Clustering in Conjunction with Wrapper Approach to Select Discriminatory Genes for Microarray Dataset Classification

With the advent of microarray technology, it is possible to measure gene expression levels of thousands of genes simultaneously. This helps us diagnose and classify some particular cancers directly using DNA microarray. High-dimensionality and small sample size of microarray datasets has made the task of classification difficult. These datasets contain a large number of redundant and irrelevant genes. For efficient classification of samples there is a need of selecting a smaller set of relevant and non-redundant genes. In this paper, we have proposed a two stage algorithm for finding a set of discriminatory genes responsible for classification of high dimensional microarray datasets. In the first stage redundancy is reduced by grouping correlated genes into clusters and selecting a representative gene from each cluster. Maximal information compression index is used to measure similarity between genes. In the second stage a wrapper based forward feature selection method is used to obtain a set of discriminatory genes for a given classifier. We have investigated three different techniques for clustering and four classifiers in our experiments. The proposed algorithm is tested on six well known publicly available datasets. Comparison with the other state-of-the-art methods show that our proposed algorithm is able to achieve better classification accuracy with less number of genes

Clustering and Community Detection in Directed Networks: A Survey

Networks (or graphs) appear as dominant structures in diverse domains, including sociology, biology, neuroscience and computer science. In most of the aforementioned cases graphs are directed - in the sense that there is directionality on the edges, making the semantics of the edges non symmetric. An interesting feature that real networks present is the clustering or community structure property, under which the graph topology is organized into modules commonly called communities or clusters. The essence here is that nodes of the same community are highly similar while on the contrary, nodes across communities present low similarity. Revealing the underlying community structure of directed complex networks has become a crucial and interdisciplinary topic with a plethora of applications. Therefore, naturally there is a recent wealth of research production in the area of mining directed graphs - with clustering being the primary method and tool for community detection and evaluation. The goal of this paper is to offer an in-depth review of the methods presented so far for clustering directed networks along with the relevant necessary methodological background and also related applications. The survey commences by offering a concise review of the fundamental concepts and methodological base on which graph clustering algorithms capitalize on. Then we present the relevant work along two orthogonal classifications. The first one is mostly concerned with the methodological principles of the clustering algorithms, while the second one approaches the methods from the viewpoint regarding the properties of a good cluster in a directed network. Further, we present methods and metrics for evaluating graph clustering results, demonstrate interesting application domains and provide promising future research directions.Comment: 86 pages, 17 figures. Physics Reports Journal (To Appear

ALIGNMENT-FREE METHODS AND ITS APPLICATIONS

Comparing biological sequences remains one of the most vital activities in Bioinformatics. Comparing biological sequences would address the relatedness between species, and find similar structures that might lead to similar functions. Sequence alignment is the default method, and has been used in the domain for over four decades. It gained a lot of trust, but limitations and even failure has been reported, especially with the new generated genomes. These new generated genomes have bigger size, and to some extent suffer errors. Such errors come mainly as a result from the sequencing machine. These sequencing errors should be considered when submitting sequences to GenBank, for sequence comparison, it is often hard to address or even trace this problem. Alignment-based methods would fail with such errors, and even if biologists still trust them, reports showed failure with these methods. The poor results of alignment-based methods with erratic sequences, motivated researchers in the domain to look for alternatives. These alternative methods are alignment-free, and would overcome the shortcomings of alignment-based methods. The work of this thesis is based on alignment-free methods, and it conducts an in-depth study to evaluate these methods, and find the right domain’s application for them. The right domain for alignment-free methods could be by applying them to data that were subjected to manufactured errors, and test the methods provide better comparison results with data that has naturally severe errors. The two techniques used in this work are compression-based and motif-based (or k-mer based, or signal based). We also addressed the selection of the used motifs in the second technique, and how to progress the results by selecting specific motifs that would enhance the quality of results. In addition, we applied an alignment-free method to a different domain, which is gene prediction. We are using alignment-free in gene prediction to speed up the process of providing high quality results, and predict accurate stretches in the DNA sequence, which would be considered parts of genes

Unsupervised Discovery and Representation of Subspace Trends in Massive Biomedical Datasets

The goal of this dissertation is to develop unsupervised algorithms for discovering previously unknown subspace trends in massive multivariate biomedical data sets without the benefit of prior information. A subspace trend is a sustained pattern of gradual/progressive changes within an unknown subset of feature dimensions. A fundamental challenge to subspace trend discovery is the presence of irrelevant data dimensions, noise, outliers, and confusion from multiple subspace trends driven by independent factors that are mixed in with each other. These factors can obscure the trends in traditional dimension reduction and projection based data visualizations. To overcome these limitations, we propose a novel graph-theoretic neighborhood similarity measure for sensing concordant progressive changes across data dimensions. Using this measure, we present an unsupervised algorithm for trend-relevant feature selection and visualization. Additionally, we propose to use an efficient online density-based representation to make the algorithm scalable for massive datasets. The representation not only assists in trend discovery, but also in cluster detection including rare populations. Our method has been successfully applied to diverse synthetic and real-world biomedical datasets, such as gene expression microarray and arbor morphology of neurons and microglia in brain tissue. Derived representations revealed biologically meaningful hidden subspace trend(s) that were obscured by irrelevant features and noise. Although our applications are mostly from the biomedical domain, the proposed algorithm is broadly applicable to exploratory analysis of high-dimensional data including visualization, hypothesis generation, knowledge discovery, and prediction in diverse other applications.Electrical and Computer Engineering, Department o

A Pipeline for Clustering by Compression with Application to Patient Stratification in Spondyloarthritis

Funding Information: The authors acknowledge Fundação para a Ciência e Tecnologia, LASIGE Research Unit, ref. UIDB/00408/2020 and ref. UIDP/00408/2020 and Instituto de Telecomunicações Research Unit, ref. UIDB/50008/2020, and UIDP/50008/2020. The authors also acknowledge the Project PREDICT (PTDC/CCI-CIF/29877/2017), funded by Fundo Europeu de Desenvolvimento Regional (FEDER), through Programa Operacional Regional LISBOA (LISBOA2020), and by national funds, through Fundacção para a Ciência e Tecnologia (FCT), and projects MATISSE (DSAIPA/DS/0026/2019), MONET (PTDC/CCI-BIO/4180/2020) and SmartGlauco (PTDC/CTM-REF/2679/2020). Publisher Copyright: © 2023 by the authors.The normalized compression distance (NCD) is a similarity measure between a pair of finite objects based on compression. Clustering methods usually use distances (e.g., Euclidean distance, Manhattan distance) to measure the similarity between objects. The NCD is yet another distance with particular characteristics that can be used to build the starting distance matrix for methods such as hierarchical clustering or K-medoids. In this work, we propose Zgli, a novel Python module that enables the user to compute the NCD between files inside a given folder. Inspired by the CompLearn Linux command line tool, this module iterates on it by providing new text file compressors, a new compression-by-column option for tabular data, such as CSV files, and an encoder for small files made up of categorical data. Our results demonstrate that compression by column can yield better results than previous methods in the literature when clustering tabular data. Additionally, the categorical encoder shows that it can augment categorical data, allowing the use of the NCD for new data types. One of the advantages is that using this new feature does not require knowledge or context of the data. Furthermore, the fact that the new proposed module is written in Python, one of the most popular programming languages for machine learning, potentiates its use by developers to tackle problems with a new approach based on compression. This pipeline was tested in clinical data and proved a promising computational strategy by providing patient stratification via clusters aiding in precision medicine.publishersversionpublishe

Automatic text summarization with Maximal Frequent Sequences

En las últimas dos décadas un aumento exponencial de la información electrónica ha provocado una gran necesidad de entender rápidamente grandes volúmenes de información. En este libro se desarrollan los métodos automáticos para producir un resumen. Un resumen es un texto corto que transmite la información más importante de un documento o de una colección de documentos. Los resúmenes utilizados en este libro son extractivos: una selección de las oraciones más importantes del texto. Otros retos consisten en generar resúmenes de manera independiente de lenguaje y dominio. Se describe la identificación de cuatro etapas para generación de resúmenes extractivos. La primera etapa es la selección de términos, en la que uno tiene que decidir qué unidades contarían como términos individuales. El proceso de estimación de la utilidad de los términos individuales se llama etapa de pesado de términos. El siguiente paso se denota como pesado de oraciones, donde todas las secuencias reciben alguna medida numérica de acuerdo con la utilidad de términos. Finalmente, el proceso de selección de las oraciones más importantes se llama selección de oraciones. Los diferentes métodos para generación de resúmenes extractivos pueden ser caracterizados como representan estas etapas. En este libro se describe la etapa de selección de términos, en la que la detección de descripciones multipalabra se realiza considerando Secuencias Frecuentes Maximales (sfms), las cuales adquieren un significado importante, mientras Secuencias Frecuentes (sf) no maximales, que son partes de otros sf, no deben de ser consideradas. En la motivación se consideró costo vs. beneficio: existen muchas sf no maximales, mientras que la probabilidad de adquirir un significado importante es baja. De todos modos, las sfms representan todas las sfs en el modo compacto: todas las sfs podrían ser obtenidas a partir de todas las sfms explotando cada sfm al conjunto de todas sus subsecuencias. Se presentan los nuevos métodos basados en grafos, algoritmos de agrupamiento y algoritmos genéticos, los cuales facilitan la tarea de generación de resúmenes de textos. Se ha experimentado diferentes combinaciones de las opciones de selección de términos, pesado de términos, pesado de oraciones y selección de oraciones para generar los resúmenes extractivos de textos independientes de lenguaje y dominio para una colección de noticias. Se ha analizado algunas opciones basadas en descripciones multipalabra considerándolas en los métodos de grafos, algoritmos de agrupamiento y algoritmos genéticos. Se han obtenido los resultados superiores al de estado de arte. Este libro está dirigido a los estudiantes y científicos del área de Lingüística Computacional, y también a quienes quieren saber sobre los recientes avances en las investigaciones de generación automática de resúmenes de textos.In the last two decades, an exponential increase in the available electronic information causes a big necessity to quickly understand large volumes of information. It raises the importance of the development of automatic methods for detecting the most relevant content of a document in order to produce a shorter text. Automatic Text Summarization (ats) is an active research area dedicated to generate abstractive and extractive summaries not only for a single document, but also for a collection of documents. Other necessity consists in finding method for ats in a language and domain independent way. In this book we consider extractive text summarization for single document task. We have identified that a typical extractive summarization method consists in four steps. First step is a term selection where one should decide what units will count as individual terms. The process of estimating the usefulness of the individual terms is called term weighting step. The next step denotes as sentence weighting where all the sentences receive some numerical measure according to the usefulness of its terms. Finally, the process of selecting the most relevant sentences calls sentence selection. Different extractive summarization methods can be characterized how they perform these steps. In this book, in the term selection step, we describe how to detect multiword descriptions considering Maximal Frequent Sequences (mfss), which bearing important meaning, while non-maximal frequent sequences (fss), those that are parts of another fs, should not be considered. Our additional motivation was cost vs. benefit considerations: there are too many non-maximal fss while their probability to bear important meaning is lower. In any case, mfss represent all fss in a compact way: all fss can be obtained from all mfss by bursting each mfs into a set of all its subsequences.New methods based on graph algorithms, genetic algorithms, and clustering algorithms which facilitate the text summarization task are presented. We have tested different combinations of term selection, term weighting, sentence weighting and sentence selection options for language-and domain-independent extractive single-document text summarization on a news report collection. We analyzed several options based on mfss, considering them with graph, genetic, and clustering algorithms. We obtained results superior to the existing state-ofthe- art methods. This book is addressed for students and scientists of the area of Computational Linguistics, and also who wants to know recent developments in the area of Automatic Text Generation of Summaries

Automatic Summarization

It has now been 50 years since the publication of Luhn’s seminal paper on automatic summarization. During these years the practical need for automatic summarization has become increasingly urgent and numerous papers have been published on the topic. As a result, it has become harder to find a single reference that gives an overview of past efforts or a complete view of summarization tasks and necessary system components. This article attempts to fill this void by providing a comprehensive overview of research in summarization, including the more traditional efforts in sentence extraction as well as the most novel recent approaches for determining important content, for domain and genre specific summarization and for evaluation of summarization. We also discuss the challenges that remain open, in particular the need for language generation and deeper semantic understanding of language that would be necessary for future advances in the field