classification rate on each class as a separate objective. This approach produces a Pareto front of non-dominated solutions that exhibit different classification trade-offs, from which the user can select one with the desired properties. The multi-objective approach is also utilised to evolve classifier ensembles, which yields an improved Pareto front of solutions. Furthermore, the selection of classifier members for the ensembles is investigated, demonstrating how this affects the performance of the resultant ensembles. This is a key to explaining why some classifier combinations fail to give fruitful solutions

Detecting Slow Wave Sleep Using a Single EEG Signal Channel

Background: In addition to the cost and complexity of processing multiple signal channels, manual sleep staging is also tedious, time consuming, and error-prone. The aim of this paper is to propose an automatic slow wave sleep (SWS) detection method that uses only one channel of the electroencephalography (EEG) signal. New Method: The proposed approach distinguishes itself from previous automatic sleep staging methods by using three specially designed feature groups. The first feature group characterizes the waveform pattern of the EEG signal. The remaining two feature groups are developed to resolve the difficulties caused by interpersonal EEG signal differences. Results and comparison with existing methods: The proposed approach was tested with 1,003 subjects, and the SWS detection results show kappa coefficient at 0.66, an accuracy level of 0.973, a sensitivity score of 0.644 and a positive predictive value of 0.709. By excluding sleep apnea patients and persons whose age is older than 55, the SWS detection results improved to kappa coefficient, 0.76; accuracy, 0.963; sensitivity, 0.758; and positive predictive value, 0.812. Conclusions: With newly developed signal features, this study proposed and tested a single-channel EEG-based SWS detection method. The effectiveness of the proposed approach was demonstrated by applying it to detect the SWS of 1003 subjects. Our test results show that a low SWS ratio and sleep apnea can degrade the performance of SWS detection. The results also show that a large and accurately staged sleep dataset is of great importance when developing automatic sleep staging methods