An all-substrings common subsequence algorithm

Given two strings A and B of lengths n(a) and n(b), n(a) <= n(b), respectively, the all-substrings longest common subsequence (ALCS) problem obtains, for every substring B` of B, the length of the longest string that is a subsequence of both A and B. The ALCS problem has many applications, such as finding approximate tandem repeats in strings, solving the circular alignment of two strings and finding the alignment of one string with several others that have a common substring. We present an algorithm to prepare the basic data structure for ALCS queries that takes O(n(a)n(b)) time and O(n(a) + n(b)) space. After this preparation, it is possible to build that allows any LCS length to be retrieved in constant time. Some trade-offs between the space required and a matrix of size O(n(b)(2)) the querying time are discussed. To our knowledge, this is the first algorithm in the literature for the ALCS problem. (C) 2007 Elsevier B.V. All rights reserved.

Analysis and performance of a UPC implementation of a parallel longest common subsequence algorithm

An important problem in computational biology is finding the longest common subsequence (LCS) of two nucleotide sequences. This paper examines the correctness and performance of a recently proposed parallel LCS algorithm that uses successor tables and pruning rules to construct a list of sets from which an LCS can be easily reconstructed. Counterexamples are given for two pruning rules that were given with the original algorithm. Because of these errors, performance measurements originally reported cannot be validated. The work presented here shows that speedup can be reliably achieved by an implementation in Unified Parallel C that runs on an Infiniband cluster. This performance is partly facilitated by exploiting the software cache of the MuPC runtime system. In addition, this implementation achieved speedup without bulk memory copy operations and the associated programming complexity of message passing.

A common Tabu search algorithm for the global optimization of engineering problems

A novel common Tabu algorithm for global optimizations of engineering problems is presented. The robustness and efficiency of the presented method are evaluated by using standard mathematical functions and hy solving a practical engineering problem. The numerical results show that the proposed method is (i) superior to the conventional Tabu search algorithm in robustness, and (ii) superior to the simulated annealing algorithm in efficiency. (C) 2001 Elsevier B.V. B.V. All rights reserved.

Intelligent Internet Data Searching

In this thesis author approaches the problem of automated text classification, which is one of basic tasks for building Intelligent Internet Search Agent. The work discusses various approaches to solving sub-problems of automated text classification, such as feature extraction and machine learning on text sources. Author also describes her own multiword approach to feature extraction and pres-ents the results of testing this approach using linear discriminant analysis based classifier, and classifier combining unsupervised learning for etalon extraction with supervised learning using common backpropagation algorithm for multilevel perceptron.

Analysis, monitoring, and management of quality of experience in video delivery services over IP

Esta tesis estudia la monitorización y gestión de la Calidad de Experiencia (QoE) en los servicios de distribución de vídeo sobre IP. Aborda el problema de cómo prevenir, detectar, medir y reaccionar a las degradaciones de la QoE desde la perspectiva de un proveedor de servicios: la solución debe ser escalable para una red IP extensa que entregue flujos individuales a miles de usuarios simultáneamente. La solución de monitorización propuesta se ha denominado QuEM(Qualitative Experience Monitoring, o Monitorización Cualitativa de la Experiencia). Se basa en la detección de las degradaciones de la calidad de servicio de red (pérdidas de paquetes, disminuciones abruptas del ancho de banda...) e inferir de cada una una descripción cualitativa de su efecto en la Calidad de Experiencia percibida (silencios, defectos en el vídeo...). Este análisis se apoya en la información de transporte y de la capa de abstracción de red de los flujos codificados, y permite caracterizar los defectos más relevantes que se observan en este tipo de servicios: congelaciones, efecto de “cuadros”, silencios, pérdida de calidad del vídeo, retardos e interrupciones en el servicio. Los resultados se han validado mediante pruebas de calidad subjetiva. La metodología usada en esas pruebas se ha desarrollado a su vez para imitar lo más posible las condiciones de visualización de un usuario de este tipo de servicios: los defectos que se evalúan se introducen de forma aleatoria en medio de una secuencia de vídeo continua. Se han propuesto también algunas aplicaciones basadas en la solución de monitorización: un sistema de protección desigual frente a errores que ofrece más protección a las partes del vídeo más sensibles a pérdidas, una solución para minimizar el impacto de la interrupción de la descarga de segmentos de Streaming Adaptativo sobre HTTP, y un sistema de cifrado selectivo que encripta únicamente las partes del vídeo más sensibles. También se ha presentado una solución de cambio rápido de canal, así como el análisis de la aplicabilidad de los resultados anteriores a un escenario de vídeo en 3D. ABSTRACT This thesis proposes a comprehensive approach to the monitoring and management of Quality of Experience (QoE) in multimedia delivery services over IP. It addresses the problem of preventing, detecting, measuring, and reacting to QoE degradations, under the constraints of a service provider: the solution must scale for a wide IP network delivering individual media streams to thousands of users. The solution proposed for the monitoring is called QuEM (Qualitative Experience Monitoring). It is based on the detection of degradations in the network Quality of Service (packet losses, bandwidth drops...) and the mapping of each degradation event to a qualitative description of its effect in the perceived Quality of Experience (audio mutes, video artifacts...). This mapping is based on the analysis of the transport and Network Abstraction Layer information of the coded stream, and allows a good characterization of the most relevant defects that exist in this kind of services: screen freezing, macroblocking, audio mutes, video quality drops, delay issues, and service outages. The results have been validated by subjective quality assessment tests. The methodology used for those test has also been designed to mimic as much as possible the conditions of a real user of those services: the impairments to evaluate are introduced randomly in the middle of a continuous video stream. Based on the monitoring solution, several applications have been proposed as well: an unequal error protection system which provides higher protection to the parts of the stream which are more critical for the QoE, a solution which applies the same principles to minimize the impact of incomplete segment downloads in HTTP Adaptive Streaming, and a selective scrambling algorithm which ciphers only the most sensitive parts of the media stream. A fast channel change application is also presented, as well as a discussion about how to apply the previous results and concepts in a 3D video scenario.

Typing less common ovarian tumors: A training tool based on a pattern-based algorithm applied to a set of 20 virtual slides.

Context: Ovarian tumors (OT) typing is a competency expected from pathologists, with significant clinical implications. OT however come in numerous different types, some rather rare, with the consequence of few opportunities for practice in some departments. Aim: Our aim was to design a tool for pathologists to train in less common OT typing. Method and Results: Representative slides of 20 less common OT were scanned (Nano Zoomer Digital Hamamatsu®) and the diagnostic algorithm proposed by Young and Scully applied to each case (Young RH and Scully RE, Seminars in Diagnostic Pathology 2001, 18: 161-235) to include: recognition of morphological pattern(s); shortlisting of differential diagnosis; proposition of relevant immunohistochemical markers. The next steps of this project will be: evaluation of the tool in several post-graduate training centers in Europe and Québec; improvement of its design based on evaluation results; diffusion to a larger public. Discussion: In clinical medicine, solving many cases is recognized as of utmost importance for a novice to become an expert. This project relies on the virtual slides technology to provide pathologists with a learning tool aimed at increasing their skills in OT typing. After due evaluation, this model might be extended to other uncommon tumors.

New developmental stages for common marmosets (Callithrix jacchus) using mass and age variables obtained by K-means algorithm and self-organizing maps (SOM)

LEÃO, Adriano de Castro; DÓRIA NETO, Adrião Duarte; SOUSA, Maria Bernardete Cordeiro de. New developmental stages for common marmosets (Callithrix jacchus) using mass and age variables obtained by K-means algorithm and self-organizing maps (SOM). Computers in Biology and Medicine, v. 39, p. 853-859, 2009

Many Facet, Common Latent Trait Polytomous IRT Model and EM Algorithm

2000 Mathematics Subject Classification: 91E45.

New developmental stages for common marmosets (Callithrix jacchus) using mass and age variables obtained by K-means algorithm and self-organizing maps (SOM)

LEÃO, Adriano de Castro; DÓRIA NETO, Adrião Duarte; SOUSA, Maria Bernardete Cordeiro de. New developmental stages for common marmosets (Callithrix jacchus) using mass and age variables obtained by K-means algorithm and self-organizing maps (SOM). Computers in Biology and Medicine, v. 39, p. 853-859, 2009

New developmental stages for common marmosets (Callithrix jacchus) using mass and age variables obtained by K-means algorithm and self-organizing maps (SOM)

LEÃO, Adriano de Castro; DÓRIA NETO, Adrião Duarte; SOUSA, Maria Bernardete Cordeiro de. New developmental stages for common marmosets (Callithrix jacchus) using mass and age variables obtained by K-means algorithm and self-organizing maps (SOM). Computers in Biology and Medicine, v. 39, p. 853-859, 2009

Estimating HIV-1 incidence using the serologic testing algorithm for recent HIV infections at HIV counseling and testing centers in the city of São Paulo, Brazil

The network of HIV counseling and testing centers in São Paulo, Brazil is a major source of data used to build epidemiological profiles of the client population. We examined HIV-1 incidence from November 2000 to April 2001, comparing epidemiological and socio-behavioral data of recently-infected individuals with those with long-standing infection. A less sensitive ELISA was employed to identify recent infection. The overall incidence of HIV-1 infection was 0.53/100/year (95% CI: 0.31-0.85/100/year): 0.77/100/year for males (95% CI: 0.42-1.27/100/year) and 0.22/100/ year (95% CI: 0.05-0.59/100/year) for females. Overall HIV-1 prevalence was 3.2% (95% CI: 2.8-3.7%), being 4.0% among males (95% CI: 3.3-4.7%) and 2.1% among females (95% CI: 1.6-2.8%). Recent infections accounted for 15% of the total (95% CI: 10.2-20.8%). Recent infection correlated with being younger and male (p = 0.019). Therefore, recent infection was more common among younger males and older females.