Bayesian Online Changepoint Detection

Changepoints are abrupt variations in the generative parameters of a data sequence. Online detection of changepoints is useful in modelling and prediction of time series in application areas such as finance, biometrics, and robotics. While frequentist methods have yielded online filtering and prediction techniques, most Bayesian papers have focused on the retrospective segmentation problem. Here we examine the case where the model parameters before and after the changepoint are independent and we derive an online algorithm for exact inference of the most recent changepoint. We compute the probability distribution of the length of the current ``run,'' or time since the last changepoint, using a simple message-passing algorithm. Our implementation is highly modular so that the algorithm may be applied to a variety of types of data. We illustrate this modularity by demonstrating the algorithm on three different real-world data sets.

Probabilistic graphical models for semi-supervised traffic classification

Traffic classification using machine learning continues to be an active research area. The majority of work in this area uses off-the-shelf machine learning tools and treats them as black-box classifiers. This approach turns all the modelling complexity into a feature selection problem. In this paper, we build a problem-specific solution to the traffic classification problem by designing a custom probabilistic graphical model. Graphical models are a modular framework to design classifiers which incorporate domain-specific knowledge. More specifically, our solution introduces semi-supervised learning which means we learn from both labelled and unlabelled traffic flows. We show that our solution performs competitively compared to previous approaches while using less data and simpler features. Copyright © 2010 ACM.

Sistema seguro de votação eletrônica multi-células

Em uso desde a Grécia antiga e atualmente massificado na maioria dos países do mundo, o sistema de votação tradicional baseado em cédulas de papel possui diversos problemas associados à segurança, tais como dificuldades para evitar coerção do eleitor, venda do voto e substituição fraudulenta do eleitor. Além de problemas de usabilidade que acarretam erros de preenchimento da cédula e um processo de apuração lento, que pode durar dias. Ao lado disso, o sistema tradicional não fornece a contraprova do voto, que permite ao eleitor conferir se o seu voto foi corretamente contabilizado na apuração. Inicialmente acreditou-se que a informatização do sistema de votação resolveria todos os problemas do sistema tradicional. Porém, com a sua implantação em alguns países o sistema de votação eletrônica não mostrou-se capaz de fornecer garantias irrefutáveis que não tivesse sido alvo de alterações fraudulentas durante o seu desenvolvimento ou operação. A má reputação do sistema eletrônico está principalmente associada à falta de transparência dos processos que, em sua maioria, não proporcionam a materialização do voto, conferido pelo eleitor para fins de contagem manual, e nem geram evidências (contraprova) da correta contabilização do voto do eleitor. O objetivo deste trabalho é propor uma arquitetura de votação eletrônica que integra, de forma segura, o anonimato e autenticidade do votante, a confidencialidade e integridade do voto/sistema. O sistema aumenta a usabilidade do esquema de votação baseado em "Três Cédulas" de papel, implementando-o computacionalmente. O esquema oferece maior credibilidade ao sistema de votação através da materialização e contraprova do voto, resistência à coerção e ao comércio do voto. Utilizando esquemas de criptografia assimétrica e segurança computacional clássica, associado a um sistema de auditoria eficiente, a proposta garante segurança e transparência nos processos envolvidos. A arquitetura de construção modular distribui a responsabilidade entre suas entidades, agregando-lhe robustez e viabilizando eleições em grande escala. O protótipo do sistema desenvolvido usando serviços web e Election Markup Language mostra a viabilidade da proposta.

Implantar un Sistema de Gestion Integral en Software libre

El proyecto de fin de carrera “Implantar un Sistema de Gestión Integral en Software libre” se ha desarrollado en la empresa Avanzosc con sede en Azkoitia. Una peculiaridad del proyecto es que a su vez se ha utilizado como cliente otra empresa, q2K, Soluciones Informáticas en Gestión Estratégica. El objetivo del proyecto es implantar en q2K un sistema de planificación de recursos empresariales (ERP, Enterprise Resource Planning), esto le permite reunir en una única aplicación todos los procesos de negocio de la empresa. La implantación de un ERP requiere de una importante inversión ya que el coste de la licencia de un sistema ERP propietario es elevado. Una interesante alternativa para evitar este desembolso es optar por un de ERP de software libre con todas las ventajas de configuración y personalización. En nuestro caso se ha adoptado OpenERP que es un software integral, modular y adaptable, adecuado para pequeñas y medianas empresas. El desarrollo del proyecto ha estado supervisado por el equipo de trabajo de Avanzosc, empresa líder en España en implantación de OpenErp, siguiendo la metodología de trabajo propia de esta empresa.

A Computational Module Assembled from Different Protease Family Motifs Identifies PI PLC from Bacillus cereus as a Putative Prolyl Peptidase with a Serine Protease Scaffold

Proteolytic enzymes have evolved several mechanisms to cleave peptide bonds. These distinct types have been systematically categorized in the MEROPS database. While a BLAST search on these proteases identifies homologous proteins, sequence alignment methods often fail to identify relationships arising from convergent evolution, exon shuffling, and modular reuse of catalytic units. We have previously established a computational method to detect functions in proteins based on the spatial and electrostatic properties of the catalytic residues (CLASP). CLASP identified a promiscuous serine protease scaffold in alkaline phosphatases (AP) and a scaffold recognizing a beta-lactam (imipenem) in a cold-active Vibrio AP. Subsequently, we defined a methodology to quantify promiscuous activities in a wide range of proteins. Here, we assemble a module which encapsulates the multifarious motifs used by protease families listed in the MEROPS database. Since APs and proteases are an integral component of outer membrane vesicles (OMV), we sought to query other OMV proteins, like phospholipase C (PLC), using this search module. Our analysis indicated that phosphoinositide-specific PLC from Bacillus cereus is a serine protease. This was validated by protease assays, mass spectrometry and by inhibition of the native phospholipase activity of PI-PLC by the well-known serine protease inhibitor AEBSF (IC50 = 0.018 mM). Edman degradation analysis linked the specificity of the protease activity to a proline in the amino terminal, suggesting that the PI-PLC is a prolyl peptidase. Thus, we propose a computational method of extending protein families based on the spatial and electrostatic congruence of active site residues.

Design and synthesis of quasi-diastereomeric molecules with unchanging central, regenerating axial and switchable helical chirality via cleavage and formation of Ni(II)–O and Ni(II)–N coordination bonds

9 p.

Failure detectors and communication efficiency in the crash and general omisión failure models

122 p.

Commercial aquaculture in Nigeria: a vertically integrated approach in the commercial freshwater farming of tilapia in floating bamboo net-hapas and cages systems

Tilapia once termed "poor man's" fish, still remains as the highly-priced food fish in many developing countries. The good attributes of this fish prompt its use in intensive aquaculture vertically integrated systems (VIS) which embrace broodstock development, hatchery/nursery and growout phase. Based on the series of studies carried out at Kainji Lake Research Institute, in New Bussa, Nigeria using Oreochromis (Tilapia niloticus) in floating bamboo hapas/cages, the recommended intensive modular systems were estimated to be capable of producing 4 million Tilapia fingerlings and 729 tons fish (Market-size) annually. Cost-benefit analysis showed the venture to have high prospects. It is recommended that priority be given to Tilapia cage culture at the national level in order to contribute immensely towards increased fish production

Itzulpen-sistema hibridoen eraikuntza EBMT bidezko itzulpen partzialak erabiliz

Proiektu honetan EBMT tekniken bidez itzulpen partzialak sortzen dituen aurreprozesu batean oinarritutako itzulpen automatikorako hibridazio-mekanismo bat garatu da, entitateen eta esaldia baino txikiagoak diren unitate sintaktikoen bidezko orokortzea darabilena. Sistema oso arina eta eskalagarria izan dadin diseinatua izan da, eta inplementazio modular, hedagarri eta eraginkor bat eskaini zaio, baliabide eta tresna ugarirekin integratuz. Egindako esperimentuetan oso emaitza positiboak eskuratu dira, proposatutako sistemak abiapuntukoarekiko hobekuntza nabarmenak ekar ditzakeela erakusten dutenak.

Improving the biological activity of pyrrole-imidazole polyamides

DNA is nature’s blueprint, holding within it the genetic code that defines the structure and function of an organism. A complex network of DNA-binding proteins called transcription factors can largely control the flow of information from DNA, so modulating the function of transcription factors is a promising approach for treating many diseases. Pyrrole-imidazole (Py-Im) polyamides are a class of DNA-binding oligomers, which can be synthetically programmed to bind a target sequence of DNA. Due to their unique shape complementarity and a series of favorable hydrogen bonding interactions that occur upon DNA-binding, Py-Im polyamides can bind to the minor groove of DNA with affinities comparable to transcription factors. Previous studies have demonstrated that these cell-permeable small molecules can enter cell nuclei and disrupt the transcription factor-DNA interface, thereby repressing transcription. As the use of Py-Im polyamides has significant potential as a type of modular therapeutic platform, the need for polyamides with extremely favorable biological properties and high potency will be essential. Described herein, a variety of studies have been performed aimed at improving the biological activity of Py-Im polyamides. To improve the biological potency and cellular uptake of these compounds, we have developed a next-generation class of polyamides bearing aryl-turn moieties, a simple structural modification that allows significant improvements in cellular uptake. This strategy was also applied to a panel of high-affinity cyclic Py-Im polyamides, again demonstrating the remarkable effect minor structural changes can have on biological activity. The solubility properties of Py-Im polyamides and use of formulating reagents with their treatment have also been examined. Finally, we describe the study of Py-Im polyamides as a potential artificial transcription factor.

Dense, efficient chip-to-chip communication at the extremes of computing

The scalability of CMOS technology has driven computation into a diverse range of applications across the power consumption, performance and size spectra. Communication is a necessary adjunct to computation, and whether this is to push data from node-to-node in a high-performance computing cluster or from the receiver of wireless link to a neural stimulator in a biomedical implant, interconnect can take up a significant portion of the overall system power budget. Although a single interconnect methodology cannot address such a broad range of systems efficiently, there are a number of key design concepts that enable good interconnect design in the age of highly-scaled CMOS: an emphasis on highly-digital approaches to solving ‘analog’ problems, hardware sharing between links as well as between different functions (such as equalization and synchronization) in the same link, and adaptive hardware that changes its operating parameters to mitigate not only variation in the fabrication of the link, but also link conditions that change over time. These concepts are demonstrated through the use of two design examples, at the extremes of the power and performance spectra.

A novel all-digital clock and data recovery technique for high-performance, high density interconnect has been developed. Two independently adjustable clock phases are generated from a delay line calibrated to 2 UI. One clock phase is placed in the middle of the eye to recover the data, while the other is swept across the delay line. The samples produced by the two clocks are compared to generate eye information, which is used to determine the best phase for data recovery. The functions of the two clocks are swapped after the data phase is updated; this ping-pong action allows an infinite delay range without the use of a PLL or DLL. The scheme's generalized sampling and retiming architecture is used in a sharing technique that saves power and area in high-density interconnect. The eye information generated is also useful for tuning an adaptive equalizer, circumventing the need for dedicated adaptation hardware.

On the other side of the performance/power spectra, a capacitive proximity interconnect has been developed to support 3D integration of biomedical implants. In order to integrate more functionality while staying within size limits, implant electronics can be embedded onto a foldable parylene (‘origami’) substrate. Many of the ICs in an origami implant will be placed face-to-face with each other, so wireless proximity interconnect can be used to increase communication density while decreasing implant size, as well as facilitate a modular approach to implant design, where pre-fabricated parylene-and-IC modules are assembled together on-demand to make custom implants. Such an interconnect needs to be able to sense and adapt to changes in alignment. The proposed array uses a TDC-like structure to realize both communication and alignment sensing within the same set of plates, increasing communication density and eliminating the need to infer link quality from a separate alignment block. In order to distinguish the communication plates from the nearby ground plane, a stimulus is applied to the transmitter plate, which is rectified at the receiver to bias a delay generation block. This delay is in turn converted into a digital word using a TDC, providing alignment information.

Convex analysis for minimizing and learning submodular set functions

The connections between convexity and submodularity are explored, for purposes of minimizing and learning submodular set functions.

First, we develop a novel method for minimizing a particular class of submodular functions, which can be expressed as a sum of concave functions composed with modular functions. The basic algorithm uses an accelerated first order method applied to a smoothed version of its convex extension. The smoothing algorithm is particularly novel as it allows us to treat general concave potentials without needing to construct a piecewise linear approximation as with graph-based techniques.

Second, we derive the general conditions under which it is possible to find a minimizer of a submodular function via a convex problem. This provides a framework for developing submodular minimization algorithms. The framework is then used to develop several algorithms that can be run in a distributed fashion. This is particularly useful for applications where the submodular objective function consists of a sum of many terms, each term dependent on a small part of a large data set.

Lastly, we approach the problem of learning set functions from an unorthodox perspective---sparse reconstruction. We demonstrate an explicit connection between the problem of learning set functions from random evaluations and that of sparse signals. Based on the observation that the Fourier transform for set functions satisfies exactly the conditions needed for sparse reconstruction algorithms to work, we examine some different function classes under which uniform reconstruction is possible.

Informática de gestión

Nivel educativo: Grado. Duración (en horas): Más de 50 horas

Developing peptide based capture agents for diagnostics and therapeutics

Iterative in situ click chemistry (IISCC) is a robust general technology for development of high throughput, inexpensive protein detection agents. In IISCC, the target protein acts as a template and catalyst, and assembles its own ligand from modular blocks of peptides. This process of ligand discovery is iterated to add peptide arms to develop a multivalent ligand with increased affinity and selectivity. The peptide based protein capture agents (PCC) should ideally have the same degree of selectivity and specificity as a monoclonal antibody, along with improved chemical stability. We had previously reported developing a PCC agent against bovine carbonic anhydrase II (bCAII) that could replace a polyclonal antibody. To further enhance the affinity or specificity of the PCC agent, I explore branching the peptide arms to develop branched PCC agents against bCAII. The developed branched capture agents have two to three fold higher affinities for the target protein. In the second part of my thesis, I describe the epitope targeting strategy, a strategy for directing the development of a peptide ligand against specific region or fragment of the protein. The strategy is successfully demonstrated by developing PCC agents with low nanomolar binding affinities that target the C-terminal hydrophobic motif of Akt2 kinase. One of the developed triligands inhibits the kinase activity of Akt. This suggests that, if targeted against the right epitope, the PCC agents can also influence the functional properties of the protein. The exquisite control of the epitope targeting strategy is further demonstrated by developing a cyclic ligand against Akt2. The cyclic ligand acts as an inhibitor by itself, without any iteration of the ligand discovery process. The epitope targeting strategy is a cornerstone of the IISCC technology and opens up new opportunities, leading to the development of protein detection agents and of modulators of protein functions.

Lightweight deformable mirrors for future space telescopes

This thesis presents a concept for ultra-lightweight deformable mirrors based on a thin substrate of optical surface quality coated with continuous active piezopolymer layers that provide modes of actuation and shape correction. This concept eliminates any kind of stiff backing structure for the mirror surface and exploits micro-fabrication technologies to provide a tight integration of the active materials into the mirror structure, to avoid actuator print-through effects. Proof-of-concept, 10-cm-diameter mirrors with a low areal density of about 0.5 kg/m² have been designed, built and tested to measure their shape-correction performance and verify the models used for design. The low cost manufacturing scheme uses replication techniques, and strives for minimizing residual stresses that deviate the optical figure from the master mandrel. It does not require precision tolerancing, is lightweight, and is therefore potentially scalable to larger diameters for use in large, modular space telescopes. Other potential applications for such a laminate could include ground-based mirrors for solar energy collection, adaptive optics for atmospheric turbulence, laser communications, and other shape control applications.

The immediate application for these mirrors is for the Autonomous Assembly and Reconfiguration of a Space Telescope (AAReST) mission, which is a university mission under development by Caltech, the University of Surrey, and JPL. The design concept, fabrication methodology, material behaviors and measurements, mirror modeling, mounting and control electronics design, shape control experiments, predictive performance analysis, and remaining challenges are presented herein. The experiments have validated numerical models of the mirror, and the mirror models have been used within a model of the telescope in order to predict the optical performance. A demonstration of this mirror concept, along with other new telescope technologies, is planned to take place during the AAReST mission.