Design methodologies and architectures of hardware-based evolutionary algorithms for aerospace optimisation applications on FPGAS

This thesis is a study of new design methods for allowing evolutionary algorithms to be more effectively utilised in aerospace optimisation applications where computation needs are high and computation platform space may be restrictive. It examines the applicability of special hardware computational platforms known as field programmable gate arrays and shows that with the right implementation methods they can offer significant benefits. This research is a step forward towards the advancement of efficient and highly automated aircraft systems for meeting compact physical constraints in aerospace platforms and providing effective performance speedups over traditional methods

Next Generation Silicon Photonic Transceiver: From Device Innovation to System Analysis

Silicon photonics is recognized as a disruptive technology that has the potential to reshape many application areas, for example, data center communication, telecommunications, high-performance computing, and sensing. The key capability that silicon photonics offers is to leverage CMOS-style design, fabrication, and test infrastructure to build compact, energy-efficient, and high-performance integrated photonic systems-on- chip at low cost. As the need to squeeze more data into a given bandwidth and a given footprint increases, silicon photonics becomes more and more promising. This work develops and demonstrates novel devices, methodologies, and architectures to resolve the challenges facing the next-generation silicon photonic transceivers. The first part of this thesis focuses on the topology optimization of passive silicon photonic devices. Specifically, a novel device optimization methodology - particle swarm optimization in conjunction with 3D finite-difference time-domain (FDTD), has been proposed and proven to be an effective way to design a wide range of passive silicon photonic devices. We demonstrate a polarization rotator and a 90◦ optical hybrid for polarization-diversity and phase-diversity communications - two important schemes to increase the communication capacity by increasing the spectral efficiency. The second part of this thesis focuses on the design and characterization of the next- generation silicon photonic transceivers. We demonstrate a polarization-insensitive WDM receiver with an aggregate data rate of 160 Gb/s. This receiver adopts a novel architecture which effectively reduces the polarization-dependent loss. In addition, we demonstrate a III-V/silicon hybrid external cavity laser with a tuning range larger than 60 nm in the C-band on a silicon-on-insulator platform. A III-V semiconductor gain chip is hybridized into the silicon chip by edge-coupling to the silicon chip. The demonstrated packaging method requires only passive alignment and is thus suitable for high-volume production. We also demonstrate all silicon-photonics-based transmission of 34 Gbaud (272 Gb/s) dual-polarization 16-QAM using our integrated laser and silicon photonic coherent transceiver. The results show no additional penalty compared to commercially available narrow linewidth tunable lasers. The last part of this thesis focuses on the chip-scale optical interconnect and presents two different types of reconfigurable memory interconnects for multi-core many-memory computing systems. These reconfigurable interconnects can effectively alleviate the memory access issues, such as non-uniform memory access, and Network-on-Chip (NoC) hot-spots that plague the many-memory computing systems by dynamically directing the available memory bandwidth to the required memory interface

Políticas de Copyright de Publicações Científicas em Repositórios Institucionais: O Caso do INESC TEC

A progressiva transformação das práticas científicas, impulsionada pelo desenvolvimento das novas Tecnologias de Informação e Comunicação (TIC), têm possibilitado aumentar o acesso à informação, caminhando gradualmente para uma abertura do ciclo de pesquisa. Isto permitirá resolver a longo prazo uma adversidade que se tem colocado aos investigadores, que passa pela existência de barreiras que limitam as condições de acesso, sejam estas geográficas ou financeiras. Apesar da produção científica ser dominada, maioritariamente, por grandes editoras comerciais, estando sujeita às regras por estas impostas, o Movimento do Acesso Aberto cuja primeira declaração pública, a Declaração de Budapeste (BOAI), é de 2002, vem propor alterações significativas que beneficiam os autores e os leitores. Este Movimento vem a ganhar importância em Portugal desde 2003, com a constituição do primeiro repositório institucional a nível nacional. Os repositórios institucionais surgiram como uma ferramenta de divulgação da produção científica de uma instituição, com o intuito de permitir abrir aos resultados da investigação, quer antes da publicação e do próprio processo de arbitragem (preprint), quer depois (postprint), e, consequentemente, aumentar a visibilidade do trabalho desenvolvido por um investigador e a respetiva instituição. O estudo apresentado, que passou por uma análise das políticas de copyright das publicações científicas mais relevantes do INESC TEC, permitiu não só perceber que as editoras adotam cada vez mais políticas que possibilitam o auto-arquivo das publicações em repositórios institucionais, como também que existe todo um trabalho de sensibilização a percorrer, não só para os investigadores, como para a instituição e toda a sociedade. A produção de um conjunto de recomendações, que passam pela implementação de uma política institucional que incentive o auto-arquivo das publicações desenvolvidas no âmbito institucional no repositório, serve como mote para uma maior valorização da produção científica do INESC TEC.The progressive transformation of scientific practices, driven by the development of new Information and Communication Technologies (ICT), which made it possible to increase access to information, gradually moving towards an opening of the research cycle. This opening makes it possible to resolve, in the long term, the adversity that has been placed on researchers, which involves the existence of barriers that limit access conditions, whether geographical or financial. Although large commercial publishers predominantly dominate scientific production and subject it to the rules imposed by them, the Open Access movement whose first public declaration, the Budapest Declaration (BOAI), was in 2002, proposes significant changes that benefit the authors and the readers. This Movement has gained importance in Portugal since 2003, with the constitution of the first institutional repository at the national level. Institutional repositories have emerged as a tool for disseminating the scientific production of an institution to open the results of the research, both before publication and the preprint process and postprint, increase the visibility of work done by an investigator and his or her institution. The present study, which underwent an analysis of the copyright policies of INESC TEC most relevant scientific publications, allowed not only to realize that publishers are increasingly adopting policies that make it possible to self-archive publications in institutional repositories, all the work of raising awareness, not only for researchers but also for the institution and the whole society. The production of a set of recommendations, which go through the implementation of an institutional policy that encourages the self-archiving of the publications developed in the institutional scope in the repository, serves as a motto for a greater appreciation of the scientific production of INESC TEC

Skaalautuvat laskentamenetelmät suuren kapasiteetin sekvensointidatan analytiikkaan populaatiogenomiikassa

High-throughput sequencing (HTS) technologies have enabled rapid DNA sequencing of whole-genomes collected from various organisms and environments, including human tissues, plants, soil, water, and air. As a result, sequencing data volumes have grown by several orders of magnitude, and the number of assembled whole-genomes is increasing rapidly as well. This whole-genome sequencing (WGS) data has revealed the genetic variation in humans and other species, and advanced various fields from human and microbial genomics to drug design and personalized medicine. The amount of sequencing data has almost doubled every six months, creating new possibilities but also big data challenges in genomics. Diverse methods used in modern computational biology require a vast amount of computational power, and advances in HTS technology are even widening the gap between the analysis input data and the analysis outcome. Currently, many of the existing genomic analysis tools, algorithms, and pipelines are not fully exploiting the power of distributed and high-performance computing, which in turn limits the analysis throughput and restrains the deployment of the applications to clinical practice in the long run. Thus, the relevance of harnessing distributed and cloud computing in bioinformatics is more significant than ever before. Besides, efficient data compression and storage methods for genomic data processing and retrieval integrated with conventional bioinformatics tools are essential. These vast datasets have to be stored and structured in formats that can be managed, processed, searched, and analyzed efficiently in distributed systems. Genomic data contain repetitive sequences, which is one key property in developing efficient compression algorithms to alleviate the data storage burden. Moreover, indexing compressed sequences appropriately for bioinformatics tools, such as read aligners, offers direct sequence search and alignment capabilities with compressed indexes. Relative Lempel-Ziv (RLZ) has been found to be an efficient compression method for repetitive genomes that complies with the data-parallel computing approach. RLZ has recently been used to build hybrid-indexes compatible with read aligners, and we focus on extending it with distributed computing. Data structures found in genomic data formats have properties suitable for parallelizing routine bioinformatics methods, e.g., sequence matching, read alignment, genome assembly, genotype imputation, and variant calling. Compressed indexing fused with the routine bioinformatics methods and data-parallel computing seems a promising approach to building population-scale genome analysis pipelines. Various data decomposition and transformation strategies are studied for optimizing data-parallel computing performance when such routine bioinformatics methods are executed in a complex pipeline. These novel distributed methods are studied in this dissertation and demonstrated in a generalized scalable bioinformatics analysis pipeline design. The dissertation starts from the main concepts of genomics and DNA sequencing technologies and builds routine bioinformatics methods on the principles of distributed and parallel computing. This dissertation advances towards designing fully distributed and scalable bioinformatics pipelines focusing on population genomic problems where the input data sets are vast and the analysis results are hard to achieve with conventional computing. Finally, the methods studied are applied in scalable population genomics applications using real WGS data and experimented with in a high performance computing cluster. The experiments include mining virus sequences from human metagenomes, imputing genotypes from large-scale human populations, sequence alignment with compressed pan-genomic indexes, and assembling reference genomes for pan-genomic variant calling.Suuren kapasiteetin sekvensointimenetelmät (High-Throughput Sequencing, HTS) ovat mahdollistaneet kokonaisten genomien nopean ja huokean sekvensoinnin eri organismeista ja ympäristöistä, mukaan lukien kudos-, maaperä-, vesistö- ja ilmastonäytteet. Tämän seurauksena sekvensointidatan ja koostettujen kokogenomien määrät ovat kasvaneet nopeasti. Kokogenomin sekvensointi on lisännyt ihmisen ja muiden lajien geneettisen perimän tietämystä ja edistänyt eri tieteenaloja ympäristötieteistä lääkesuunnitteluun ja yksilölliseen lääketieteeseen. Sekvensointidatan määrä on lähes kaksinkertaistunut puolivuosittain, mikä on luonut uusia mahdollisuuksia läpimurtoihin, mutta myös suuria datankäsittelyn haasteita. Nykyaikaisessa laskennallisessa biologiassa käytettävät monimutkaiset analyysimenetelmät vaativat yhä enemmän laskentatehoa HTS-datan kasvaessa, ja siksi HTS-menetelmien edistyminen kasvattaa kuilua raakadatasta lopullisiin analyysituloksiin. Useat tällä hetkellä käytetyistä genomianalyysityökaluista, algoritmeista ja ohjelmistoista eivät hyödynnä hajautetun laskennan tehoa kokonaisvaltaisesti, mikä puolestaan ​​hidastaa uusimpien analyysitulosten saamista ja rajoittaa tieteellisten ohjelmistojen käyttöönottoa kliinisessä lääketieteessä pitkällä aikavälillä. Näin ollen hajautetun ja pilvilaskennan hyödyntämisen merkitys bioinformatiikassa on tärkeämpää kuin koskaan ennen. Genomitiedon suoraa hakua ja käsittelyä tukevat pakkaus- ja tallennusmenetelmät mahdollistavat nopean ja tilatehokkaan genomianalytiikan. Uusia hajautettuihin järjestelmiin soveltuvia tietorakenteita tarvitaan, jotta näitä suuria datamääriä voidaan hallita, käsitellä, hakea ja analysoida tehokkaasti. Genomidata sisältää runsaasti toistuvia sekvenssejä, mikä on yksi keskeinen ominaisuus kehitettäessä tehokkaita pakkausalgoritmeja tiedontallennustaakkaa ja analysointia keventämään. Lisäksi pakattujen sekvenssien indeksointi yhdistettynä sekvenssilinjausmenetelmiin mahdollistaa sekvenssien satunnaishaun ja suoran linjauksen pakattuihin sekvensseihin. Relative Lempel-Ziv (RLZ) pakkausmenetelmä on todettu tehokkaaksi toistuville genomisekvensseille rinnakkaislaskentaa hyödyntäen. RLZ-menetelmää on viime aikoina sovellettu sekvenssilinjaukseen yhteensopiviin hybridi-indekseihin, joita tässä työssä on nopeutettu hajautetulla laskennalla. Genomiikan dataformaateista löytyvillä tietorakenteilla on ominaisuuksia, jotka soveltuvat hajautettuun sekvenssihakuun, sekvenssilinjaukseen, genomien koostamiseen, genotyyppien imputointiin ja varianttien havaitsemiseen. Pakattu indeksointi sovellettuna hajautetulla laskennalla tehostettuihin menetelmiin vaikuttaa lupaavalta lähestymistavalta populaatiogenomiikan analyysiohjelmistojen mukauttamiseksi suuriin datamääriin. Erilaisia ​​tiedon osittamis- ja muunnosstrategioita hyödynnetään suorituskyvyn tehostamiseen monivaiheisessa hajautetussa genomidatan prosessoinnissa. Näitä uusia skaalautuvia hajautettuja laskentamenetelmiä tutkitaan tässä väitöskirjassa ja demonstroidaan yleisluontoisella bioinformatiikan analyysiohjelmiston arkkitehtuurilla. Tässä työssä johdatellaan genomiikan ja DNA-sekvensointitekniikoiden peruskäsitteisiin ja esitellään rutiininomaisia ​​bioinformatiikan menetelmiä perustuen hajautetun ja rinnakkaislaskennan periaatteille. Väitöskirjassa edetään kohti täysin hajautettujen ja skaalautuvien bioinformatiikan ohjelmistojen suunnittelua keskittyen populaatiogenomiikan ongelmiin, joissa syötedatan määrät ovat suuria ja analyysitulosten saavuttaminen on hidasta tai jopa mahdotonta tavanomaisella laskennalla. Lopuksi tutkittuja menetelmiä sovelletaan tässä työssä kehitettyihin skaalautuviin populaatiogenomiikan sovelluksiin, joita koestetaan kokogenomidatalla supertietokoneen laskentaklusterissa. Kokeet sisältävät virussekvenssien louhintaa ihmisten metagenominäytteistä, genotyyppien täydentämistä (imputointia) suurista ihmispopulaatioista ja pan-genomisen indeksin pakkaamista sekvenssilinjauksen nopeuttamista varten. Lisäksi pakattua pan-genomia kokeillaan referenssigenomin koostamiseen populaatioon perustuvien varianttien havaitsemista varten

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Towards a Common Software/Hardware Methodology for Future Advanced Driver Assistance Systems

The European research project DESERVE (DEvelopment platform for Safe and Efficient dRiVE, 2012-2015) had the aim of designing and developing a platform tool to cope with the continuously increasing complexity and the simultaneous need to reduce cost for future embedded Advanced Driver Assistance Systems (ADAS). For this purpose, the DESERVE platform profits from cross-domain software reuse, standardization of automotive software component interfaces, and easy but safety-compliant integration of heterogeneous modules. This enables the development of a new generation of ADAS applications, which challengingly combine different functions, sensors, actuators, hardware platforms, and Human Machine Interfaces (HMI). This book presents the different results of the DESERVE project concerning the ADAS development platform, test case functions, and validation and evaluation of different approaches. The reader is invited to substantiate the content of this book with the deliverables published during the DESERVE project. Technical topics discussed in this book include:Modern ADAS development platforms;Design space exploration;Driving modelling;Video-based and Radar-based ADAS functions;HMI for ADAS;Vehicle-hardware-in-the-loop validation system

Towards a Common Software/Hardware Methodology for Future Advanced Driver Assistance Systems

The European research project DESERVE (DEvelopment platform for Safe and Efficient dRiVE, 2012-2015) had the aim of designing and developing a platform tool to cope with the continuously increasing complexity and the simultaneous need to reduce cost for future embedded Advanced Driver Assistance Systems (ADAS). For this purpose, the DESERVE platform profits from cross-domain software reuse, standardization of automotive software component interfaces, and easy but safety-compliant integration of heterogeneous modules. This enables the development of a new generation of ADAS applications, which challengingly combine different functions, sensors, actuators, hardware platforms, and Human Machine Interfaces (HMI). This book presents the different results of the DESERVE project concerning the ADAS development platform, test case functions, and validation and evaluation of different approaches. The reader is invited to substantiate the content of this book with the deliverables published during the DESERVE project. Technical topics discussed in this book include:Modern ADAS development platforms;Design space exploration;Driving modelling;Video-based and Radar-based ADAS functions;HMI for ADAS;Vehicle-hardware-in-the-loop validation system

Topical Workshop on Electronics for Particle Physics

The purpose of the workshop was to present results and original concepts for electronics research and development relevant to particle physics experiments as well as accelerator and beam instrumentation at future facilities; to review the status of electronics for the LHC experiments; to identify and encourage common efforts for the development of electronics; and to promote information exchange and collaboration in the relevant engineering and physics communities