Kahden merkkijonon pisimmän yhteisen alijonon ongelma ja sen ratkaiseminen

Tämä tutkielma kuuluu merkkijonoalgoritmiikan piiriin. Merkkijono S on merkkijonojen X[1..m] ja Y[1..n] yhteinen alijono, mikäli se voidaan muodostaa poistamalla X:stä 0..m ja Y:stä 0..n kappaletta merkkejä mielivaltaisista paikoista. Jos yksikään X:n ja Y:n yhteinen alijono ei ole S:ää pidempi, sanotaan, että S on X:n ja Y:n pisin yhteinen alijono (lyh. PYA). Tässä työssä keskitytään kahden merkkijonon PYAn ratkaisemiseen, mutta ongelma on yleistettävissä myös useammalle jonolle. PYA-ongelmalle on sovelluskohteita – paitsi tietojenkäsittelytieteen niin myös bioinformatiikan osa-alueilla. Tunnetuimpia niistä ovat tekstin ja kuvien tiivistäminen, tiedostojen versionhallinta, hahmontunnistus sekä DNA- ja proteiiniketjujen rakennetta vertaileva tutkimus. Ongelman ratkaisemisen tekee hankalaksi ratkaisualgoritmien riippuvuus syötejonojen useista eri parametreista. Näitä ovat syötejonojen pituuden lisäksi mm. syöttöaakkoston koko, syötteiden merkkijakauma, PYAn suhteellinen osuus lyhyemmän syötejonon pituudesta ja täsmäävien merkkiparien lukumäärä. Täten on vaikeaa kehittää algoritmia, joka toimisi tehokkaasti kaikille ongelman esiintymille. Tutkielman on määrä toimia yhtäältä käsikirjana, jossa esitellään ongelman peruskäsitteiden kuvauksen jälkeen jo aikaisemmin kehitettyjä tarkkoja PYAalgoritmeja. Niiden tarkastelu on ryhmitelty algoritmin toimintamallin mukaan joko rivi, korkeuskäyrä tai diagonaali kerrallaan sekä monisuuntaisesti prosessoiviin. Tarkkojen menetelmien lisäksi esitellään PYAn pituuden ylä- tai alarajan laskevia heuristisia menetelmiä, joiden laskemia tuloksia voidaan hyödyntää joko sellaisinaan tai ohjaamaan tarkan algoritmin suoritusta. Tämä osuus perustuu tutkimusryhmämme julkaisemiin artikkeleihin. Niissä käsitellään ensimmäistä kertaa heuristiikoilla tehostettuja tarkkoja menetelmiä. Toisaalta työ sisältää laajahkon empiirisen tutkimusosuuden, jonka tavoitteena on ollut tehostaa olemassa olevien tarkkojen algoritmien ajoaikaa ja muistinkäyttöä. Kyseiseen tavoitteeseen on pyritty ohjelmointiteknisesti esittelemällä algoritmien toimintamallia hyvin tukevia tietorakenteita ja rajoittamalla algoritmien suorittamaa tuloksetonta laskentaa parantamalla niiden kykyä havainnoida suorituksen aikana saavutettuja välituloksia ja hyödyntää niitä. Tutkielman johtopäätöksinä voidaan yleisesti todeta tarkkojen PYA-algoritmien heuristisen esiprosessoinnin lähes systemaattisesti pienentävän niiden suoritusaikaa ja erityisesti muistintarvetta. Lisäksi algoritmin käyttämällä tietorakenteella on ratkaiseva vaikutus laskennan tehokkuuteen: mitä paikallisempia haku- ja päivitysoperaatiot ovat, sitä tehokkaampaa algoritmin suorittama laskenta on.

Memory studies - kohti tutkimusalueen vakiintumista

Teemanumero 2/2011: Media ja menneisyys.

Evaluation of Bubble Formation and Break Up in Suppression Pools by Using Pattern Recognition Methods

During a possible loss of coolant accident in BWRs, a large amount of steam will be released from the reactor pressure vessel to the suppression pool. Steam will be condensed into the suppression pool causing dynamic and structural loads to the pool. The formation and break up of bubbles can be measured by visual observation using a suitable pattern recognition algorithm. The aim of this study was to improve the preliminary pattern recognition algorithm, developed by Vesa Tanskanen in his doctoral dissertation, by using MATLAB. Video material from the PPOOLEX test facility, recorded during thermal stratification and mixing experiments, was used as a reference in the development of the algorithm. The developed algorithm consists of two parts: the pattern recognition of the bubbles and the analysis of recognized bubble images. The bubble recognition works well, but some errors will appear due to the complex structure of the pool. The results of the image analysis were reasonable. The volume and the surface area of the bubbles were not evaluated. Chugging frequencies calculated by using FFT fitted well into the results of oscillation frequencies measured in the experiments. The pattern recognition algorithm works in the conditions it is designed for. If the measurement configuration will be changed, some modifications have to be done. Numerous improvements are proposed for the future 3D equipment.

Lectio praecursoria : Systems between information and knowledge : in a memory management model of an extended enterprise

VTT Jouni Meriluodon valtio-opin alaan kuuluva väitöskirja Systems between information and knowledge : in a memory management model of an extended enterprise tarkastettiin 21.6.2011 Helsingin yliopistossa.

Memory Effects in the Dynamics of Open Quantum Systems

In this Thesis various aspects of memory effects in the dynamics of open quantum systems are studied. We develop a general theoretical framework for open quantum systems beyond the Markov approximation which allows us to investigate different sources of memory effects and to develop methods for harnessing them in order to realise controllable open quantum systems. In the first part of the Thesis a characterisation of non-Markovian dynamics in terms of information flow is developed and applied to study different sources of memory effects. Namely, we study nonlocal memory effects which arise due to initial correlations between two local environments and further the memory effects induced by initial correlations between the open system and the environment. The last part focuses on describing two all-optical experiment in which through selective preparation of the initial environment states the information flow between the system and the environment can be controlled. In the first experiment the system is driven from the Markovian to the non- Markovian regime and the degree of non-Markovianity is determined. In the second experiment we observe the nonlocal nature of the memory effects and provide a novel method to experimentally quantify frequency correlations in photonic environments via polarisation measurements.

Neurocognitive changes in early-stage Parkinson's disease : functional and structural brain correlates of memory and verbal functions

Resultaten påvisade små, men mätbara försämringar i minnes- och verbal förmåga hos personer som haft Parkinsons sjukdom under tre år. Jämfört med en kontrollgrupp uppvisade Parkinsonpatienter avvikande responser i hjärnans elektriska aktivitet under en korttidsminnesuppgift, och de presterade även sämre i olika typer av andra minnesuppgifter. Försämring i en specifik typ av minnesuppgift korrelerade med förminskad volym i höger hjärnhalva. Samband hittades också mellan sämre verbal förmåga och förminskad volym i djupa hjärnstrukturer. Förminskad hjärnvolym har tidigare påvisats hos dementa patienter i senare sjukdomsstadier. Forskningsresultaten bidrar med ny kunskap om kognitiva symptom och deras neurala bakgrund vid Parkinsons sjukdom. De tyder också på att tidig kognitiv funktionsnedsättning kan identifieras, vilket kan bidra till utvecklingen av sjukdomens behandling. Parkinsons sjukdom är den näst vanligaste neurogeriatriska sjukdomen efter Alzheimers sjukdom. Symptomen uppstår som följd av förminskad produktion av hjärnans transmittorämne dopamin. Parkinsons sjukdom har traditionellt betraktats som en progressiv motorisk sjukdom. Ny forskning tyder på att multipla hjärnsystem skadas, vilket resulterar i att även tankeprocesser påverkas. 75-80% uppskattas insjukna i demens 10-15 år efter diagnos, men det kognitiva sjukdomsförloppet och orsaken till demenssymptomen är tillsvidare okänd. I Finland uppskattas ca 10-12 000 personer ha Parkinsons sjukdom, varav ca 3 000 uppskattas ha demens. ----------------------------------------------------------------------------------------------------------------------------------------------------- Tutkimuksessa todettiin lieviä muutoksia muisti- ja kielellisissä toiminnoissa alle kolme vuotta sairastaneilla Parkinson-potilailla. Potilailla havaittiin poikkeavia aivosähkötoiminnan vasteita lyhytkestoista muistia mittaavan tehtävän aikana. Potilaat suoriutuivat myös verrokkiryhmää heikommin useissa muistitehtävissä. Heikentynyt tahaton muisti liittyi pienempään aivokuoren harmaan aineen paikalliseen tilavuuteen. Heikompi kielellinen suoriutuminen liittyi pienempään harmaan aineen tilavuuteen aivojen syvissä rakenteissa. Pienentyneitä aivorakenteiden tilavuuksia on aiemmin todettu dementoituneilla Parkinson-potilailla sairauden myöhemmissä vaiheissa. Tutkimustulokset tuovat uutta tietoa Parkinsonin taudin kognitiivisista oireista ja niiden aivoperäisestä taustasta. Tulosten perusteella on mahdollista tunnistaa jo varhaisia kognitiivisia muutoksia, mikä voi mahdollistaa tehokkaamman hoidon kohdentamisen. Parkinsonin tauti on Alzheimerin taudin jälkeen toiseksi yleisin neurogeriatrinen sairaus. Oirekuva liittyy aivojen dopaminergisen järjestelmän rappeutumiseen. Perinteisesti liikehäiriösairaudeksi luokiteltu sairaus vaurioittaa lukuisia muita aivojärjestelmiä aiheuttaen muutoksia myös mm. ajattelutoiminnoissa. Pitkään sairastaneista 75–80 prosentilla esiintyy dementiaoireita, mutta oireiden syy ja kehityskaari tunnetaan toistaiseksi huonosti. Suomessa on arviolta 10–12 000 Parkinson-potilasta, joista noin 3 000 arvioidaan kärsivän dementiaoireista.

Spontaneous Focusing on Numerosity in the Development of Early Mathematical Skills

The aim of the present set of longitudinal studies was to explore 3-7-year-old children.s Spontaneous FOcusing on Numerosity (SFON) and its relation to early mathematical development. The specific goals were to capture in method and theory the distinct process by which children focus on numerosity as a part of their activities involving exact number recognition, and individual differences in this process that may be informative in the development of more complex number skills. Over the course of conducting the five studies, fifteen novel tasks were progressively developed for the SFON assessments. In the tasks, confounding effects of insufficient number recognition, verbal comprehension, other procedural skills as well as working memory capacity were aimed to be controlled. Furthermore, how children.s individual differences in SFON are related to their development of number sequence, subitizing-based enumeration, object counting and basic arithmetic skills was explored. The effect of social interaction on SFON was tested. Study I captured the first phase of the 3-year longitudinal study with 39 children. It was investigated whether there were differences in 3-year-old children.s tendency to focus on numerosity, and whether these differences were related to the children.s development of cardinality recognition skills from the age of 3 to 4 years. It was found that the two groups of children formed on the basis of their amount of SFON tendency at the age of 3 years differed in their development of recognising and producing small numbers. The children whose SFON tendency was very predominant developed faster in cardinality related skills from the age of 3 to 4 years than the children whose SFON tendency was not as predominant. Thus, children.s development in cardinality recognition skills is related to their SFON tendency. Studies II and III were conducted to investigate, firstly, children.s individual differences in SFON, and, secondly, whether children.s SFON is related to their counting development. Altogether nine tasks were designed for the assessments of spontaneous and guided focusing on numerosity. The longitudinal data of 39 children in Study II from the age of 3.5 to 6 years showed individual differences in SFON at the ages of 4, 5 and 6 years, as well as stability in children.s SFON across tasks used at different ages. The counting skills were assessed at the ages of 3.5, 5 and 6 years. Path analyses indicated a reciprocal tendency in the relationship between SFON and counting development. In Study III, these results on the individual differences in SFON tendency, the stability of SFON across different tasks and the relationship of SFON and mathematical skills were confirmed by a larger-scale cross-sectional study of 183 on average 6.5-year-old children (range 6;0-7;0 years). The significant amount of unique variance that SFON accounted for number sequence elaboration, object counting and basic arithmetic skills stayed statistically significant (partial correlations varying from .27 to .37) when the effects of non-verbal IQ and verbal comprehension were controlled. In addition, to confirm that the SFON tasks assess SFON tendency independently from enumeration skills, guided focusing tasks were used for children who had failed in SFON tasks. It was explored whether these children were able to proceed in similar tasks to SFON tasks once they were guided to focus on number. The results showed that these children.s poor performance in the SFON tasks was not caused by their deficiency in executing the tasks but on lacking focusing on numerosity. The longitudinal Study IV of 39 children aimed at increasing the knowledge of associations between children.s long-term SFON tendency, subitizing-based enumeration and verbal counting skills. Children were tested twice at the age of 4-5 years on their SFON, and once at the age of 5 on their subitizing-based enumeration, number sequence production, as well as on their skills for counting of objects. Results showed considerable stability in SFON tendency measured at different ages, and that there is a positive direct association between SFON and number sequence production. The association between SFON and object counting skills was significantly mediated by subitizing-based enumeration. These results indicate that the associations between the child.s SFON and sub-skills of verbal counting may differ on the basis of how significant a role understanding the cardinal meanings of number words plays in learning these skills. The specific goal of Study V was to investigate whether it is possible to enhance 3-year old children.s SFON tendency, and thus start children.s deliberate practice in early mathematical skills. Participants were 3-year-old children in Finnish day care. The SFON scores and cardinality-related skills of the experimental group of 17 children were compared to the corresponding results of the 17 children in the control group. The results show an experimental effect on SFON tendency and subsequent development in cardinality-related skills during the 6-month period from pretest to delayed posttest in the children with some initial SFON tendency in the experimental group. Social interaction has an effect on children.s SFON tendency. The results of the five studies assert that within a child.s existing mathematical competence, it is possible to distinguish a separate process, which refers to the child.s tendency to spontaneously focus on numerosity. Moreover, there are significant individual differences in children.s SFON at the age of 3-7 years. Moderate stability was found in this tendency across different tasks assessed both at the same and at different ages. Furthermore, SFON tendency is related to the development of early mathematical skills. Educational implications of the findings emphasise, first, the importance of regarding focusing on numerosity as a separate, essential process in the assessments of young children.s mathematical skills. Second, the substantial individual differences in SFON tendency during the childhood years suggest that uncovering and modeling this kind of mathematically meaningful perceiving of the surroundings and tasks could be an efficient tool for promoting young children.s mathematical development, and thus prevent later failures in learning mathematical skills. It is proposed to consider focusing on numerosity as one potential sub-process of activities involving exact number recognition in future studies.

Between Memory and Strategy: Media Discourse Analysis of an Industrial Shutdown

In 2006 UPM was able to gain a level of social legitimacy that allowed it to carry out one of the largest industrial restructuring programmes in Finnish industrial history, shut down major operations in Finland and still appear to be functioning in the interests of the nation as well as itself. This study considers and examines various contexts of this shutdown with the aim of demonstrating how profoundly mediated such organizational events are though they appear to be produced primarily through strategic company decisions. The study aims to examine the processes of mediation at two levels. At one level, through close analysis of press releases and newspaper reports in local and national newspapers, the study presents a discursive analysis of the Voikkaa case. The discursive analysis focuses on providing historical contexts for understanding why this organizational event was also an occasion for reimagining the past and future of the Finnish nation; spatial contexts for understanding the differing struggles over the meaning of the event nationally and regionally; and the temporal dynamics of the media reports. At another level, the study considers and refines methods for reading and analyzing mediation in organization studies. Bringing together recent research of media text–based legitimation studies, emerging research on organizational memory and organizational death and a Foucaultian analytics of power, this work suggests that organizational research needs to be less concerned with particular typologies and narratives of shutdowns, and more curious about the processes of mediation through which organizational events are imagined and remembered.

Semantic and fuzzy modelling for human behaviour recognition in smart spaces : a case study on ambient assisted living.

Human activity recognition in everyday environments is a critical, but challenging task in Ambient Intelligence applications to achieve proper Ambient Assisted Living, and key challenges still remain to be dealt with to realize robust methods. One of the major limitations of the Ambient Intelligence systems today is the lack of semantic models of those activities on the environment, so that the system can recognize the speci c activity being performed by the user(s) and act accordingly. In this context, this thesis addresses the general problem of knowledge representation in Smart Spaces. The main objective is to develop knowledge-based models, equipped with semantics to learn, infer and monitor human behaviours in Smart Spaces. Moreover, it is easy to recognize that some aspects of this problem have a high degree of uncertainty, and therefore, the developed models must be equipped with mechanisms to manage this type of information. A fuzzy ontology and a semantic hybrid system are presented to allow modelling and recognition of a set of complex real-life scenarios where vagueness and uncertainty are inherent to the human nature of the users that perform it. The handling of uncertain, incomplete and vague data (i.e., missing sensor readings and activity execution variations, since human behaviour is non-deterministic) is approached for the rst time through a fuzzy ontology validated on real-time settings within a hybrid data-driven and knowledgebased architecture. The semantics of activities, sub-activities and real-time object interaction are taken into consideration. The proposed framework consists of two main modules: the low-level sub-activity recognizer and the high-level activity recognizer. The rst module detects sub-activities (i.e., actions or basic activities) that take input data directly from a depth sensor (Kinect). The main contribution of this thesis tackles the second component of the hybrid system, which lays on top of the previous one, in a superior level of abstraction, and acquires the input data from the rst module's output, and executes ontological inference to provide users, activities and their in uence in the environment, with semantics. This component is thus knowledge-based, and a fuzzy ontology was designed to model the high-level activities. Since activity recognition requires context-awareness and the ability to discriminate among activities in di erent environments, the semantic framework allows for modelling common-sense knowledge in the form of a rule-based system that supports expressions close to natural language in the form of fuzzy linguistic labels. The framework advantages have been evaluated with a challenging and new public dataset, CAD-120, achieving an accuracy of 90.1% and 91.1% respectively for low and high-level activities. This entails an improvement over both, entirely data-driven approaches, and merely ontology-based approaches. As an added value, for the system to be su ciently simple and exible to be managed by non-expert users, and thus, facilitate the transfer of research to industry, a development framework composed by a programming toolbox, a hybrid crisp and fuzzy architecture, and graphical models to represent and con gure human behaviour in Smart Spaces, were developed in order to provide the framework with more usability in the nal application. As a result, human behaviour recognition can help assisting people with special needs such as in healthcare, independent elderly living, in remote rehabilitation monitoring, industrial process guideline control, and many other cases. This thesis shows use cases in these areas.

Collective Memory Embodied in Poetry as Poison. The Mnemonic Role of Romantic Poets Discussed on the Basis of Adam Mickiewicz’ Konrad Wallenrod and Forefathers (Part III)

This thesis constitutes an interdisciplinary approach to the Polish Romanticism combining literature studies with memory studies, nationalism research and psychoanalysis. This phenomenon-based study attempts to answer the question, how the Polish national poet Adam Mickiewicz (1798–1855) – or more exactly the implied authors in his works – perceived the role of poetry in mnemonic terms and how it changes in course of time. Consequently, ‘memory in literature’ (Astrin Erll and Ansger Nünning) is discussed here. Two pieces of writing by Mickiewicz – Konrad Wallenrod [1828] and the third part of Forefathers [1832], where a bard respectively a poetic genius appears – are seen as meta-texts defining goals of poets in time of the political non-existence of a state. Poetry is supposed to keep memory of the glorious past alive, kindle the love for the motherland, support the collective identity of a group and initiate a liberation movement. Poets function as memory guards, leaders of the nation and prophets. Thus, literature is a medium of collective memory – it stores crucial contents, transmits them and acts as a cue. Nevertheless, shifting the focus from the community towards well-being of individuals, which is consistent with the postmodern thinking, the impact that poetry has on members of a given memory culture (Jan Assmann) can be described in ‘vampiric’ terms (Maria Janion). Poetry embodying collective memory may be compared to ‘poison’, ‘infecting’ people with a nationalistic way of thinking to their disadvantage as far as their personal lives are concerned.

Automatic recognition of fish from video sequences

The problem of automatic recognition of the fish from the video sequences is discussed in this Master’s Thesis. This is a very urgent issue for many organizations engaged in fish farming in Finland and Russia because the process of automation control and counting of individual species is turning point in the industry. The difficulties and the specific features of the problem have been identified in order to find a solution and propose some recommendations for the components of the automated fish recognition system. Methods such as background subtraction, Kalman filtering and Viola-Jones method were implemented during this work for detection, tracking and estimation of fish parameters. Both the results of the experiments and the choice of the appropriate methods strongly depend on the quality and the type of a video which is used as an input data. Practical experiments have demonstrated that not all methods can produce good results for real data, whereas on synthetic data they operate satisfactorily.

Conflicting Memory in Estonia: How Do Estonian Russian-speakers Understand the Events of 1939-40?

This thesis studies the collective memory of the Russian-speaking minority living in Estonia. The minority is exposed to two national narratives regarding the incorporation of Estonia into the Soviet Union in 1940. According to the Estonian narrative, Estonia was occupied and annexed by the Soviet Union while the Soviet-Russian narrative sees the actions to have been legal and voluntary. This thesis firstly examines thoughts the existence of these two opposing narratives evoke among the Russian-speaking minority and secondly it explores whether the views of the minority compare with the two official yet divergent narratives. The study focuses on the second and third generation minority members. The topic belongs to the field of memory studies. The objective is to understand the views the Russian minority have towards the controversial events of the years 1939-40. To accomplish the objectives set, a web-based survey using open-ended and multiple-choice questions was conducted. The open-ended questions addressed the main research questions while the multiple-choice questions contributed to forming a more comprehensive understanding of the subject in question. In order to interpret the data, qualitative content analysis has been applied. Based on the findings, the Russian-speaking minority respondents’ understanding of the events of 1939-40 could be described as fragmented, inconsistent and including viewpoints that resulted from the merger of different storylines. There is no single cohesive or coherent narrative of the past amongst the minority. In addition to that, their views do not generally comply with the narrative of the Russian Federation as often referred to in literature, even though the minority respondents do not want to see the Soviet involvement as critically as the Estonian narrative does. Many respondents conceive the events of 1939-40 as ambiguous revealing the ability to be tolerant and receptive in their views regarding the past.

Recognition of nucleic acids by metal ion complexes

Metal-ion-mediated base-pairing of nucleic acids has attracted considerable attention during the past decade, since it offers means to expand the genetic code by artificial base-pairs, to create predesigned molecular architecture by metal-ion-mediated inter- or intra-strand cross-links, or to convert double stranded DNA to a nano-scale wire. Such applications largely depend on the presence of a modified nucleobase in both strands engaged in the duplex formation. Hybridization of metal-ion-binding oligonucleotide analogs with natural nucleic acid sequences has received much less attention in spite of obvious applications. While the natural oligonucleotides hybridize with high selectivity, their affinity for complementary sequences is inadequate for a number of applications. In the case of DNA, for example, more than 10 consecutive Watson-Crick base pairs are required for a stable duplex at room temperature, making targeting of sequences shorter than this challenging. For example, many types of cancer exhibit distinctive profiles of oncogenic miRNA, the diagnostics of which is, however, difficult owing to the presence of only short single stranded loop structures. Metallo-oligonucleotides, with their superior affinity towards their natural complements, would offer a way to overcome the low stability of short duplexes. In this study a number of metal-ion-binding surrogate nucleosides were prepared and their interaction with nucleoside 5´-monophosphates (NMPs) has been investigated by 1H NMR spectroscopy. To find metal ion complexes that could discriminate between natural nucleobases upon double helix formation, glycol nucleic acid (GNA) sequences carrying a PdII ion with vacant coordination sites at a predetermined position were synthesized and their affinity to complementary as well as mismatched counterparts quantified by UV-melting measurements.