Fast protein superfamily classification using principal component null space analysis.

The protein family classification problem, which consists of determining the family memberships of given unknown protein sequences, is very important for a biologist for many practical reasons, such as drug discovery, prediction of molecular functions and medical diagnosis. Neural networks and Bayesian methods have performed well on the protein classification problem, achieving accuracy ranging from 90% to 98% while running relatively slowly in the learning stage. In this thesis, we present a principal component null space analysis (PCNSA) linear classifier to the problem and report excellent results compared to those of neural networks and support vector machines. The two main parameters of PCNSA are linked to the high dimensionality of the dataset used, and were optimized in an exhaustive manner to maximize accuracy. Paper copy at Leddy Library: Theses & Major Papers - Basement, West Bldg. / Call Number: Thesis2005 .F74. Source: Masters Abstracts International, Volume: 44-03, page: 1400. Thesis (M.Sc.)--University of Windsor (Canada), 2005

Plant protein-coding gene families: emerging bioinformatics approaches

Protein-coding gene families are sets of similar genes with a shared evolutionary origin and, generally, with similar biological functions. In plants, the size and role of gene families has been only partially addressed. However, suitable bioinformatics tools are being developed to cluster the enormous number of sequences currently available in databases. Specifically, comparative genomic databases promise to become powerful tools for gene family annotation in plant clades. In this review, I evaluate the data retrieved from various gene family databases, the ease with which they can be extracted and how useful the extracted information is

Identification des régimes et regroupement des séquences pour la prévision des marchés financiers

Abstract : Regime switching analysis is extensively advocated to capture complex behaviors underlying financial time series for market prediction. Two main disadvantages in current approaches of regime identification are raised in the literature: 1) the lack of a mechanism for identifying regimes dynamically, restricting them to switching among a fixed set of regimes with a static transition probability matrix; 2) failure to utilize cross-sectional regime dependencies among time series, since not all the time series are synchronized to the same regime. As the numerical time series can be symbolized into categorical sequences, a third issue raises: 3) the lack of a meaningful and effective measure of the similarity between chronological dependent categorical values, in order to identify sequence clusters that could serve as regimes for market forecasting. In this thesis, we propose a dynamic regime identification model that can identify regimes dynamically with a time-varying transition probability, to address the first issue. For the second issue, we propose a cluster-based regime identification model to account for the cross-sectional regime dependencies underlying financial time series for market forecasting. For the last issue, we develop a dynamic order Markov model, making use of information underlying frequent consecutive patterns and sparse patterns, to identify the clusters that could serve as regimes identified on categorized financial time series. Experiments on synthetic and real-world datasets show that our two regime models show good performance on both regime identification and forecasting, while our dynamic order Markov clustering model also demonstrates good performance on identifying clusters from categorical sequences.L'analyse de changement de régime est largement préconisée pour capturer les comportements complexes sous-jacents aux séries chronologiques financières pour la prédiction du marché. Deux principaux problèmes des approches actuelles d'identifica-tion de régime sont soulevés dans la littérature. Il s’agit de: 1) l'absence d'un mécanisme d'identification dynamique des régimes. Ceci limite la commutation entre un ensemble fixe de régimes avec une matrice de probabilité de transition statique; 2) l’incapacité à utiliser les dépendances transversales des régimes entre les séries chronologiques, car toutes les séries chronologiques ne sont pas synchronisées sur le même régime. Étant donné que les séries temporelles numériques peuvent être symbolisées en séquences catégorielles, un troisième problème se pose: 3) l'absence d'une mesure significative et efficace de la similarité entre les séries chronologiques dépendant des valeurs catégorielles pour identifier les clusters de séquences qui pourraient servir de régimes de prévision du marché. Dans cette thèse, nous proposons un modèle d'identification de régime dynamique qui identifie dynamiquement des régimes avec une probabilité de transition variable dans le temps afin de répondre au premier problème. Ensuite, pour adresser le deuxième problème, nous proposons un modèle d'identification de régime basé sur les clusters. Notre modèle considère les dépendances transversales des régimes sous-jacents aux séries chronologiques financières avant d’effectuer la prévision du marché. Pour terminer, nous abordons le troisième problème en développant un modèle de Markov d'ordre dynamique, en utilisant les informations sous-jacentes aux motifs consécutifs fréquents et aux motifs clairsemés, pour identifier les clusters qui peuvent servir de régimes identifiés sur des séries chronologiques financières catégorisées. Nous avons mené des expériences sur des ensembles de données synthétiques et du monde réel. Nous démontrons que nos deux modèles de régime présentent de bonnes performances à la fois en termes d'identification et de prévision de régime, et notre modèle de clustering de Markov d'ordre dynamique produit également de bonnes performances dans l'identification de clusters à partir de séquences catégorielles

Algorithms for Gene Clustering Analysis on Genomes

The increased availability of data in biological databases provides many opportunities for understanding biological processes through these data. As recent attention has shifted from sequence analysis to higher-level analysis of genes across multiple genomes, there is a need to develop efficient algorithms for these large-scale applications that can help us understand the functions of genes. The overall objective of my research was to develop improved methods which can automatically assign groups of functionally related genes in large-scale data sets by applying new gene clustering algorithms. Proposed gene clustering algorithms that can help us understand gene function and genome evolution include new algorithms for protein family classification, a window-based strategy for gene clustering on chromosomes, and an exhaustive strategy that allows all clusters of small size to be enumerated. I investigate the problems of gene clustering in multiple genomes, and define gene clustering problems using mathematical methodology and solve the problems by developing efficient and effective algorithms. For protein family classification, I developed two supervised classification algorithms that can assign proteins to existing protein families in public databases and, by taking into account similarities between the unclassified proteins, allows for progressive construction of new families from proteins that cannot be assigned. This approach is useful for rapid assignment of protein sequences from genome sequencing projects to protein families. A comparative analysis of the method to other previously developed methods shows that the algorithm has a higher accuracy rate and lower mis-classification rate when compared to algorithms that are based on the use of multiple sequence alignments and hidden Markov models. The proposed algorithm performs well even on families with very few proteins and on families with low sequence similarity. Apart from the analysis of individual sequences, identifying genomic regions that descended from a common ancestor helps us study gene function and genome evolution. In distantly related genomes, clusters of homologous gene pairs serve as evidence used in function prediction, operon detection, etc. Thus, reliable identification of gene clusters is critical to functional annotation and analysis of genes. I developed an efficient gene clustering algorithm that can be applied on hundreds of genomes at the same time. This approach allows for large-scale study of evolutionary relationships of gene clusters and study of operon formation and destruction. By placing a stricter limit on the maximum cluster size, I developed another algorithm that uses a different formulation based on constraining the overall size of a cluster and statistical estimates that allow direct comparisons of clusters of different size. A comparative analysis of proposed algorithms shows that more biological insight can be obtained by analyzing gene clusters across hundreds of genomes, which can help us understand operon occurrences, gene orientations and gene rearrangements

On Prediction Using Variable Order Markov Models

This paper is concerned with algorithms for prediction of discrete sequences over a finite alphabet, using variable order Markov models. The class of such algorithms is large and in principle includes any lossless compression algorithm. We focus on six prominent prediction algorithms, including Context Tree Weighting (CTW), Prediction by Partial Match (PPM) and Probabilistic Suffix Trees (PSTs). We discuss the properties of these algorithms and compare their performance using real life sequences from three domains: proteins, English text and music pieces. The comparison is made with respect to prediction quality as measured by the average log-loss. We also compare classification algorithms based on these predictors with respect to a number of large protein classification tasks. Our results indicate that a "decomposed" CTW (a variant of the CTW algorithm) and PPM outperform all other algorithms in sequence prediction tasks. Somewhat surprisingly, a different algorithm, which is a modification of the Lempel-Ziv compression algorithm, significantly outperforms all algorithms on the protein classification problems