Language complexity of rotations and Sturmian sequences

AbstractGiven a rotation of the circle, we study the complexity of formal languages that are generated by the itineraries of interval covers. These languages are regular iff the rotation is rational. In the case of irrational rotations, our study reduces to that of the language complexity of the corresponding Sturmian sequences. We show that for a large class of irrationals, including e, all quadratic numbers and more generally all Hurwitz numbers, the corresponding languages can be recognized by a nondeterministic Turing machine in linear time (in other words, belongs to NLIN)

Energy-Efficient and Reliable Computing in Dark Silicon Era

Dark silicon denotes the phenomenon that, due to thermal and power constraints, the fraction of transistors that can operate at full frequency is decreasing in each technology generation. Moore’s law and Dennard scaling had been backed and coupled appropriately for five decades to bring commensurate exponential performance via single core and later muti-core design. However, recalculating Dennard scaling for recent small technology sizes shows that current ongoing multi-core growth is demanding exponential thermal design power to achieve linear performance increase. This process hits a power wall where raises the amount of dark or dim silicon on future multi/many-core chips more and more. Furthermore, from another perspective, by increasing the number of transistors on the area of a single chip and susceptibility to internal defects alongside aging phenomena, which also is exacerbated by high chip thermal density, monitoring and managing the chip reliability before and after its activation is becoming a necessity. The proposed approaches and experimental investigations in this thesis focus on two main tracks: 1) power awareness and 2) reliability awareness in dark silicon era, where later these two tracks will combine together. In the first track, the main goal is to increase the level of returns in terms of main important features in chip design, such as performance and throughput, while maximum power limit is honored. In fact, we show that by managing the power while having dark silicon, all the traditional benefits that could be achieved by proceeding in Moore’s law can be also achieved in the dark silicon era, however, with a lower amount. Via the track of reliability awareness in dark silicon era, we show that dark silicon can be considered as an opportunity to be exploited for different instances of benefits, namely life-time increase and online testing. We discuss how dark silicon can be exploited to guarantee the system lifetime to be above a certain target value and, furthermore, how dark silicon can be exploited to apply low cost non-intrusive online testing on the cores. After the demonstration of power and reliability awareness while having dark silicon, two approaches will be discussed as the case study where the power and reliability awareness are combined together. The first approach demonstrates how chip reliability can be used as a supplementary metric for power-reliability management. While the second approach provides a trade-off between workload performance and system reliability by simultaneously honoring the given power budget and target reliability

Novel computational techniques for mapping and classifying Next-Generation Sequencing data

Since their emergence around 2006, Next-Generation Sequencing technologies have been revolutionizing biological and medical research. Quickly obtaining an extensive amount of short or long reads of DNA sequence from almost any biological sample enables detecting genomic variants, revealing the composition of species in a metagenome, deciphering cancer biology, decoding the evolution of living or extinct species, or understanding human migration patterns and human history in general. The pace at which the throughput of sequencing technologies is increasing surpasses the growth of storage and computer capacities, which creates new computational challenges in NGS data processing. In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved. However, the vast majority of mappers follow the same paradigm and only little attention has been paid to non-standard mapping approaches. Here, we propound the so-called dynamic mapping that we show to significantly improve the resulting alignments compared to traditional mapping approaches. Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads. We provide the first comprehensive overview of this method and demonstrate its qualities using Dynamic Mapping Simulator, a pipeline that compares various dynamic mapping scenarios to static mapping and iterative referencing. An important component of a dynamic mapper is an online consensus caller, i.e., a program collecting alignment statistics and guiding updates of the reference in the online fashion. We provide Ococo, the first online consensus caller that implements a smart statistics for individual genomic positions using compact bit counters. Beyond its application to dynamic mapping, Ococo can be employed as an online SNP caller in various analysis pipelines, enabling SNP calling from a stream without saving the alignments on disk. Metagenomic classification of NGS reads is another major topic studied in the thesis. Having a database with thousands of reference genomes placed on a taxonomic tree, the task is to rapidly assign a huge amount of NGS reads to tree nodes, and possibly estimate the relative abundance of involved species. In this thesis, we propose improved computational techniques for this task. In a series of experiments, we show that spaced seeds consistently improve the classification accuracy. We provide Seed-Kraken, a spaced seed extension of Kraken, the most popular classifier at present. Furthermore, we suggest ProPhyle, a new indexing strategy based on a BWT-index, obtaining a much smaller and more informative index compared to Kraken. We provide a modified version of BWA that improves the BWT-index for a quick k-mer look-up

Automatic Pain Assessment by Learning from Multiple Biopotentials

Kivun täsmällinen arviointi on tärkeää kivunhallinnassa, erityisesti sairaan- hoitoa vaativille ipupotilaille. Kipu on subjektiivista, sillä se ei ole pelkästään aistituntemus, vaan siihen saattaa liittyä myös tunnekokemuksia. Tällöin itsearviointiin perustuvat kipuasteikot ovat tärkein työkalu, niin auan kun potilas pystyy kokemuksensa arvioimaan. Arviointi on kuitenkin haasteellista potilailla, jotka eivät itse pysty kertomaan kivustaan. Kliinisessä hoito- työssä kipua pyritään objektiivisesti arvioimaan esimerkiksi havainnoimalla fysiologisia muuttujia kuten sykettä ja käyttäytymistä esimerkiksi potilaan kasvonilmeiden perusteella. Tutkimuksen päätavoitteena on automatisoida arviointiprosessi hyödyntämällä koneoppimismenetelmiä yhdessä biosignaalien prosessointnin kanssa. Tavoitteen saavuttamiseksi mitattiin autonomista keskushermoston toimintaa kuvastavia biopotentiaaleja: sydänsähkökäyrää, galvaanista ihoreaktiota ja kasvolihasliikkeitä mittaavaa lihassähkökäyrää. Mittaukset tehtiin terveillä vapaaehtoisilla, joille aiheutettiin kokeellista kipuärsykettä. Järestelmän kehittämiseen tarvittavaa tietokantaa varten rakennettiin biopotentiaaleja keräävä Internet of Things -pohjainen tallennusjärjestelmä. Koostetun tietokannan avulla kehitettiin biosignaaleille prosessointimenetelmä jatku- vaan kivun arviointiin. Signaaleista eroteltiin piirteitä sekuntitasoon mukautetuilla aikaikkunoilla. Piirteet visualisoitiin ja tarkasteltiin eri luokittelijoilla kivun ja kiputason tunnistamiseksi. Parhailla luokittelumenetelmillä saavutettiin kivuntunnistukseen 90% herkkyyskyky (sensitivity) ja 84% erottelukyky (specificity) ja kivun voimakkuuden arviointiin 62,5% tarkkuus (accuracy). Tulokset vahvistavat kyseisen käsittelytavan käyttökelpoisuuden erityis- esti tunnistettaessa kipua yksittäisessä arviointi-ikkunassa. Tutkimus vahvistaa biopotentiaalien avulla kehitettävän automatisoidun kivun arvioinnin toteutettavuuden kokeellisella kivulla, rohkaisten etenemään todellisen kivun tutkimiseen samoilla menetelmillä. Menetelmää kehitettäessä suoritettiin lisäksi vertailua ja yhteenvetoa automaattiseen kivuntunnistukseen kehitettyjen eri tutkimusten välisistä samankaltaisuuksista ja eroista. Tarkastelussa löytyi signaalien eroavaisuuksien lisäksi tutkimusmuotojen aiheuttamaa eroa arviointitavoitteisiin, mikä hankaloitti tutkimusten vertailua. Lisäksi pohdit- tiin mitkä perinteisten prosessointitapojen osiot rajoittavat tai edistävät ennustekykyä ja miten, sekä tuoko optimointi läpimurtoa järjestelmän näkökulmasta.Accurate pain assessment plays an important role in proper pain management, especially among hospitalized people experience acute pain. Pain is subjective in nature which is not only a sensory feeling but could also combine affective factors. Therefore self-report pain scales are the main assessment tools as long as patients are able to self-report. However, it remains a challenge to assess the pain from the patients who cannot self-report. In clinical practice, physiological parameters like heart rate and pain behaviors including facial expressions are observed as empirical references to infer pain objectively. The main aim of this study is to automate such process by leveraging machine learning methods and biosignal processing. To achieve this goal, biopotentials reflecting autonomic nervous system activities including electrocardiogram and galvanic skin response, and facial expressions measured with facial electromyograms were recorded from healthy volunteers undergoing experimental pain stimulus. IoT-enabled biopotential acquisition systems were developed to build the database aiming at providing compact and wearable solutions. Using the database, a biosignal processing flow was developed for continuous pain estimation. Signal features were extracted with customized time window lengths and updated every second. The extracted features were visualized and fed into multiple classifiers trained to estimate the presence of pain and pain intensity separately. Among the tested classifiers, the best pain presence estimating sensitivity achieved was 90% (specificity 84%) and the best pain intensity estimation accuracy achieved was 62.5%. The results show the validity of the proposed processing flow, especially in pain presence estimation at window level. This study adds one more piece of evidence on the feasibility of developing an automatic pain assessment tool from biopotentials, thus providing the confidence to move forward to real pain cases. In addition to the method development, the similarities and differences between automatic pain assessment studies were compared and summarized. It was found that in addition to the diversity of signals, the estimation goals also differed as a result of different study designs which made cross dataset comparison challenging. We also tried to discuss which parts in the classical processing flow would limit or boost the prediction performance and whether optimization can bring a breakthrough from the system’s perspective

On Security and Privacy for Networked Information Society : Observations and Solutions for Security Engineering and Trust Building in Advanced Societal Processes

Our society has developed into a networked information society, in which all aspects of human life are interconnected via the Internet — the backbone through which a significant part of communications traffic is routed. This makes the Internet arguably the most important piece of critical infrastructure in the world. Securing Internet communications for everyone using it is extremely important, as the continuing growth of the networked information society relies upon fast, reliable and secure communications. A prominent threat to the security and privacy of Internet users is mass surveillance of Internet communications. The methods and tools used to implement mass surveillance capabilities on the Internet pose a danger to the security of all communications, not just the intended targets. When we continue to further build the networked information upon the unreliable foundation of the Internet we encounter increasingly complex problems,which are the main focus of this dissertation. As the reliance on communication technology grows in a society, so does the importance of information security. At this stage, information security issues become separated from the purely technological domain and begin to affect everyone in society. The approach taken in this thesis is therefore both technical and socio-technical. The research presented in this PhD thesis builds security in to the networked information society and provides parameters for further development of a safe and secure networked information society. This is achieved by proposing improvements on a multitude of layers. In the technical domain we present an efficient design flow for secure embedded devices that use cryptographic primitives in a resource-constrained environment, examine and analyze threats to biometric passport and electronic voting systems, observe techniques used to conduct mass Internet surveillance, and analyze the security of Finnish web user passwords. In the socio-technical domain we examine surveillance and how it affects the citizens of a networked information society, study methods for delivering efficient security education, examine what is essential security knowledge for citizens, advocate mastery over surveillance data by the targeted citizens in the networked information society, and examine the concept of forced trust that permeates all topics examined in this work.Yhteiskunta, jossa elämme, on muovautunut teknologian kehityksen myötä todelliseksi tietoyhteiskunnaksi. Monet verkottuneen tietoyhteiskunnan osa-alueet ovat kokeneet muutoksen tämän kehityksen seurauksena. Tämän muutoksen keskiössä on Internet: maailmanlaajuinen tietoverkko, joka mahdollistaa verkottuneiden laitteiden keskenäisen viestinnän ennennäkemättömässä mittakaavassa. Internet on muovautunut ehkä keskeisimmäksi osaksi globaalia viestintäinfrastruktuuria, ja siksi myös globaalin viestinnän turvaaminen korostuu tulevaisuudessa yhä enemmän. Verkottuneen tietoyhteiskunnan kasvu ja kehitys edellyttävät vakaan, turvallisen ja nopean viestintäjärjestelmän olemassaoloa. Laajamittainen tietoverkkojen joukkovalvonta muodostaa merkittävän uhan tämän järjestelmän vakaudelle ja turvallisuudelle. Verkkovalvonnan toteuttamiseen käytetyt menetelmät ja työkalut eivät vain anna mahdollisuutta tarkastella valvonnan kohteena olevaa viestiliikennettä, vaan myös vaarantavat kaiken Internet-liikenteen ja siitä riippuvaisen toiminnan turvallisuuden. Kun verkottunutta tietoyhteiskuntaa rakennetaan tämän kaltaisia valuvikoja ja haavoittuvuuksia sisältävän järjestelmän varaan, keskeinen uhkatekijä on, että yhteiskunnan ydintoiminnot ovat alttiina ulkopuoliselle vaikuttamiselle. Näiden uhkatekijöiden ja niiden taustalla vaikuttavien mekanismien tarkastelu on tämän väitöskirjatyön keskiössä. Koska työssä on teknisen sisällön lisäksi vahva yhteiskunnallinen elementti, tarkastellaan tiukan teknisen tarkastelun sijaan aihepiirä laajemmin myös yhteiskunnallisesta näkökulmasta. Tässä väitöskirjassa pyritään rakentamaan kokonaiskuvaa verkottuneen tietoyhteiskunnan turvallisuuteen, toimintaan ja vakauteen vaikuttavista tekijöistä, sekä tuomaan esiin uusia ratkaisuja ja avauksia eri näkökulmista. Työn tavoitteena on osaltaan mahdollistaa entistä turvallisemman verkottuneen tietoyhteiskunnan rakentaminen tulevaisuudessa. Teknisestä näkökulmasta työssä esitetään suunnitteluvuo kryptografisia primitiivejä tehokkaasti hyödyntäville rajallisen laskentatehon sulautetuviiille järjestelmille, analysoidaan biometrisiin passeihin, kansainväliseen passijärjestelmään, sekä sähköiseen äänestykseen kohdistuvia uhkia, tarkastellaan joukkovalvontaan käytettyjen tekniikoiden toimintaperiaatteita ja niiden aiheuttamia uhkia, sekä tutkitaan suomalaisten Internet-käyttäjien salasanatottumuksia verkkosovelluksissa. Teknis-yhteiskunnallisesta näkökulmasta työssä tarkastellaan valvonnan teoriaa ja perehdytään siihen, miten valvonta vaikuttaa verkottuneen tietoyhteiskunnan kansalaisiin. Lisäksi kehitetään menetelmiä parempaan tietoturvaopetukseen kaikilla koulutusasteilla, määritellään keskeiset tietoturvatietouden käsitteet, tarkastellaan mahdollisuutta soveltaa tiedon herruuden periaatetta verkottuneen tietoyhteiskunnan kansalaisistaan keräämän tiedon hallintaan ja käyttöön, sekä tutkitaan luottamuksen merkitystä yhteiskunnan ydintoimintojen turvallisuudelle ja toiminnalle, keskittyen erityisesti pakotetun luottamuksen vaikutuksiin

Design for energy-efficient and reliable fog-assisted healthcare IoT systems

Cardiovascular disease and diabetes are two of the most dangerous diseases as they are the leading causes of death in all ages. Unfortunately, they cannot be completely cured with the current knowledge and existing technologies. However, they can be effectively managed by applying methods of continuous health monitoring. Nonetheless, it is difficult to achieve a high quality of healthcare with the current health monitoring systems which often have several limitations such as non-mobility support, energy inefficiency, and an insufficiency of advanced services. Therefore, this thesis presents a Fog computing approach focusing on four main tracks, and proposes it as a solution to the existing limitations. In the first track, the main goal is to introduce Fog computing and Fog services into remote health monitoring systems in order to enhance the quality of healthcare. In the second track, a Fog approach providing mobility support in a real-time health monitoring IoT system is proposed. The handover mechanism run by Fog-assisted smart gateways helps to maintain the connection between sensor nodes and the gateways with a minimized latency. Results show that the handover latency of the proposed Fog approach is 10%-50% less than other state-of-the-art mobility support approaches. In the third track, the designs of four energy-efficient health monitoring IoT systems are discussed and developed. Each energy-efficient system and its sensor nodes are designed to serve a specific purpose such as glucose monitoring, ECG monitoring, or fall detection; with the exception of the fourth system which is an advanced and combined system for simultaneously monitoring many diseases such as diabetes and cardiovascular disease. Results show that these sensor nodes can continuously work, depending on the application, up to 70-155 hours when using a 1000 mAh lithium battery. The fourth track mentioned above, provides a Fog-assisted remote health monitoring IoT system for diabetic patients with cardiovascular disease. Via several proposed algorithms such as QT interval extraction, activity status categorization, and fall detection algorithms, the system can process data and detect abnormalities in real-time. Results show that the proposed system using Fog services is a promising approach for improving the treatment of diabetic patients with cardiovascular disease

The Use of digital games to enhance the physical exercise activity of the elderly : a case of Finland

According to the World Health Organization (WHO), population ageing is a global phenomenon, which brings both challenges and opportunities for society. The current longer expected lifespan can create opportunities for the elderly to contribute in many ways to their families and communities. However, it greatly depends on their quality of life, which is affected by many factors, including physical and functional health, social well-being, and cognitive abilities. The WHO (2012) states that physical health is one of the indicators for the elderly’s quality of life, and it declines with increasing age. Participation in regular physical exercises can help the elderly improve their physical and mental health, and this has been aided by the use of modern technologies to promote the elderly’s physical and functional health. Of these latest technologies, digital games have shown promise to improve and enhance the elderly’s physical activities through fun and engaging gameplay. The literature highlights that some commercial games in the market (e.g. Microsoft Kinect- Sports and Nintendo Wii Sports games) have the potential to improve the elderly’s physical health such as gait, balance, and fall prevention. However, researchers argue that these commercial games are not designed specifically for the elderly and their physical exercise activities. They state that most commercial games are not user-friendly for the elderly whose functional and physical abilities are limited due to their advanced years. The literature points out that more studies need to be undertaken to understand the usability and usefulness of digital games for physical exercise activities so that game designers can create elderly-friendly digital games in the future. In Finland, the government has been focusing on promoting healthy ageing and increasing home care services for the elderly. In recent years, Finnish researchers have used digital games to promote older Finns’ healthy and active ageing. The existing literature, whilst showing the potential of digital games for elderly Finns’ physical health, also acknowledges further research is needed particularly in the context of Finland. Thus, in this study, we aimed at investigating digital games to specifically assess their applications for older Finns’ physical activities, focusing on the quality of users’ experiences, and their reported ease of use and perceived usefulness. We used the mixed methods approach, which applies both qualitative and quantitative research methods. The study design included four stages: requirements gathering, analysis and design, prototyping, and evaluation. Firstly, we conducted pre-studies to elicit users’ requirements. This was followed by the analysis of the resulting data to identify trends and patterns, which fuelled ideas in the brainstorming game design and development phases. The final product was a digital game-based physical exercise called the Skiing Game. We then evaluated the Skiing Game in Finland with 21 elderly Finns (M=7, F=14, Average Age =76). By using questionnaires, observation, and interviews, we investigated user experiences, focusing on the game’s usability, and usefulness for enhancing the physical activity and wellbeing of the elderly. We also conducted a comparative test of the Skiing Game in Japan with 24 elderly Japanese participants (M=12, F=12, Average Age = 72) to further understand non-Finnish elderly users’ experiences. The findings from the usability study of the Skiing Game in Finland demonstrated that elderly Finns had a positive experience in the gameplay, and their motivation was noticeably high. It also confirmed that elderly Finns have a genuine interest in digital game-based exercises and strong intentions to play digital games as a form of physical exercise in the future. Although prior to the study most of them had negative views and misconceptions about digital games, after the gameplay their attitudes were decidedly positive. They acknowledged that whilst playing digital games could be an alternative way of exercising for them their use would primarily be when they don’t have access to their usual non-digital physical exercise. The Japanese usability of the Skiing Game showed that the elderly Japanese people also had positive user experiences in playing digital games, and also intend to use them in the future. Similarly, after playing the game they reported that their attitudes towards digital games become positive, and indicated playing digital games could be an alternative way of exercising. Although the comparison of the two studies suggests that the elderly Finns had relatively more positive experiences whilst playing the Skiing Game, compared to their Japanese counterparts, in general, both groups had a positive experience in the gameplay and showed interest in digital games as an alternative exercise. Based on the usability lessons learned from these two studies, recommendations for practitioners and designers regarding improvements in game design and development are made in this report. Implementing these modifications into future designs and further development of digital games for the elderly will improve their commercial viability and user uptake. The findings from this study can provide valuable insights, particularly for Finnish policymakers and healthcare practitioners who are keen to introduce digital games into the aged-care sector in Finland. The studies have also provided valuable insights into the optimal methods for introducing Finnish digital games to international markets, in particular, digital games tailored specifically for the physical exercise needs and motivations of the elderly. By taking into consideration the limitations of the study, we provide our future studies and further improvements of the game to be conducted