Network signatures based on gene pair expression ratios improve classification and the analysis of muscle-invasive urothelial cancer

Urothelial cancer (UC) is highly recurrent and can progress from non-invasive (NMIUC) to a more aggressive muscle-invasive (MIUC) subtype that invades the muscle tissue layer of the bladder. We present a proof of principle study that network-based features of gene pairs can be used to improve classifier performance and the functional analysis of urothelial cancer gene expression data. In the first step of our procedure each individual sample of a UC gene expression dataset is inflated by gene pair expression ratios that are defined based on a given network structure. In the second step an elastic net feature selection procedure for network-based signatures is applied to discriminate between NMIUC and MIUC samples. We performed a repeated random subsampling cross validation in three independent datasets. The network signatures were characterized by a functional enrichment analysis and studied for the enrichment of known cancer genes. We observed that the network-based gene signatures from meta collections of proteinprotein interaction (PPI) databases such as CPDB and the PPI databases HPRD and BioGrid improved the classification performance compared to single gene based signatures. The network based signatures that were derived from PPI databases showed a prominent enrichment of cancer genes (e.g., TP53, TRIM27 and HNRNPA2Bl). We provide a novel integrative approach for large-scale gene expression analysis for the identification and development of novel diagnostical targets in bladder cancer. Further, our method allowed to link cancer gene associations to network-based expression signatures that are not observed in gene-based expression signatures.

An analysis on the network access pricing rules

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Neural Network based studies on Spectroscopic Analysis and Image Processing

International School of Photonics, Cochin University of Science and Technology

Availability analysis of GMPLS connections based on physical network topology

This paper presents a study of connection availability in GMPLS over optical transport networks (OTN) taking into account different network topologies. Two basic path protection schemes are considered and compared with the no protection case. The selected topologies are heterogeneous in geographic coverage, network diameter, link lengths, and average node degree. Connection availability is also computed considering the reliability data of physical components and a well-known network availability model. Results show several correspondences between suitable path protection algorithms and several network topology characteristics

Simple Analysis of Network Datasets

Linux commands that are generally useful for analyzing data; it is very easy to reduce phenomena such as links, nodes, URLs or downloads, to multiply repeating identifiers and then sorting and counting appearances.

Configuración de la interfaz discurso-gramática en el lenguaje del profesor de preescolar en el aula ILE : presentación de una red sistémica como herramienta para un análisis sistemático de las funciones reguladoras. Modelling the discourse-grammar interface of ELF pre-school teacher talk (native and non-native) : proposal of a system network enabling the systematic analysis of regulatory functions.

Esta investigación pretende alcanzar dos objetivos. Cubrir el vacío existente en los estudios de las funciones comunicativas del habla de profesores, en este caso de inglés como Lengua Extranjera (ILE) destinado a nivel preescolar, y configurar una interfaz discurso-gramática de las funciones reguladoras del lenguaje.. En primer lugar, para lograr un análisis discursivo-semántico, en este trabajo se diseña la Red Sistémica de Funciones Reguladoras, RSFR, una herramienta que resume las diferentes opciones discursivo-semánticas de los contextos de las funciones reguladoras. A continuación, se analizan los datos en el estrato léxico-gramatical para facilitar conclusiones sobre la relación función-realización formal. Por último se exponen las similitudes y diferencias en la producción lingüística de las funciones reguladoras entre profesores nativos y no nativos.. Las aportaciones más destacadas de esta investigación son cuatro: hacer posible un estudio sistemático del significado mediante el diseño de una herramienta; la propuesta de una taxonomía de funciones reguladoras; el análisis de la dependencia entre las funciones reguladoras, y sus realizaciones lingüísticas; y las diferencias encontradas en la comparación del discurso del profesor nativo y no-nativo..

Neural network basis function center selection using cluster analysis

This paper deals with the selection of centres for radial basis function (RBF) networks. A novel mean-tracking clustering algorithm is described as a way in which centers can be chosen based on a batch of collected data. A direct comparison is made between the mean-tracking algorithm and k-means clustering and it is shown how mean-tracking clustering is significantly better in terms of achieving an RBF network which performs accurate function modelling.