A Comparison of Multi-instance Learning Algorithms

Motivated by various challenging real-world applications, such as drug activity prediction and image retrieval, multi-instance (MI) learning has attracted considerable interest in recent years. Compared with standard supervised learning, the MI learning task is more difficult as the label information of each training example is incomplete. Many MI algorithms have been proposed. Some of them are specifically designed for MI problems whereas others have been upgraded or adapted from standard single-instance learning algorithms. Most algorithms have been evaluated on only one or two benchmark datasets, and there is a lack of systematic comparisons of MI learning algorithms. This thesis presents a comprehensive study of MI learning algorithms that aims to compare their performance and find a suitable way to properly address different MI problems. First, it briefly reviews the history of research on MI learning. Then it discusses five general classes of MI approaches that cover a total of 16 MI algorithms. After that, it presents empirical results for these algorithms that were obtained from 15 datasets which involve five different real-world application domains. Finally, some conclusions are drawn from these results: (1) applying suitable standard single-instance learners to MI problems can often generate the best result on the datasets that were tested, (2) algorithms exploiting the standard asymmetric MI assumption do not show significant advantages over approaches using the so-called collective assumption, and (3) different MI approaches are suitable for different application domains, and no MI algorithm works best on all MI problems

Alleviating Naive Bayes attribute independence assumption by attribute weighting

Despite the simplicity of the Naive Bayes classifier, it has continued to perform well against more sophisticated newcomers and has remained, therefore, of great interest to the machine learning community. Of numerous approaches to refining the naive Bayes classifier, attribute weighting has received less attention than it warrants. Most approaches, perhaps influenced by attribute weighting in other machine learning algorithms, use weighting to place more emphasis on highly predictive attributes than those that are less predictive. In this paper, we argue that for naive Bayes attribute weighting should instead be used to alleviate the conditional independence assumption. Based on this premise, we propose a weighted naive Bayes algorithm, called WANBIA, that selects weights to minimize either the negative conditional log likelihood or the mean squared error objective functions. We perform extensive evaluations and find that WANBIA is a competitive alternative to state of the art classifiers like Random Forest, Logistic Regression and A1DE. © 2013 Nayyar A. Zaidi, Jesus Cerquides, Mark J. Carman and Geoffrey I. Webb.This research has been supported by the Australian Research Council under grant DP110101427 and Asian Office of Aerospace Research and Development, Air Force Office of Scientific Research under contract FA23861214030. The authors would like to thank Mark Hall for providing the code for CFS and MH. The authors would also like to thank anonymous reviewers for their insightful comments that helped improving the paper tremendously.Peer Reviewe

Application of data mining in scheduling of single machine system

The rapidly growing field of data mining has the potential of improving performance of existing scheduling systems. Such systems generate large amounts of data, which is often not utilized to its potential. The problem is whether it is possible to discover the implicit knowledge behind scheduling practice and then, with this knowledge, we could improve current scheduling practice. In this dissertation, we propose a novel methodology for generating scheduling rules using a data-driven approach. We show how to use data mining to discover previously unknown dispatching rules by applying the learning algorithms directly to production data. We also consider how by using this new approach unexpected knowledge and insights can be obtained, in a manner that would not be possible if an explicit model of the system or the basic scheduling rules had to be obtained beforehand. However, direct data mining of production data can at least mimic scheduling practices. The problem is whether scheduling practice could be improved with the knowledge discovered by data mining. We propose to combine data mining with optimization for effective production. In this approach, we use a genetic algorithm to find a heuristic solution to the optimal instances selection problem, and then induce a decision tree from this subset of instances. The optimal instance selection can be viewed as determining the best practices from what has been done in the past, and the data mining can then learn new dispatching rules from those best practices

Learning Instance Weights in Multi-Instance Learning

Multi-instance (MI) learning is a variant of supervised machine learning, where each learning example contains a bag of instances instead of just a single feature vector. MI learning has applications in areas such as drug activity prediction, fruit disease management and image classification. This thesis investigates the case where each instance has a weight value determining the level of influence that it has on its bag's class label. This is a more general assumption than most existing approaches use, and thus is more widely applicable. The challenge is to accurately estimate these weights in order to make predictions at the bag level. An existing approach known as MILES is retroactively identified as an algorithm that uses instance weights for MI learning, and is evaluated using a variety of base learners on benchmark problems. New algorithms for learning instance weights for MI learning are also proposed and rigorously evaluated on both artificial and real-world datasets. The new algorithms are shown to achieve better root mean squared error rates than existing approaches on artificial data generated according to the algorithms' underlying assumptions. Experimental results also demonstrate that the new algorithms are competitive with existing approaches on real-world problems

Intelligent and Improved Self-Adaptive Anomaly based Intrusion Detection System for Networks

With the advent of digital technology, computer networks have developed rapidly at an unprecedented pace contributing tremendously to social and economic development. They have become the backbone for all critical sectors and all the top Multi-National companies. Unfortunately, security threats for computer networks have increased dramatically over the last decade being much brazen and bolder. Intrusions or attacks on computers and networks are activities or attempts to jeopardize main system security objectives, which called as confidentiality, integrity and availability. They lead mostly in great financial losses, massive sensitive data leaks, thereby decreasing efficiency and the quality of productivity of an organization. There is a great need for an effective Network Intrusion Detection System (NIDS), which are security tools designed to interpret the intrusion attempts in incoming network traffic, thereby achieving a solid line of protection against inside and outside intruders. In this work, we propose to optimize a very popular soft computing tool prevalently used for intrusion detection namely Back Propagation Neural Network (BPNN) using a novel machine learning framework called “ISAGASAA”, based on Improved Self-Adaptive Genetic Algorithm (ISAGA) and Simulated Annealing Algorithm (SAA). ISAGA is our variant of standard Genetic Algorithm (GA), which is developed based on GA improved through an Adaptive Mutation Algorithm (AMA) and optimization strategies. The optimization strategies carried out are Parallel Processing (PP) and Fitness Value Hashing (FVH) that reduce execution time, convergence time and save processing power. While, SAA was incorporated to ISAGA in order to optimize its heuristic search. Experimental results based on Kyoto University benchmark dataset version 2015 demonstrate that our optimized NIDS based BPNN called “ANID BPNN-ISAGASAA” outperforms several state-of-art approaches in terms of detection rate and false positive rate. Moreover, improvement of GA through FVH and PP saves processing power and execution time. Thus, our model is very much convenient for network anomaly detection.

Statistical and Machine Learning Models to Predict Programming Performance

This thesis details a longitudinal study on factors that influence introductory programming success and on the development of machine learning models to predict incoming student performance. Although numerous studies have developed models to predict programming success, the models struggled to achieve high accuracy in predicting the likely performance of incoming students. Our approach overcomes this by providing a machine learning technique, using a set of three significant factors, that can predict whether students will be ‘weak’ or ‘strong’ programmers with approximately 80% accuracy after only three weeks of programming experience. This thesis makes three fundamental contributions. The first contribution is a longitudinal study identifying factors that influence introductory programming success, investigating 25 factors at four different institutions. Evidence of the importance of mathematics, comfort-level and computer game-playing as predictors of programming performance is provided. A number of new instruments were developed by the author and a programming self-esteem measure was shown to out-perform other previous comparable comfort-level measures in predicting programming performance. The second contribution of the thesis is an analysis of the use of machine learning (ML) algorithms to predict performance and is a first attempt to investigate the effectiveness of a variety of ML algorithms to predict introductory programming performance. The ML models built as part of this research are the most effective models so far developed. The models are effective even when students have just commenced a programming module. Consequently, timely interventions can be put in place to prevent struggling students from failing. The third contribution of the thesis is the recommendation of an algorithm, based on detailed statistical analysis that should be used by the computer science education community to predict the likely performance of incoming students. Optimisations were carried out to investigate if prediction accuracy could be further increased and an ensemble algorithm, StackingC, was shown to improve prediction performance. The factors identified in this thesis and the associated machine learning models provide a means to predict accurately programming performance when students have only completed preliminary programming concepts. This has not previously been possible

Adaptive rule-based malware detection employing learning classifier systems

Efficient and accurate malware detection is increasingly becoming a necessity for society to operate. Existing malware detection systems have excellent performance in identifying known malware for which signatures are available, but poor performance in anomaly detection for zero day exploits for which signatures have not yet been made available or targeted attacks against a specific entity. The primary goal of this thesis is to provide evidence for the potential of learning classier systems to improve the accuracy of malware detection. A customized system based on a state-of-the-art learning classier system is presented for adaptive rule-based malware detection, which combines a rule-based expert system with evolutionary algorithm based reinforcement learning, thus creating a self-training adaptive malware detection system which dynamically evolves detection rules. This system is analyzed on a benchmark of malicious and non-malicious files. Experimental results show that the system can outperform C4.5, a well-known non-adaptive machine learning algorithm, under certain conditions. The results demonstrate the system\u27s ability to learn effective rules from repeated presentations of a tagged training set and show the degree of generalization achieved on an independent test set. This thesis is an extension and expansion of the work published in the Security, Trust, and Privacy for Software Applications workshop in COMPSAC 2011 - the 35th Annual IEEE Signature Conference on Computer Software and Applications --Abstract, page iii

Combining classification algorithms

Dissertação de Doutoramento em Ciência de Computadores apresentada à Faculdade de Ciências da Universidade do PortoA capacidade de um algoritmo de aprendizagem induzir, para um determinado problema, uma boa generalização depende da linguagem de representação usada para generalizar os exemplos. Como diferentes algoritmos usam diferentes linguagens de representação e estratégias de procura, são explorados espaços diferentes e são obtidos resultados diferentes. O problema de encontrar a representação mais adequada para o problema em causa, é uma área de investigação bastante activa. Nesta dissertação, em vez de procurar métodos que fazem o ajuste aos dados usando uma única linguagem de representação, apresentamos uma família de algoritmos, sob a designação genérica de Generalização em Cascata, onde o espaço de procura contem modelos que utilizam diferentes linguagens de representação. A ideia básica do método consiste em utilizar os algoritmos de aprendizagem em sequência. Em cada iteração ocorre um processo com dois passos. No primeiro passo, um classificador constrói um modelo. No segundo passo, o espaço definido pelos atributos é estendido pela inserção de novos atributos gerados utilizando este modelo. Este processo de construção de novos atributos constrói atributos na linguagem de representação do classificador usado para construir o modelo. Se posteriormente na sequência, um classificador utiliza um destes novos atributos para construir o seu modelo, a sua capacidade de representação foi estendida. Desta forma as restrições da linguagem de representação dosclassificadores utilizados a mais alto nível na sequência, são relaxadas pela incorporação de termos da linguagem derepresentação dos classificadores de base. Esta é a metodologia base subjacente ao sistema Ltree e à arquitecturada Generalização em Cascata.O método é apresentado segundo duas perspectivas. Numa primeira parte, é apresentado como uma estratégia paraconstruir árvores de decisão multivariadas. É apresentado o sistema Ltree que utiliza como operador para a construção de atributos um discriminante linear. ..

Predictive Modelling Approach to Data-Driven Computational Preventive Medicine

This thesis contributes novel predictive modelling approaches to data-driven computational preventive medicine and offers an alternative framework to statistical analysis in preventive medicine research. In the early parts of this research, this thesis presents research by proposing a synergy of machine learning methods for detecting patterns and developing inexpensive predictive models from healthcare data to classify the potential occurrence of adverse health events. In particular, the data-driven methodology is founded upon a heuristic-systematic assessment of several machine-learning methods, data preprocessing techniques, models’ training estimation and optimisation, and performance evaluation, yielding a novel computational data-driven framework, Octopus. Midway through this research, this thesis advances research in preventive medicine and data mining by proposing several new extensions in data preparation and preprocessing. It offers new recommendations for data quality assessment checks, a novel multimethod imputation (MMI) process for missing data mitigation, a novel imbalanced resampling approach, and minority pattern reconstruction (MPR) led by information theory. This thesis also extends the area of model performance evaluation with a novel classification performance ranking metric called XDistance. In particular, the experimental results show that building predictive models with the methods guided by our new framework (Octopus) yields domain experts' approval of the new reliable models’ performance. Also, performing the data quality checks and applying the MMI process led healthcare practitioners to outweigh predictive reliability over interpretability. The application of MPR and its hybrid resampling strategies led to better performances in line with experts' success criteria than the traditional imbalanced data resampling techniques. Finally, the use of the XDistance performance ranking metric was found to be more effective in ranking several classifiers' performances while offering an indication of class bias, unlike existing performance metrics The overall contributions of this thesis can be summarised as follow. First, several data mining techniques were thoroughly assessed to formulate the new Octopus framework to produce new reliable classifiers. In addition, we offer a further understanding of the impact of newly engineered features, the physical activity index (PAI) and biological effective dose (BED). Second, the newly developed methods within the new framework. Finally, the newly accepted developed predictive models help detect adverse health events, namely, visceral fat-associated diseases and advanced breast cancer radiotherapy toxicity side effects. These contributions could be used to guide future theories, experiments and healthcare interventions in preventive medicine and data mining

Grammatical evolution decision trees for detecting gene-gene interactions

<p>Abstract</p> <p>Background</p> <p>A fundamental goal of human genetics is the discovery of polymorphisms that predict common, complex diseases. It is hypothesized that complex diseases are due to a myriad of factors including environmental exposures and complex genetic risk models, including gene-gene interactions. Such epistatic models present an important analytical challenge, requiring that methods perform not only statistical modeling, but also variable selection to generate testable genetic model hypotheses. This challenge is amplified by recent advances in genotyping technology, as the number of potential predictor variables is rapidly increasing.</p> <p>Methods</p> <p>Decision trees are a highly successful, easily interpretable data-mining method that are typically optimized with a hierarchical model building approach, which limits their potential to identify interacting effects. To overcome this limitation, we utilize evolutionary computation, specifically grammatical evolution, to build decision trees to detect and model gene-gene interactions. In the current study, we introduce the Grammatical Evolution Decision Trees (GEDT) method and software and evaluate this approach on simulated data representing gene-gene interaction models of a range of effect sizes. We compare the performance of the method to a traditional decision tree algorithm and a random search approach and demonstrate the improved performance of the method to detect purely epistatic interactions.</p> <p>Results</p> <p>The results of our simulations demonstrate that GEDT has high power to detect even very moderate genetic risk models. GEDT has high power to detect interactions with and without main effects.</p> <p>Conclusions</p> <p>GEDT, while still in its initial stages of development, is a promising new approach for identifying gene-gene interactions in genetic association studies.</p