Data mining in bioinformatics using Weka

The Weka machine learning workbench provides a general purpose environment for automatic classification, regression, clustering and feature selection-common data mining problems in bioinformatics research. It contains an extensive collection of machine learning algorithms and data exploration and the experimental comparison of different machine learning techniques on the same problem. Weka can process data given in the form of a single relational table. Its main objectives are to (a) assist users in extracting useful information from data and (b) enable them to easily identify a suitable algorithm for generating an accurate predictive model from it

Dynamic Rule Covering Classification in Data Mining with Cyber Security Phishing Application

Data mining is the process of discovering useful patterns from datasets using intelligent techniques to help users make certain decisions. A typical data mining task is classification, which involves predicting a target variable known as the class in previously unseen data based on models learnt from an input dataset. Covering is a well-known classification approach that derives models with If-Then rules. Covering methods, such as PRISM, have a competitive predictive performance to other classical classification techniques such as greedy, decision tree and associative classification. Therefore, Covering models are appropriate decision-making tools and users favour them carrying out decisions. Despite the use of Covering approach in data processing for different classification applications, it is also acknowledged that this approach suffers from the noticeable drawback of inducing massive numbers of rules making the resulting model large and unmanageable by users. This issue is attributed to the way Covering techniques induce the rules as they keep adding items to the rule’s body, despite the limited data coverage (number of training instances that the rule classifies), until the rule becomes with zero error. This excessive learning overfits the training dataset and also limits the applicability of Covering models in decision making, because managers normally prefer a summarised set of knowledge that they are able to control and comprehend rather a high maintenance models. In practice, there should be a trade-off between the number of rules offered by a classification model and its predictive performance. Another issue associated with the Covering models is the overlapping of training data among the rules, which happens when a rule’s classified data are discarded during the rule discovery phase. Unfortunately, the impact of a rule’s removed data on other potential rules is not considered by this approach. However, When removing training data linked with a rule, both frequency and rank of other rules’ items which have appeared in the removed data are updated. The impacted rules should maintain their true rank and frequency in a dynamic manner during the rule discovery phase rather just keeping the initial computed frequency from the original input dataset. In response to the aforementioned issues, a new dynamic learning technique based on Covering and rule induction, that we call Enhanced Dynamic Rule Induction (eDRI), is developed. eDRI has been implemented in Java and it has been embedded in WEKA machine learning tool. The developed algorithm incrementally discovers the rules using primarily frequency and rule strength thresholds. These thresholds in practice limit the search space for both items as well as potential rules by discarding any with insufficient data representation as early as possible resulting in an efficient training phase. More importantly, eDRI substantially cuts down the number of training examples scans by continuously updating potential rules’ frequency and strength parameters in a dynamic manner whenever a rule gets inserted into the classifier. In particular, and for each derived rule, eDRI adjusts on the fly the remaining potential rules’ items frequencies as well as ranks specifically for those that appeared within the deleted training instances of the derived rule. This gives a more realistic model with minimal rules redundancy, and makes the process of rule induction efficient and dynamic and not static. Moreover, the proposed technique minimises the classifier’s number of rules at preliminary stages by stopping learning when any rule does not meet the rule’s strength threshold therefore minimising overfitting and ensuring a manageable classifier. Lastly, eDRI prediction procedure not only priorities using the best ranked rule for class forecasting of test data but also restricts the use of the default class rule thus reduces the number of misclassifications. The aforementioned improvements guarantee classification models with smaller size that do not overfit the training dataset, while maintaining their predictive performance. The eDRI derived models particularly benefit greatly users taking key business decisions since they can provide a rich knowledge base to support their decision making. This is because these models’ predictive accuracies are high, easy to understand, and controllable as well as robust, i.e. flexible to be amended without drastic change. eDRI applicability has been evaluated on the hard problem of phishing detection. Phishing normally involves creating a fake well-designed website that has identical similarity to an existing business trustful website aiming to trick users and illegally obtain their credentials such as login information in order to access their financial assets. The experimental results against large phishing datasets revealed that eDRI is highly useful as an anti-phishing tool since it derived manageable size models when compared with other traditional techniques without hindering the classification performance. Further evaluation results using other several classification datasets from different domains obtained from University of California Data Repository have corroborated eDRI’s competitive performance with respect to accuracy, number of knowledge representation, training time and items space reduction. This makes the proposed technique not only efficient in inducing rules but also effective

CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules

Nowadays, knowledge extraction methods from Next Generation Sequencing data are highly requested. In this work, we focus on RNA-seq gene expression analysis and specifically on case-control studies with rule-based supervised classification algorithms that build a model able to discriminate cases from controls. State of the art algorithms compute a single classification model that contains few features (genes). On the contrary, our goal is to elicit a higher amount of knowledge by computing many classification models, and therefore to identify most of the genes related to the predicted class

Ensemble based on randomised neural networks for online data stream regression in presence of concept drift

The big data paradigm has posed new challenges for the Machine Learning algorithms, such as analysing continuous flows of data, in the form of data streams, and dealing with the evolving nature of the data, which cause a phenomenon often referred to in the literature as concept drift. Concept drift is caused by inconsistencies between the optimal hypotheses in two subsequent chunks of data, whereby the concept underlying a given process evolves over time, which can happen due to several factors including change in consumer preference, economic dynamics, or environmental conditions. This thesis explores the problem of data stream regression with the presence of concept drift. This problem requires computationally efficient algorithms that are able to adapt to the various types of drift that may affect the data. The development of effective algorithms for data streams with concept drift requires several steps that are discussed in this research. The first one is related to the datasets required to assess the algorithms. In general, it is not possible to determine the occurrence of concept drift on real-world datasets; therefore, synthetic datasets where the various types of concept drift can be simulated are required. The second issue is related to the choice of the algorithm. The ensemble algorithms show many advantages to deal with concept drifting data streams, which include flexibility, computational efficiency and high accuracy. For the design of an effective ensemble, this research analyses the use of randomised Neural Networks as base models, along with their optimisation. The optimisation of the randomised Neural Networks involves design and tuning hyperparameters which may substantially affect its performance. The optimisation of the base models is an important aspect to build highly accurate and computationally efficient ensembles. To cope with the concept drift, the existing methods either require setting fixed updating points, which may result in unnecessary computations or slow reaction to concept drift, or rely on drifting detection mechanism, which may be ineffective due to the difficulty to detect drift in real applications. Therefore, the research contributions of this thesis include the development of a new approach for synthetic dataset generation, development of a new hyperparameter optimisation algorithm that reduces the search effort and the need of prior assumptions compared to existing methods, the analysis of the effects of randomised Neural Networks hyperparameters, and the development of a new ensemble algorithm based on bagging meta-model that reduces the computational effort over existing methods and uses an innovative updating mechanism to cope with concept drift. The algorithms have been tested on synthetic datasets and validated on four real-world datasets from various application domains

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

Ensemble deep learning: A review

Ensemble learning combines several individual models to obtain better generalization performance. Currently, deep learning models with multilayer processing architecture is showing better performance as compared to the shallow or traditional classification models. Deep ensemble learning models combine the advantages of both the deep learning models as well as the ensemble learning such that the final model has better generalization performance. This paper reviews the state-of-art deep ensemble models and hence serves as an extensive summary for the researchers. The ensemble models are broadly categorised into ensemble models like bagging, boosting and stacking, negative correlation based deep ensemble models, explicit/implicit ensembles, homogeneous /heterogeneous ensemble, decision fusion strategies, unsupervised, semi-supervised, reinforcement learning and online/incremental, multilabel based deep ensemble models. Application of deep ensemble models in different domains is also briefly discussed. Finally, we conclude this paper with some future recommendations and research directions

LC an effective classification based association rule mining algorithm

Classification using association rules is a research field in data mining that primarily uses association rule discovery techniques in classification benchmarks. It has been confirmed by many research studies in the literature that classification using association tends to generate more predictive classification systems than traditional classification data mining techniques like probabilistic, statistical and decision tree. In this thesis, we introduce a novel data mining algorithm based on classification using association called “Looking at the Class” (LC), which can be used in for mining a range of classification data sets. Unlike known algorithms in classification using the association approach such as Classification based on Association rule (CBA) system and Classification based on Predictive Association (CPAR) system, which merge disjoint items in the rule learning step without anticipating the class label similarity, the proposed algorithm merges only items with identical class labels. This saves too many unnecessary items combining during the rule learning step, and consequently results in large saving in computational time and memory. Furthermore, the LC algorithm uses a novel prediction procedure that employs multiple rules to make the prediction decision instead of a single rule. The proposed algorithm has been evaluated thoroughly on real world security data sets collected using an automated tool developed at Huddersfield University. The security application which we have considered in this thesis is about categorizing websites based on their features to legitimate or fake which is a typical binary classification problem. Also, experimental results on a number of UCI data sets have been conducted and the measures used for evaluation is the classification accuracy, memory usage, and others. The results show that LC algorithm outperformed traditional classification algorithms such as C4.5, PART and Naïve Bayes as well as known classification based association algorithms like CBA with respect to classification accuracy, memory usage, and execution time on most data sets we consider

Predicting software faults in large space systems using machine learning techniques

Recently, the use of machine learning (ML) algorithms has proven to be of great practical value in solving a variety of engineering problems including the prediction of failure, fault, and defect-proneness as the space system software becomes complex. One of the most active areas of recent research in ML has been the use of ensemble classifiers. How ML techniques (or classifiers) could be used to predict software faults in space systems, including many aerospace systems is shown, and further use ensemble individual classifiers by having them vote for the most popular class to improve system software fault-proneness prediction. Benchmarking results on four NASA public datasets show the Naive Bayes classifier as more robust software fault prediction while most ensembles with a decision tree classifier as one of its components achieve higher accuracy rates