Support vector machine and parametric wavelet-based texture classification of stem cell images

Thesis (S.M.)--Massachusetts Institute of Technology, Sloan School of Management, Operations Research Center, 2004.Includes bibliographical references (p. 117-121).This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Stem (cell research is one of the most promising and cutting-edge fields i the miedical sciences. It is believed that this innovative research will lead to life-saving treatments in the coming years. As part of their work, stem cell researchers must first determine which of their stem cell colonies are of sufficiently high quality to be suitable for experimental studies and therapeutic treatments. Since colony texture is a major discriminating feature in determining quality. we introduce a non-invasive, semi-automated texture-based stem cell colony classification methodology to aid researchers in colony quality control. We first consider the general problem of textural image segmentation. In a new approach to this problem. we characterize image texture by the subband energies of the image's wavelet decomposition, and we employ a non-parametric support vector machine to perform the classification that yields the segmentation. We also adapt a parametric wavelet-based classifier that utilizes the Kullback-Leibler distance. We apply both methods to a set of benchmark textural images, report low segmentation error rates and comment on the applicability of and tradeoffs between the non-parametric and parametric segmentation methods.(cont.) We then apply the two classifiers to the segmentation of stem cell colony images into regions of varying quality. This provides stem cell researchers with a rich set of descriptive graphical representations of their colonies to aid in quality control. From these graphical representatiolns, we extract colony-wise textural features to which we add colony-wise border features. Taken together, these features characterize overall colony quality. Using these features as inputs to a multiclass support vector machine, we successfully categorize full stem cell colonies into several quality categories. This methodology provides stem cell researchers with a novel, non-invasive quantitative quality control tool.by Christopher G. Jeffreys.S.M

Boosted Feature Generation for Classification Problems Involving High Numbers of Inputs and Classes

Classification problems involving high numbers of inputs and classes play an important role in the field of machine learning. Image classification, in particular, is a very active field of research with numerous applications. In addition to their high number, inputs of image classification problems often show significant correlation. Also, in proportion to the number of inputs, the number of available training samples is usually low. Therefore techniques combining low susceptibility to overfitting with good classification performance have to be found. Since for many tasks data has to be processed in real time, computational efficiency is crucial as well. Boosting is a machine learning technique, which is used successfully in a number of application areas, in particular in the field of machine vision. Due to it's modular design and flexibility, Boosting can be adapted to new problems easily. In addition, techniques for optimizing classifiers produced by Boosting with respect to computational efficiency exist. Boosting builds linear ensembles of base classifiers in a stage-wise fashion. Sample-weights reflect whether training samples are hard-to-classify or not. Therefore Boosting is able to adapt to the given classification problem over the course of training. The present work deals with the design of techniques for adapting Boosting to problems involving high numbers of inputs and classes. In the first part, application of Boosting to multi-class problems is analyzed. After giving an overview of existing approaches, a new formulation for base-classifiers solving multi-class problems by splitting them into pair-wise binary subproblems is presented. Experimental evaluation shows the good performance and computational efficiency of the proposed technique compared to state-of-the-art techniques. In the second part of the work, techniques that use Boosting for feature generation are presented. These techniques use the distribution of sample weights, produced by Boosting, to learn features that are adapted to the problems solved in each Boosting stage. By using smoothing-spline base classifiers, gradient descent schemes can be incorporated to find features that minimize the cost function of the current base classifier. Experimental evaluation shows, that Boosting with linear projective features significantly outperforms state-of-the-art approaches like e.g. SVM and Random Forests. In order to be applicable to image classification problems, the presented feature generation scheme is extended to produce shift-invariant features. The utilized features are inspired by the features used in Convolutional Neural Networks and perform a combination of convolution and subsampling. Experimental evaluation for classification of handwritten digits and car side-views shows that the proposed system is competitive to the best published results. The presented scheme has the advantages of being very simple and involving a low number of design parameters only

Relational clustering models for knowledge discovery and recommender systems

Cluster analysis is a fundamental research field in Knowledge Discovery and Data Mining (KDD). It aims at partitioning a given dataset into some homogeneous clusters so as to reflect the natural hidden data structure. Various heuristic or statistical approaches have been developed for analyzing propositional datasets. Nevertheless, in relational clustering the existence of multi-type relationships will greatly degrade the performance of traditional clustering algorithms. This issue motivates us to find more effective algorithms to conduct the cluster analysis upon relational datasets. In this thesis we comprehensively study the idea of Representative Objects for approximating data distribution and then design a multi-phase clustering framework for analyzing relational datasets with high effectiveness and efficiency. The second task considered in this thesis is to provide some better data models for people as well as machines to browse and navigate a dataset. The hierarchical taxonomy is widely used for this purpose. Compared with manually created taxonomies, automatically derived ones are more appealing because of their low creation/maintenance cost and high scalability. Up to now, the taxonomy generation techniques are mainly used to organize document corpus. We investigate the possibility of utilizing them upon relational datasets and then propose some algorithmic improvements. Another non-trivial problem is how to assign suitable labels for the taxonomic nodes so as to credibly summarize the content of each node. Unfortunately, this field has not been investigated sufficiently to the best of our knowledge, and so we attempt to fill the gap by proposing some novel approaches. The final goal of our cluster analysis and taxonomy generation techniques is to improve the scalability of recommender systems that are developed to tackle the problem of information overload. Recent research in recommender systems integrates the exploitation of domain knowledge to improve the recommendation quality, which however reduces the scalability of the whole system at the same time. We address this issue by applying the automatically derived taxonomy to preserve the pair-wise similarities between items, and then modeling the user visits by another hierarchical structure. Experimental results show that the computational complexity of the recommendation procedure can be greatly reduced and thus the system scalability be improved

Applications of Artificial Intelligence to Cryptography

This paper considers some recent advances in the field of Cryptography using Artificial Intelligence (AI). It specifically considers the applications of Machine Learning (ML) and Evolutionary Computing (EC) to analyze and encrypt data. A short overview is given on Artificial Neural Networks (ANNs) and the principles of Deep Learning using Deep ANNs. In this context, the paper considers: (i) the implementation of EC and ANNs for generating unique and unclonable ciphers; (ii) ML strategies for detecting the genuine randomness (or otherwise) of finite binary strings for applications in Cryptanalysis. The aim of the paper is to provide an overview on how AI can be applied for encrypting data and undertaking cryptanalysis of such data and other data types in order to assess the cryptographic strength of an encryption algorithm, e.g. to detect patterns of intercepted data streams that are signatures of encrypted data. This includes some of the authors’ prior contributions to the field which is referenced throughout. Applications are presented which include the authentication of high-value documents such as bank notes with a smartphone. This involves using the antenna of a smartphone to read (in the near field) a flexible radio frequency tag that couples to an integrated circuit with a non-programmable coprocessor. The coprocessor retains ultra-strong encrypted information generated using EC that can be decrypted on-line, thereby validating the authenticity of the document through the Internet of Things with a smartphone. The application of optical authentication methods using a smartphone and optical ciphers is also briefly explored

Parallelizing support vector machines for scalable image annotation

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Machine learning techniques have facilitated image retrieval by automatically classifying and annotating images with keywords. Among them Support Vector Machines (SVMs) are used extensively due to their generalization properties. However, SVM training is notably a computationally intensive process especially when the training dataset is large. In this thesis distributed computing paradigms have been investigated to speed up SVM training, by partitioning a large training dataset into small data chunks and process each chunk in parallel utilizing the resources of a cluster of computers. A resource aware parallel SVM algorithm is introduced for large scale image annotation in parallel using a cluster of computers. A genetic algorithm based load balancing scheme is designed to optimize the performance of the algorithm in heterogeneous computing environments. SVM was initially designed for binary classifications. However, most classification problems arising in domains such as image annotation usually involve more than two classes. A resource aware parallel multiclass SVM algorithm for large scale image annotation in parallel using a cluster of computers is introduced. The combination of classifiers leads to substantial reduction of classification error in a wide range of applications. Among them SVM ensembles with bagging is shown to outperform a single SVM in terms of classification accuracy. However, SVM ensembles training are notably a computationally intensive process especially when the number replicated samples based on bootstrapping is large. A distributed SVM ensemble algorithm for image annotation is introduced which re-samples the training data based on bootstrapping and training SVM on each sample in parallel using a cluster of computers. The above algorithms are evaluated in both experimental and simulation environments showing that the distributed SVM algorithm, distributed multiclass SVM algorithm, and distributed SVM ensemble algorithm, reduces the training time significantly while maintaining a high level of accuracy in classifications

Timely Classification of Encrypted or ProtocolObfuscated Internet Traffic Using Statistical Methods

Internet traffic classification aims to identify the type of application or protocol that generated a particular packet or stream of packets on the network. Through traffic classification, Internet Service Providers (ISPs), governments, and network administrators can access basic functions and several solutions, including network management, advanced network monitoring, network auditing, and anomaly detection. Traffic classification is essential as it ensures the Quality of Service (QoS) of the network, as well as allowing efficient resource planning. With the increase of encrypted or obfuscated protocol traffic on the Internet and multilayer data encapsulation, some classical classification methods have lost interest from the scientific community. The limitations of traditional classification methods based on port numbers and payload inspection to classify encrypted or obfuscated Internet traffic have led to significant research efforts focused on Machine Learning (ML) based classification approaches using statistical features from the transport layer. In an attempt to increase classification performance, Machine Learning strategies have gained interest from the scientific community and have shown promise in the future of traffic classification, specially to recognize encrypted traffic. However, ML approach also has its own limitations, as some of these methods have a high computational resource consumption, which limits their application when classifying large traffic or realtime flows. Limitations of ML application have led to the investigation of alternative approaches, including featurebased procedures and statistical methods. In this sense, statistical analysis methods, such as distances and divergences, have been used to classify traffic in large flows and in realtime. The main objective of statistical distance is to differentiate flows and find a pattern in traffic characteristics through statistical properties, which enable classification. Divergences are functional expressions often related to information theory, which measure the degree of discrepancy between any two distributions. This thesis focuses on proposing a new methodological approach to classify encrypted or obfuscated Internet traffic based on statistical methods that enable the evaluation of network traffic classification performance, including the use of computational resources in terms of CPU and memory. A set of traffic classifiers based on KullbackLeibler and JensenShannon divergences, and Euclidean, Hellinger, Bhattacharyya, and Wootters distances were proposed. The following are the four main contributions to the advancement of scientific knowledge reported in this thesis. First, an extensive literature review on the classification of encrypted and obfuscated Internet traffic was conducted. The results suggest that portbased and payloadbased methods are becoming obsolete due to the increasing use of traffic encryption and multilayer data encapsulation. MLbased methods are also becoming limited due to their computational complexity. As an alternative, Support Vector Machine (SVM), which is also an ML method, and the KolmogorovSmirnov and Chisquared tests can be used as reference for statistical classification. In parallel, the possibility of using statistical methods for Internet traffic classification has emerged in the literature, with the potential of good results in classification without the need of large computational resources. The potential statistical methods are Euclidean Distance, Hellinger Distance, Bhattacharyya Distance, Wootters Distance, as well as KullbackLeibler (KL) and JensenShannon divergences. Second, we present a proposal and implementation of a classifier based on SVM for P2P multimedia traffic, comparing the results with KolmogorovSmirnov (KS) and Chisquare tests. The results suggest that SVM classification with Linear kernel leads to a better classification performance than KS and Chisquare tests, depending on the value assigned to the Self C parameter. The SVM method with Linear kernel and suitable values for the Self C parameter may be a good choice to identify encrypted P2P multimedia traffic on the Internet. Third, we present a proposal and implementation of two classifiers based on KL Divergence and Euclidean Distance, which are compared to SVM with Linear kernel, configured with the standard Self C parameter, showing a reduced ability to classify flows based solely on packet sizes compared to KL and Euclidean Distance methods. KL and Euclidean methods were able to classify all tested applications, particularly streaming and P2P, where for almost all cases they efficiently identified them with high accuracy, with reduced consumption of computational resources. Based on the obtained results, it can be concluded that KL and Euclidean Distance methods are an alternative to SVM, as these statistical approaches can operate in realtime and do not require retraining every time a new type of traffic emerges. Fourth, we present a proposal and implementation of a set of classifiers for encrypted Internet traffic, based on JensenShannon Divergence and Hellinger, Bhattacharyya, and Wootters Distances, with their respective results compared to those obtained with methods based on Euclidean Distance, KL, KS, and ChiSquare. Additionally, we present a comparative qualitative analysis of the tested methods based on Kappa values and Receiver Operating Characteristic (ROC) curves. The results suggest average accuracy values above 90% for all statistical methods, classified as ”almost perfect reliability” in terms of Kappa values, with the exception of KS. This result indicates that these methods are viable options to classify encrypted Internet traffic, especially Hellinger Distance, which showed the best Kappa values compared to other classifiers. We conclude that the considered statistical methods can be accurate and costeffective in terms of computational resource consumption to classify network traffic. Our approach was based on the classification of Internet network traffic, focusing on statistical distances and divergences. We have shown that it is possible to classify and obtain good results with statistical methods, balancing classification performance and the use of computational resources in terms of CPU and memory. The validation of the proposal supports the argument of this thesis, which proposes the implementation of statistical methods as a viable alternative to Internet traffic classification compared to methods based on port numbers, payload inspection, and ML.A classificação de tráfego Internet visa identificar o tipo de aplicação ou protocolo que gerou um determinado pacote ou fluxo de pacotes na rede. Através da classificação de tráfego, Fornecedores de Serviços de Internet (ISP), governos e administradores de rede podem ter acesso às funções básicas e várias soluções, incluindo gestão da rede, monitoramento avançado de rede, auditoria de rede e deteção de anomalias. Classificar o tráfego é essencial, pois assegura a Qualidade de Serviço (QoS) da rede, além de permitir planear com eficiência o uso de recursos. Com o aumento de tráfego cifrado ou protocolo ofuscado na Internet e do encapsulamento de dados multicamadas, alguns métodos clássicos da classificação perderam interesse de investigação da comunidade científica. As limitações dos métodos tradicionais da classificação com base no número da porta e na inspeção de carga útil payload para classificar o tráfego de Internet cifrado ou ofuscado levaram a esforços significativos de investigação com foco em abordagens da classificação baseadas em técnicas de Aprendizagem Automática (ML) usando recursos estatísticos da camada de transporte. Na tentativa de aumentar o desempenho da classificação, as estratégias de Aprendizagem Automática ganharam o interesse da comunidade científica e se mostraram promissoras no futuro da classificação de tráfego, principalmente no reconhecimento de tráfego cifrado. No entanto, a abordagem em ML também têm as suas próprias limitações, pois alguns desses métodos possuem um elevado consumo de recursos computacionais, o que limita a sua aplicação para classificação de grandes fluxos de tráfego ou em tempo real. As limitações no âmbito da aplicação de ML levaram à investigação de abordagens alternativas, incluindo procedimentos baseados em características e métodos estatísticos. Neste sentido, os métodos de análise estatística, tais como distâncias e divergências, têm sido utilizados para classificar tráfego em grandes fluxos e em tempo real. A distância estatística possui como objetivo principal diferenciar os fluxos e permite encontrar um padrão nas características de tráfego através de propriedades estatísticas, que possibilitam a classificação. As divergências são expressões funcionais frequentemente relacionadas com a teoria da informação, que mede o grau de discrepância entre duas distribuições quaisquer. Esta tese focase na proposta de uma nova abordagem metodológica para classificação de tráfego cifrado ou ofuscado da Internet com base em métodos estatísticos que possibilite avaliar o desempenho da classificação de tráfego de rede, incluindo a utilização de recursos computacionais, em termos de CPU e memória. Foi proposto um conjunto de classificadores de tráfego baseados nas Divergências de KullbackLeibler e JensenShannon e Distâncias Euclidiana, Hellinger, Bhattacharyya e Wootters. A seguir resumemse os tese. Primeiro, realizámos uma ampla revisão de literatura sobre classificação de tráfego cifrado e ofuscado de Internet. Os resultados sugerem que os métodos baseados em porta e baseados em carga útil estão se tornando obsoletos em função do crescimento da utilização de cifragem de tráfego e encapsulamento de dados multicamada. O tipo de métodos baseados em ML também está se tornando limitado em função da complexidade computacional. Como alternativa, podese utilizar a Máquina de Vetor de Suporte (SVM), que também é um método de ML, e os testes de KolmogorovSmirnov e Quiquadrado como referência de comparação da classificação estatística. Em paralelo, surgiu na literatura a possibilidade de utilização de métodos estatísticos para classificação de tráfego de Internet, com potencial de bons resultados na classificação sem aporte de grandes recursos computacionais. Os métodos estatísticos potenciais são as Distâncias Euclidiana, Hellinger, Bhattacharyya e Wootters, além das Divergências de Kullback–Leibler (KL) e JensenShannon. Segundo, apresentamos uma proposta e implementação de um classificador baseado na Máquina de Vetor de Suporte (SVM) para o tráfego multimédia P2P (PeertoPeer), comparando os resultados com os testes de KolmogorovSmirnov (KS) e Quiquadrado. Os resultados sugerem que a classificação da SVM com kernel Linear conduz a um melhor desempenho da classificação do que os testes KS e Quiquadrado, dependente do valor atribuído ao parâmetro Self C. O método SVM com kernel Linear e com valores adequados para o parâmetro Self C pode ser uma boa escolha para identificar o tráfego Par a Par (P2P) multimédia cifrado na Internet. Terceiro, apresentamos uma proposta e implementação de dois classificadores baseados na Divergência de KullbackLeibler (KL) e na Distância Euclidiana, sendo comparados com a SVM com kernel Linear, configurado para o parâmestro Self C padrão, apresenta reduzida capacidade de classificar fluxos com base apenas nos tamanhos dos pacotes em relação aos métodos KL e Distância Euclidiana. Os métodos KL e Euclidiano foram capazes de classificar todas as aplicações testadas, destacandose streaming e P2P, onde para quase todos os casos foi eficiente identificálas com alta precisão, com reduzido consumo de recursos computacionais.Com base nos resultados obtidos, podese concluir que os métodos KL e Distância Euclidiana são uma alternativa à SVM, porque essas abordagens estatísticas podem operar em tempo real e não precisam de retreinamento cada vez que surge um novo tipo de tráfego. Quarto, apresentamos uma proposta e implementação de um conjunto de classificadores para o tráfego de Internet cifrado, baseados na Divergência de JensenShannon e nas Distâncias de Hellinger, Bhattacharyya e Wootters, sendo os respetivos resultados comparados com os resultados obtidos com os métodos baseados na Distância Euclidiana, KL, KS e Quiquadrado. Além disso, apresentamos uma análise qualitativa comparativa dos métodos testados com base nos valores de Kappa e Curvas Característica de Operação do Receptor (ROC). Os resultados sugerem valores médios de precisão acima de 90% para todos os métodos estatísticos, classificados como “confiabilidade quase perfeita” em valores de Kappa, com exceçãode KS. Esse resultado indica que esses métodos são opções viáveis para a classificação de tráfego cifrado da Internet, em especial a Distância de Hellinger, que apresentou os melhores resultados do valor de Kappa em comparaçãocom os demais classificadores. Concluise que os métodos estatísticos considerados podem ser precisos e económicos em termos de consumo de recursos computacionais para classificar o tráfego da rede. A nossa abordagem baseouse na classificação de tráfego de rede Internet, focando em distâncias e divergências estatísticas. Nós mostramos que é possível classificar e obter bons resultados com métodos estatísticos, equilibrando desempenho de classificação e uso de recursos computacionais em termos de CPU e memória. A validação da proposta sustenta o argumento desta tese, que propõe a implementação de métodos estatísticos como alternativa viável à classificação de tráfego da Internet em relação aos métodos com base no número da porta, na inspeção de carga útil e de ML.Thesis prepared at Instituto de Telecomunicações Delegação da Covilhã and at the Department of Computer Science of the University of Beira Interior, and submitted to the University of Beira Interior for discussion in public session to obtain the Ph.D. Degree in Computer Science and Engineering. This work has been funded by Portuguese FCT/MCTES through national funds and, when applicable, cofunded by EU funds under the project UIDB/50008/2020, and by operation Centro010145FEDER000019 C4 Centro de Competências em Cloud Computing, cofunded by the European Regional Development Fund (ERDF/FEDER) through the Programa Operacional Regional do Centro (Centro 2020). This work has also been funded by CAPES (Brazilian Federal Agency for Support and Evaluation of Graduate Education) within the Ministry of Education of Brazil under a scholarship supported by the International Cooperation Program CAPES/COFECUB Project 9090134/ 2013 at the University of Beira Interior