Identification of pathway and gene markers using enhanced directed random walk for multiclass cancer expression data

Cancer markers play a significant role in the diagnosis of the origin of cancers and in the detection of cancers from initial treatments. This is a challenging task owing to the heterogeneity nature of cancers. Identification of these markers could help in improving the survival rate of cancer patients, in which dedicated treatment can be provided according to the diagnosis or even prevention. Previous investigations show that the use of pathway topology information could help in the detection of cancer markers from gene expression. Such analysis reduces its complexity from thousands of genes to a few hundreds of pathways. However, most of the existing methods group different cancer subtypes into just disease samples, and consider all pathways contribute equally in the analysis process. Meanwhile, the interaction between multiple genes and the genes with missing edges has been ignored in several other methods, and hence could lead to the poor performance of the identification of cancer markers from gene expression. Thus, this research proposes enhanced directed random walk to identify pathway and gene markers for multiclass cancer gene expression data. Firstly, an improved pathway selection with analysis of variances (ANOVA) that enables the consideration of multiple cancer subtypes is performed, and subsequently the integration of k-mean clustering and average silhouette method in the directed random walk that considers the interaction of multiple genes is also conducted. The proposed methods are tested on benchmark gene expression datasets (breast, lung, and skin cancers) and biological pathways. The performance of the proposed methods is then measured and compared in terms of classification accuracy and area under the receiver operating characteristics curve (AUC). The results indicate that the proposed methods are able to identify a list of pathway and gene markers from the datasets with better classification accuracy and AUC. The proposed methods have improved the classification performance in the range of between 1% and 35% compared with existing methods. Cell cycle and p53 signaling pathway were found significantly associated with breast, lung, and skin cancers, while the cell cycle was highly enriched with squamous cell carcinoma and adenocarcinoma

Click Fraud Detection in Online and In-app Advertisements: A Learning Based Approach

Click Fraud is the fraudulent act of clicking on pay-per-click advertisements to increase a site’s revenue, to drain revenue from the advertiser, or to inflate the popularity of content on social media platforms. In-app advertisements on mobile platforms are among the most common targets for click fraud, which makes companies hesitant to advertise their products. Fraudulent clicks are supposed to be caught by ad providers as part of their service to advertisers, which is commonly done using machine learning methods. However: (1) there is a lack of research in current literature addressing and evaluating the different techniques of click fraud detection and prevention, (2) threat models composed of active learning systems (smart attackers) can mislead the training process of the fraud detection model by polluting the training data, (3) current deep learning models have significant computational overhead, (4) training data is often in an imbalanced state, and balancing it still results in noisy data that can train the classifier incorrectly, and (5) datasets with high dimensionality cause increased computational overhead and decreased classifier correctness -- while existing feature selection techniques address this issue, they have their own performance limitations. By extending the state-of-the-art techniques in the field of machine learning, this dissertation provides the following solutions: (i) To address (1) and (2), we propose a hybrid deep-learning-based model which consists of an artificial neural network, auto-encoder and semi-supervised generative adversarial network. (ii) As a solution for (3), we present Cascaded Forest and Extreme Gradient Boosting with less hyperparameter tuning. (iii) To overcome (4), we propose a row-wise data reduction method, KSMOTE, which filters out noisy data samples both in the raw data and the synthetically generated samples. (iv) For (5), we propose different column-reduction methods such as multi-time-scale Time Series analysis for fraud forecasting, using binary labeled imbalanced datasets and hybrid filter-wrapper feature selection approaches

An enhanced binary bat and Markov clustering algorithms to improve event detection for heterogeneous news text documents

Event Detection (ED) works on identifying events from various types of data. Building an ED model for news text documents greatly helps decision-makers in various disciplines in improving their strategies. However, identifying and summarizing events from such data is a non-trivial task due to the large volume of published heterogeneous news text documents. Such documents create a high-dimensional feature space that influences the overall performance of the baseline methods in ED model. To address such a problem, this research presents an enhanced ED model that includes improved methods for the crucial phases of the ED model such as Feature Selection (FS), ED, and summarization. This work focuses on the FS problem by automatically detecting events through a novel wrapper FS method based on Adapted Binary Bat Algorithm (ABBA) and Adapted Markov Clustering Algorithm (AMCL), termed ABBA-AMCL. These adaptive techniques were developed to overcome the premature convergence in BBA and fast convergence rate in MCL. Furthermore, this study proposes four summarizing methods to generate informative summaries. The enhanced ED model was tested on 10 benchmark datasets and 2 Facebook news datasets. The effectiveness of ABBA-AMCL was compared to 8 FS methods based on meta-heuristic algorithms and 6 graph-based ED methods. The empirical and statistical results proved that ABBAAMCL surpassed other methods on most datasets. The key representative features demonstrated that ABBA-AMCL method successfully detects real-world events from Facebook news datasets with 0.96 Precision and 1 Recall for dataset 11, while for dataset 12, the Precision is 1 and Recall is 0.76. To conclude, the novel ABBA-AMCL presented in this research has successfully bridged the research gap and resolved the curse of high dimensionality feature space for heterogeneous news text documents. Hence, the enhanced ED model can organize news documents into distinct events and provide policymakers with valuable information for decision making

Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics

DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and expressed proteins. The ability to predict whether a given mutation is disease-causing or harmless is of great importance for the early detection of patients with a high risk of developing a particular disease and would pave the way for personalized medicine and diagnostics. Here we review existing methods and techniques to study and predict the effects of DNA mutations from three different perspectives: in silico, in vitro and in vivo. It is emphasized that the problem is complicated and successful detection of a pathogenic mutation frequently requires a combination of several methods and a knowledge of the biological phenomena associated with the corresponding macromolecules

Bioinformatics Applications Based On Machine Learning

The great advances in information technology (IT) have implications for many sectors, such as bioinformatics, and has considerably increased their possibilities. This book presents a collection of 11 original research papers, all of them related to the application of IT-related techniques within the bioinformatics sector: from new applications created from the adaptation and application of existing techniques to the creation of new methodologies to solve existing problems

Computational Optimizations for Machine Learning

The present book contains the 10 articles finally accepted for publication in the Special Issue “Computational Optimizations for Machine Learning” of the MDPI journal Mathematics, which cover a wide range of topics connected to the theory and applications of machine learning, neural networks and artificial intelligence. These topics include, among others, various types of machine learning classes, such as supervised, unsupervised and reinforcement learning, deep neural networks, convolutional neural networks, GANs, decision trees, linear regression, SVM, K-means clustering, Q-learning, temporal difference, deep adversarial networks and more. It is hoped that the book will be interesting and useful to those developing mathematical algorithms and applications in the domain of artificial intelligence and machine learning as well as for those having the appropriate mathematical background and willing to become familiar with recent advances of machine learning computational optimization mathematics, which has nowadays permeated into almost all sectors of human life and activity

Applied Metaheuristic Computing

For decades, Applied Metaheuristic Computing (AMC) has been a prevailing optimization technique for tackling perplexing engineering and business problems, such as scheduling, routing, ordering, bin packing, assignment, facility layout planning, among others. This is partly because the classic exact methods are constrained with prior assumptions, and partly due to the heuristics being problem-dependent and lacking generalization. AMC, on the contrary, guides the course of low-level heuristics to search beyond the local optimality, which impairs the capability of traditional computation methods. This topic series has collected quality papers proposing cutting-edge methodology and innovative applications which drive the advances of AMC

Machine learning assisted optimization with applications to diesel engine optimization with the particle swarm optimization algorithm

A novel approach to incorporating Machine Learning into optimization routines is presented. An approach which combines the benefits of ML, optimization, and meta-model searching is developed and tested on a multi-modal test problem; a modified Rastragin\u27s function. An enhanced Particle Swarm Optimization method was derived from the initial testing. Optimization of a diesel engine was carried out using the modified algorithm demonstrating an improvement of 83% compared with the unmodified PSO algorithm. Additionally, an approach to enhancing the training of ML models by leveraging Virtual Sensing as an alternative to standard multi-layer neural networks is presented. Substantial gains were made in the prediction of Particulate matter, reducing the MMSE by 50% and improving the correlation R^2 from 0.84 to 0.98. Improvements were made in models of PM, NOx, HC, CO, and Fuel Consumption using the method, while training times and convergence reliability were simultaneously improved over the traditional approach