Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data

<p>Abstract</p> <p>Background</p> <p>Clustering-based methods on gene-expression analysis have been shown to be useful in biomedical applications such as cancer subtype discovery. Among them, Matrix factorization (MF) is advantageous for clustering gene expression patterns from DNA microarray experiments, as it efficiently reduces the dimension of gene expression data. Although several MF methods have been proposed for clustering gene expression patterns, a systematic evaluation has not been reported yet.</p> <p>Results</p> <p>Here we evaluated the clustering performance of orthogonal and non-orthogonal MFs by a total of nine measurements for performance in four gene expression datasets and one well-known dataset for clustering. Specifically, we employed a non-orthogonal MF algorithm, BSNMF (Bi-directional Sparse Non-negative Matrix Factorization), that applies bi-directional sparseness constraints superimposed on non-negative constraints, comprising a few dominantly co-expressed genes and samples together. Non-orthogonal MFs tended to show better clustering-quality and prediction-accuracy indices than orthogonal MFs as well as a traditional method, K-means. Moreover, BSNMF showed improved performance in these measurements. Non-orthogonal MFs including BSNMF showed also good performance in the functional enrichment test using Gene Ontology terms and biological pathways.</p> <p>Conclusions</p> <p>In conclusion, the clustering performance of orthogonal and non-orthogonal MFs was appropriately evaluated for clustering microarray data by comprehensive measurements. This study showed that non-orthogonal MFs have better performance than orthogonal MFs and <it>K</it>-means for clustering microarray data.</p

A Comparative Study of Efficient Initialization Methods for the K-Means Clustering Algorithm

K-means is undoubtedly the most widely used partitional clustering algorithm. Unfortunately, due to its gradient descent nature, this algorithm is highly sensitive to the initial placement of the cluster centers. Numerous initialization methods have been proposed to address this problem. In this paper, we first present an overview of these methods with an emphasis on their computational efficiency. We then compare eight commonly used linear time complexity initialization methods on a large and diverse collection of data sets using various performance criteria. Finally, we analyze the experimental results using non-parametric statistical tests and provide recommendations for practitioners. We demonstrate that popular initialization methods often perform poorly and that there are in fact strong alternatives to these methods.Comment: 17 pages, 1 figure, 7 table

Meta-optimizations for Cluster Analysis

This dissertation thesis deals with advances in the automation of cluster analysis.This dissertation thesis deals with advances in the automation of cluster analysis

A Process for Extracting Knowledge in Design for the Developing World

The aim of this study was to develop the process necessary to identify design knowledge shared across product classes and contexts in Design for the Developing World. A process for extracting design knowledge in the field of Design for the Developing World was developed based on the Knowledge Discovery in Databases framework. This process was applied to extract knowledge from a sample dataset of 48 products and small-scale technologies. Unsupervised cluster analysis revealed two distinct product groups, cluster X-AA and cluster Z-AC-AD. Unique attributes of cluster XX-AA include local manufacture, local maintenance and service, human-power, distribution by a non-governmental organization, income-generation, and application in water/sanitation or agriculture sectors. The label Locally Oriented Design for the Developing World was assigned to this group based on the dominant features represented. Unique attributes of cluster Z-AC-AD include electric-power, distribution by a private organization, and application in the health or energy/communication sectors. The label Globally Oriented Design for the Developing World was assigned to this group. These findings were corroborated by additional analyses that suggest certain design knowledge is shared across classes and contexts within groups of products. The results suggest that at least two of these groups exist, which can serve as an initial framework for organizing the literature related to inter-context and inter-class design knowledge. Design knowledge was extracted from each group by collecting known approaches, principles, and methods from available literature. This knowledge may be applied as design guidance in future work by identifying a product group corresponding to the design scenario and sourcing the related set of knowledge

Behaviour modelling with data obtained from the Internet and contributions to cluster validation

[EN]This PhD thesis makes contributions in modelling behaviours found in different types of data acquired from the Internet and in the field of clustering evaluation. Two different types of Internet data were processed, on the one hand, internet traffic with the objective of attack detection and on the other hand, web surfing activity with the objective of web personalization, both data being of sequential nature. To this aim, machine learning techniques were applied, mostly unsupervised techniques. Moreover, contributions were made in cluster evaluation, in order to make easier the selection of the best partition in clustering problems. With regard to network attack detection, first, gureKDDCup database was generated which adds payload data to KDDCup99 connection attributes because it is essential to detect non-flood attacks. Then, by modelling this data a network Intrusion Detection System (nIDS) was proposed where context-independent payload processing was done obtaining satisfying detection rates. In the web mining context web surfing activity was modelled for web personalization. In this context, generic and non-invasive systems to extract knowledge were proposed just using the information stored in webserver log files. Contributions were done in two senses: in problem detection and in link suggestion. In the first application a meaningful list of navigation attributes was proposed for each user session to group and detect different navigation profiles. In the latter, a general and non-invasive link suggestion system was proposed which was evaluated with satisfactory results in a link prediction context. With regard to the analysis of Cluster Validity Indices (CVI), the most extensive CVI comparison found up to a moment was carried out using a partition similarity measure based evaluation methodology. Moreover, we analysed the behaviour of CVIs in a real web mining application with elevated number of clusters in which they tend to be unstable. We proposed a procedure which automatically selects the best partition analysing the slope of different CVI values.[EU]Doktorego-tesi honek internetetik eskuratutako datu mota ezberdinetan aurkitutako portaeren modelugintzan eta multzokatzeen ebaluazioan egiten ditu bere ekarpenak. Zehazki, bi mota ezberdinetako interneteko datuak prozesatu dira: batetik, interneteko trafikoa, erasoak hautemateko helburuarekin; eta bestetik, web nabigazioen jarduera, weba pertsonalizatzeko helburuarekin; bi datu motak izaera sekuentzialekoak direlarik. Helburu hauek lortzeko, ikasketa automatikoko teknikak aplikatu dira, nagusiki gainbegiratu-gabeko teknikak. Testuinguru honetan, multzokatzeen partizio onenaren aukeraketak dakartzan arazoak gutxitzeko multzokatzeen ebaluazioan ere ekarpenak egin dira. Sareko erasoen hautemateari dagokionez, lehenik gureKDDCup datubasea eratu da KDDCup99-ko konexio atributuei payload-ak (sareko paketeen datu eremuak) gehituz, izan ere, ez-flood erasoak (pakete gutxi erabiltzen dituzten erasoak) hautemateko ezinbestekoak baitira. Ondoren, datu hauek modelatuz testuinguruarekiko independenteak diren payload prozesaketak oinarri dituen sareko erasoak hautemateko sistema (network Intrusion Detection System (nIDS)) bat proposatu da maila oneko eraso hautemate-tasak lortuz. Web meatzaritzaren testuinguruan, weba pertsonalizatzeko helburuarekin web nabigazioen jarduera modelatu da. Honetarako, web zerbizarietako lorratz fitxategietan metatutako informazioa soilik erabiliz ezagutza erabilgarria erauziko duen sistema orokor eta ez-inbasiboak proposatu dira. Ekarpenak bi zentzutan eginaz: arazoen hautematean eta esteken iradokitzean. Lehen aplikazioan sesioen nabigazioa adierazteko atributu esanguratsuen zerrenda bat proposatu da, gero nabigazioak multzokatu eta nabigazio profil ezberdinak hautemateko. Bigarren aplikazioan, estekak iradokitzeko sistema orokor eta ez-inbasibo bat proposatu da, eta berau, estekak aurresateko testuinguruan ebaluatu da emaitza onak lortuz. Multzokatzeak balioztatzeko indizeen (Cluster Validity Indices (CVI)) azterketari dagokionez, gaurdaino aurkitu den CVI-en konparaketa zabalena burutu da partizioen antzekotasun neurrian oinarritutako ebaluazio metodologia erabiliz. Gainera, CVI-en portaera aztertu da egiazko web meatzaritza aplikazio batean normalean baino multzo kopuru handiagoak dituena, non CVI-ek ezegonkorrak izateko joera baitute. Arazo honi aurre eginaz, CVI ezberdinek partizio ezberdinetarako lortzen dituzten balioen maldak aztertuz automatikoki partiziorik onena hautatzen duen prozedura proposatu da.[ES]Esta tesis doctoral hace contribuciones en el modelado de comportamientos encontrados en diferentes tipos de datos adquiridos desde internet y en el campo de la evaluación del clustering. Dos tipos de datos de internet han sido procesados: en primer lugar el tráfico de internet con el objetivo de detectar ataques; y en segundo lugar la actividad generada por los usuarios web con el objetivo de personalizar la web; siendo los dos tipos de datos de naturaleza secuencial. Para este fin, se han aplicado técnicas de aprendizaje automático, principalmente técnicas no-supervisadas. Además, se han hecho aportaciones en la evaluación de particiones de clusters para facilitar la selección de la mejor partición de clusters. Respecto a la detección de ataques en la red, primero, se generó la base de datos gureKDDCup que añade el payload (la parte de contenido de los paquetes de la red) a los atributos de la conexión de KDDCup99 porque el payload es esencial para la detección de ataques no-flood (ataques que utilizan pocos paquetes). Después, se propuso un sistema de detección de intrusos (network Intrusion Detection System (IDS)) modelando los datos de gureKDDCup donde se propusieron varios preprocesos del payload independientes del contexto obteniendo resultados satisfactorios. En el contexto de la minerı́a web, se ha modelado la actividad de la navegación web para la personalización web. En este contexto se propondrán sistemas genéricos y no-invasivos para la extracción del conocimiento, utilizando únicamente la información almacenada en los ficheros log de los servidores web. Se han hecho aportaciones en dos sentidos: en la detección de problemas y en la sugerencia de links. En la primera aplicación, se propuso una lista de atributos significativos para representar las sesiones de navegación web para después agruparlos y detectar diferentes perfiles de navegación. En la segunda aplicación, se propuso un sistema general y no-invasivo para sugerir links y se evaluó en el contexto de predicción de links con resultados satisfactorios. Respecto al análisis de ı́ndices de validación de clusters (Cluster Validity Indices (CVI)), se ha realizado la más amplia comparación encontrada hasta el momento que utiliza la metodologı́a de evaluación basada en medidas de similitud de particiones. Además, se ha analizado el comportamiento de los CVIs en una aplicación real de minerı́a web con un número elevado de clusters, contexto en el que los CVIs tienden a ser inestables, ası́ que se propuso un procedimiento para la selección automática de la mejor partición en base a la pendiente de los valores de diferentes CVIs.Grant of the Basque Government (ref.: BFI08.226); Grant of Ministry of Economy and Competitiveness of the Spanish Government (ref.: BES-2011-045989); Research stay grant of Spanish Ministry of Economy and Competitiveness (ref.: EEBB-I-14-08862); University of the Basque Country UPV/EHU (BAILab, grant UFI11/45); Department of Education, Universities and Research of the Basque Government (grant IT-395-10); Ministry of Economy and Competitiveness of the Spanish Government and by the European Regional Development Fund - ERDF (eGovernAbility, grant TIN2014-52665-C2-1-R)

Redefining NBA Basketball Positions Through Visualization and Mega-Cluster Analysis

Basketball players have historically been classified based on one of five positions, namely Point Guards, Shooting Guards, Small Forwards, and Centers. While grouping players into these five categories may provide general descriptions of their perceived role, these standard positions fall short of describing players based on their true abilities and performance. This MS thesis proposes a method to group players of the National Basketball Association (NBA) from the past 20 seasons into more meaningful and specific player positions. We systematically group these players into nine distinct categories, and we draw from a vast array of visualization tools, techniques, and software to view and analyze these new player positions and compare them to the standard roles currently used by the basketball community. These visualization tools and methods allow us to view highly complex data with many variables in low-dimensional plots that are both meaningful and interpretable. Each season’s nine player positions are then grouped into nine overall positions across the 20-year span and their unique attributes and behaviors will be explored in depth. All of the player tables, the individual player position assignments, and many other relevant data tables are assembled and included on a single online repository for public access and use

Robust techniques and applications in fuzzy clustering

This dissertation addresses issues central to frizzy classification. The issue of sensitivity to noise and outliers of least squares minimization based clustering techniques, such as Fuzzy c-Means (FCM) and its variants is addressed. In this work, two novel and robust clustering schemes are presented and analyzed in detail. They approach the problem of robustness from different perspectives. The first scheme scales down the FCM memberships of data points based on the distance of the points from the cluster centers. Scaling done on outliers reduces their membership in true clusters. This scheme, known as the Mega-clustering, defines a conceptual mega-cluster which is a collective cluster of all data points but views outliers and good points differently (as opposed to the concept of Dave\u27s Noise cluster). The scheme is presented and validated with experiments and similarities with Noise Clustering (NC) are also presented. The other scheme is based on the feasible solution algorithm that implements the Least Trimmed Squares (LTS) estimator. The LTS estimator is known to be resistant to noise and has a high breakdown point. The feasible solution approach also guarantees convergence of the solution set to a global optima. Experiments show the practicability of the proposed schemes in terms of computational requirements and in the attractiveness of their simplistic frameworks. The issue of validation of clustering results has often received less attention than clustering itself. Fuzzy and non-fuzzy cluster validation schemes are reviewed and a novel methodology for cluster validity using a test for random position hypothesis is developed. The random position hypothesis is tested against an alternative clustered hypothesis on every cluster produced by the partitioning algorithm. The Hopkins statistic is used as a basis to accept or reject the random position hypothesis, which is also the null hypothesis in this case. The Hopkins statistic is known to be a fair estimator of randomness in a data set. The concept is borrowed from the clustering tendency domain and its applicability to validating clusters is shown here. A unique feature selection procedure for use with large molecular conformational datasets with high dimensionality is also developed. The intelligent feature extraction scheme not only helps in reducing dimensionality of the feature space but also helps in eliminating contentious issues such as the ones associated with labeling of symmetric atoms in the molecule. The feature vector is converted to a proximity matrix, and is used as an input to the relational fuzzy clustering (FRC) algorithm with very promising results. Results are also validated using several cluster validity measures from literature. Another application of fuzzy clustering considered here is image segmentation. Image analysis on extremely noisy images is carried out as a precursor to the development of an automated real time condition state monitoring system for underground pipelines. A two-stage FCM with intelligent feature selection is implemented as the segmentation procedure and results on a test image are presented. A conceptual framework for automated condition state assessment is also developed