Stacked Generalization (SG) is an ensemble learning technique, which aims to increase the performance of individual classifiers by combining them under a hierarchical architecture. This study consists of two major parts. In the first part, the performance of Stacked Generalization technique is analyzed with respect to the performance of the individual classifiers and the content of the training data. In the second part, based on the findings for a new class of algorithms, called Meta-Fuzzified Yield Value (Meta-FYV) is introduced. The first part introduces and verifies two hypotheses by a set of controlled experiments to assure the performance gain for SG. The learning mechanisms of SG to achieve high performance are explored and the relationship between the performance of the individual classifiers and that of SG is investigated. It is shown that if the samples in the training set are correctly classified by at least one base layer classifier, then, the generalization performance of the SG is increased, compared to the performance of the individual classifiers. In the second hypothesis, the effect of the spurious samples, which are not correctly labeled by any of the base layer classifiers, is investigated. In the second part of the thesis, six theorems are constructed based on the analysis of the feature spaces and the stacked generalization architecture. Based on the theorems and hypothesis, a new class of SG algorithms is proposed. The experiments are performed on both Corel data and synthetically generated data, using parallel programming techniques, on a high performance cluster.

Ensemble learning is a promising direction of research in machine learning, in which an ensemble classifier gives better predictive and more robust performance for classification problems by combining other learners. Meanwhile agent-based systems provide frameworks to share knowledge from multiple agents in an open context. This thesis combines multi-agent knowledge sharing with ensemble methods to produce a new style of learning system for open environments. We now are surrounded by many smart objects such as wireless sensors, ambient communication devices, mobile medical devices and even information supplied via other humans. When we coordinate smart objects properly, we can produce a form of collective intelligence from their collaboration. Traditional ensemble methods and agent-based systems have complementary advantages and disadvantages in this context. Traditional ensemble methods show better classification performance, while agent-based systems might not guarantee their performance for classification. Traditional ensemble methods work as closed and centralised systems (so they cannot handle classifiers in an open context), while agent-based systems are natural vehicles for classifiers in an open context. We designed an open and social ensemble learning architecture, named J-model, to merge the conflicting benefits of the two research domains. The J-model architecture is based on a service choreography approach for coordinating classifiers. Coordination protocols are defined by interaction models that describe how classifiers will interact with one another in a peer-to-peer manner. The peer ranking algorithm recommends more appropriate classifiers to participate in an interaction model to boost the success rate of results of their interactions. Coordinated participant classifiers who are recommended by the peer ranking algorithm become an ensemble classifier within J-model. We evaluated J-model’s classification performance with 13 UCI machine learning benchmark data sets and a virtual screening problem as a realistic classification problem. J-model showed better performance of accuracy, for 9 benchmark sets out of 13 data sets, than 8 other representative traditional ensemble methods. J-model gave better results of specificity for 7 benchmark sets. In the virtual screening problem, J-model gave better results for 12 out of 16 bioassays than already published results. We defined different interaction models for each specific classification task and the peer ranking algorithm was used across all the interaction models. Our research contributions to knowledge are as follows. First, we showed that service choreography can be an effective ensemble coordination method for classifiers in an open context. Second, we used interaction models that implement task specific coordinations of classifiers to solve a variety of representative classification problems. Third, we designed the peer ranking algorithm which is generally and independently applicable to the task of recommending appropriate member classifiers from a classifier pool based on an open pool of interaction models and classifiers.

We propose a new ensemble algorithm: the meta-boosting algorithm. This algorithm enables the original Adaboost algorithm to improve the decisions made by different WeakLearners utilizing the meta-learning approach. Better accuracy results are achieved since this algorithm reduces both bias and variance. However, higher accuracy also brings higher computational complexity, especially on big data. We then propose the parallelized meta-boosting algorithm: Parallelized-Meta-Learning (PML) using the MapReduce programming paradigm on Hadoop. The experimental results on the Amazon EC2 cloud computing infrastructure show that PML reduces the computation complexity enormously while retaining lower error rates than the results on a single computer. As we know MapReduce has its inherent weakness that it cannot directly support iterations in an algorithm, our approach is a win-win method, since it not only overcomes this weakness, but also secures good accuracy performance. The comparison between this approach and a contemporary algorithm AdaBoost.PL is also performed.

abstract: Ensemble learning methods like bagging, boosting, adaptive boosting, stacking have traditionally shown promising results in improving the predictive accuracy in classification. These techniques have recently been widely used in various domains and applications owing to the improvements in computational efficiency and distributed computing advances. However, with the advent of wide variety of applications of machine learning techniques to class imbalance problems, further focus is needed to evaluate, improve and optimize other performance measures such as sensitivity (true positive rate) and specificity (true negative rate) in classification. This thesis demonstrates a novel approach to evaluate and optimize the performance measures (specifically sensitivity and specificity) using ensemble learning methods for classification that can be especially useful in class imbalanced datasets. In this thesis, ensemble learning methods (specifically bagging and boosting) are used to optimize the performance measures (sensitivity and specificity) on a UC Irvine (UCI) 130 hospital diabetes dataset to predict if a patient will be readmitted to the hospital based on various feature vectors. From the experiments conducted, it can be empirically concluded that, by using ensemble learning methods, although accuracy does improve to some margin, both sensitivity and specificity are optimized significantly and consistently over different cross validation approaches. The implementation and evaluation has been done on a subset of the large UCI 130 hospital diabetes dataset. The performance measures of ensemble learners are compared to the base machine learning classification algorithms such as Naive Bayes, Logistic Regression, k Nearest Neighbor, Decision Trees and Support Vector Machines. / Dissertation/Thesis / Masters Thesis Computer Science 2017

Missense mutations account for more than 50% of the mutations known to be involved in human inherited diseases. Missense classification is a challenging task that involves sequencing of the genome, identifying the variations, and assessing their deleteriousness. This is a very laborious, time and cost intensive task to be carried out in the laboratory. Advancements in bioinformatics have led to several large-scale next-generation genome sequencing projects, and subsequently the identification of genome variations. Several studies have combined this data with information on established deleterious and neutral variants to develop machine learning based classifiers. There are significant issues with the missense classifiers due to which missense classification is still an open area of research. These issues can be classified under two broad categories: (a) Dataset overlap issue - where the performance estimates reported by the state-of-the-art classifiers are overly optimistic as they have often been evaluated on datasets that have significant overlaps with their training datasets. Also, there is no comparative analysis of these tools using a common benchmark dataset that contains no overlap with the training datasets, therefore making it impossible to identify the best classifier among them. Also, such a common benchmark dataset is not available. (b) Inadequate capture of vital biological information of the protein and mutations - such as conservation of long-range amino acid dependencies, changes in certain physico-chemical properties of the wild-type and mutant amino acids, due to the mutation. It is also not clear how to extract and use this information. Also, some classifiers use structural information that is not available for all proteins. In this study, we compiled a new dataset, containing around 2 - 15% overlap with the popularly used training datasets, with 18,036 mutations in 5,642 proteins. We reviewed and evaluated 15 state-of-the-art missense classifiers - SIFT, PANTHER, PROVEAN, PhD-SNP, Mutation Assessor, FATHMM, SNPs&GO, SNPs&GO3D, nsSNPAnalyzer, PolyPhen-2, SNAP, MutPred, PON-P2, CONDEL and MetaSNP, using the six metrics - accuracy, sensitivity, specificity, precision, NPV and MCC. When evaluated on our dataset, we observe huge performance drops from what has been claimed. Average drop in the performance for these 13 classifiers are around 15% in accuracy, 17% in sensitivity, 14% in specificity, 7% in NPV, 24% in precision and 30% in MCC. With this we show that the performance of these tools is not consistent on different datasets, and thus not reliable for practical use in a clinical setting. As we observed that the performance of the existing classifiers is poor in general, we tried to develop a new classifier that is robust and performs consistently across datasets, and better than the state-of-the-art classifiers. We developed a novel method of capturing long-range amino acid dependency conservation by boosting the conservation frequencies of substrings of amino acids of various lengths around the mutation position using AdaBoost learning algorithm. This score alone performed equivalently to the sequence conservation based tools in classifying missense mutations. Popularly used sequence conservation properties was combined with this boosted long-range dependency conservation scores using AdaBoost algorithm. This reduced the class bias, and improved the overall accuracy of the classifier. We trained a third classifier by incorporating changes in 21 important physico-chemical properties, due to the mutation. In this case, we observed that the overall performance further improved and the class bias further reduced. The performance of our final classifier is comparable with the state-of-the-art classifiers. We did not find any significant improvement, but the class-specific accuracies and precisions are marginally better by around 1-2% than those of the existing classifiers. In order to understand our classifier better, we dissected our benchmark dataset into: (a) seen and unseen proteins, and (b) pure and mixed proteins, and analysed the performance in detail. Finally we concluded that our classifier performs consistently across each of these categories of seen, unseen, pure and mixed protein.

abstract: This dissertation investigates the classification of systemic lupus erythematosus (SLE) in the presence of non-SLE alternatives, while developing novel curve classification methodologies with wide ranging applications. Functional data representations of plasma thermogram measurements and the corresponding derivative curves provide predictors yet to be investigated for SLE identification. Functional nonparametric classifiers form a methodological basis, which is used herein to develop a) the family of ESFuNC segment-wise curve classification algorithms and b) per-pixel ensembles based on logistic regression and fused-LASSO. The proposed methods achieve test set accuracy rates as high as 94.3%, while returning information about regions of the temperature domain that are critical for population discrimination. The undertaken analyses suggest that derivate-based information contributes significantly in improved classification performance relative to recently published studies on SLE plasma thermograms. / Dissertation/Thesis / Doctoral Dissertation Applied Mathematics 2018

Text classification for companies is becoming more important in a world where an increasing amount of digital data are made available. The aim is to research whether five different machine learning algorithms can be used to automate the process of classification of invoice data and see which one gets the highest accuracy. Algorithms are in a later stage combined for an attempt to achieve higher results. N-grams are used, and results are compared in form of total accuracy of classification for each algorithm. A library in Python, called scikit-learn, implementing the chosen algorithms, was used. Data is collected and generated to represent data present on a real invoice where data has been extracted. Results from this thesis show that it is possible to use machine learning for this type of problem. The highest scoring algorithm (LinearSVC from scikit-learn) classifies 86% of all samples correctly. This is a margin of 16% above the acceptable level of 70%.

Concept drift refers to a problem that is caused by a change in the data distribution in data mining. This leads to reduction in the accuracy of the current model that is used to examine the underlying data distribution of the concept to be discovered. A number of techniques have been introduced to address this issue, in a supervised learning (or classification) setting. In a classification setting, the target concept (or class) to be learned is known. One of these techniques is called “Ensemble learning”, which refers to using multiple trained classifiers in order to get better predictions by using some voting scheme. In a traditional ensemble, the underlying base classifiers are all of the same type. Recent research extends the idea of ensemble learning to the idea of using committees, where a committee consists of diverse classifiers. This is the main difference between the regular ensemble classifiers and the committee learning algorithms. Committees are able to use diverse learning methods simultaneously and dynamically take advantage of the most accurate classifiers as the data change. In addition, some committees are able to replace their members when they perform poorly. This thesis presents two new algorithms that address concept drifts. The first algorithm has been designed to systematically introduce gradual and sudden concept drift scenarios into datasets. In order to save time and avoid memory consumption, the Concept Drift Introducer (CDI) algorithm divides the number of drift scenarios into phases. The main advantage of using phases is that it allows us to produce a highly scalable concept drift detector that evaluates each phase, instead of evaluating each individual drift scenario. We further designed a novel algorithm to handle concept drift. Our Dynamic Committee for Concept Drift (DCCD) algorithm uses a voted committee of hypotheses that vote on the best base classifier, based on its predictive accuracy. The novelty of DCCD lies in the fact that we employ diverse heterogeneous classifiers in one committee in an attempt to maximize diversity. DCCD detects concept drifts by using the accuracy and by weighing the committee members by adding one point to the most accurate member. The total loss in accuracy for each member is calculated at the end of each point of measurement, or phase. The performance of the committee members are evaluated to decide whether a member needs to be replaced or not. Moreover, DCCD detects the worst member in the committee and then eliminates this member by using a weighting mechanism. Our experimental evaluation centers on evaluating the performance of DCCD on various datasets of different sizes, with different levels of gradual and sudden concept drift. We further compare our algorithm to another state-of-the-art algorithm, namely the MultiScheme approach. The experiments indicate the effectiveness of our DCCD method under a number of diverse circumstances. The DCCD algorithm generally generates high performance results, especially when the number of concept drifts is large in a dataset. For the size of the datasets used, our results showed that DCCD produced a steady improvement in performance when applied to small datasets. Further, in large and medium datasets, our DCCD method has a comparable, and often slightly higher, performance than the MultiScheme technique. The experimental results also show that the DCCD algorithm limits the loss in accuracy over time, regardless of the size of the dataset.

We propose a new ensemble algorithm: the meta-boosting algorithm. This algorithm enables the original Adaboost algorithm to improve the decisions made by different WeakLearners utilizing the meta-learning approach. Better accuracy results are achieved since this algorithm reduces both bias and variance. However, higher accuracy also brings higher computational complexity, especially on big data. We then propose the parallelized meta-boosting algorithm: Parallelized-Meta-Learning (PML) using the MapReduce programming paradigm on Hadoop. The experimental results on the Amazon EC2 cloud computing infrastructure show that PML reduces the computation complexity enormously while retaining lower error rates than the results on a single computer. As we know MapReduce has its inherent weakness that it cannot directly support iterations in an algorithm, our approach is a win-win method, since it not only overcomes this weakness, but also secures good accuracy performance. The comparison between this approach and a contemporary algorithm AdaBoost.PL is also performed.

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