Search Interfaces on the Web: Querying and Characterizing

Current-day web search engines (e.g., Google) do not crawl and index a significant portion of theWeb and, hence, web users relying on search engines only are unable to discover and access a large amount of information from the non-indexable part of the Web. Specifically, dynamic pages generated based on parameters provided by a user via web search forms (or search interfaces) are not indexed by search engines and cannot be found in searchers’ results. Such search interfaces provide web users with an online access to myriads of databases on the Web. In order to obtain some information from a web database of interest, a user issues his/her query by specifying query terms in a search form and receives the query results, a set of dynamic pages that embed required information from a database. At the same time, issuing a query via an arbitrary search interface is an extremely complex task for any kind of automatic agents including web crawlers, which, at least up to the present day, do not even attempt to pass through web forms on a large scale. In this thesis, our primary and key object of study is a huge portion of the Web (hereafter referred as the deep Web) hidden behind web search interfaces. We concentrate on three classes of problems around the deep Web: characterization of deep Web, finding and classifying deep web resources, and querying web databases. Characterizing deep Web: Though the term deep Web was coined in 2000, which is sufficiently long ago for any web-related concept/technology, we still do not know many important characteristics of the deep Web. Another matter of concern is that surveys of the deep Web existing so far are predominantly based on study of deep web sites in English. One can then expect that findings from these surveys may be biased, especially owing to a steady increase in non-English web content. In this way, surveying of national segments of the deep Web is of interest not only to national communities but to the whole web community as well. In this thesis, we propose two new methods for estimating the main parameters of deep Web. We use the suggested methods to estimate the scale of one specific national segment of the Web and report our findings. We also build and make publicly available a dataset describing more than 200 web databases from the national segment of the Web. Finding deep web resources: The deep Web has been growing at a very fast pace. It has been estimated that there are hundred thousands of deep web sites. Due to the huge volume of information in the deep Web, there has been a significant interest to approaches that allow users and computer applications to leverage this information. Most approaches assumed that search interfaces to web databases of interest are already discovered and known to query systems. However, such assumptions do not hold true mostly because of the large scale of the deep Web – indeed, for any given domain of interest there are too many web databases with relevant content. Thus, the ability to locate search interfaces to web databases becomes a key requirement for any application accessing the deep Web. In this thesis, we describe the architecture of the I-Crawler, a system for finding and classifying search interfaces. Specifically, the I-Crawler is intentionally designed to be used in deepWeb characterization studies and for constructing directories of deep web resources. Unlike almost all other approaches to the deep Web existing so far, the I-Crawler is able to recognize and analyze JavaScript-rich and non-HTML searchable forms. Querying web databases: Retrieving information by filling out web search forms is a typical task for a web user. This is all the more so as interfaces of conventional search engines are also web forms. At present, a user needs to manually provide input values to search interfaces and then extract required data from the pages with results. The manual filling out forms is not feasible and cumbersome in cases of complex queries but such kind of queries are essential for many web searches especially in the area of e-commerce. In this way, the automation of querying and retrieving data behind search interfaces is desirable and essential for such tasks as building domain-independent deep web crawlers and automated web agents, searching for domain-specific information (vertical search engines), and for extraction and integration of information from various deep web resources. We present a data model for representing search interfaces and discuss techniques for extracting field labels, client-side scripts and structured data from HTML pages. We also describe a representation of result pages and discuss how to extract and store results of form queries. Besides, we present a user-friendly and expressive form query language that allows one to retrieve information behind search interfaces and extract useful data from the result pages based on specified conditions. We implement a prototype system for querying web databases and describe its architecture and components design.

Modelling of the PWR PACTEL vertical steam generator with the TRACE code

The behavior of the nuclear power plants must be known in all operational situations. Thermal hydraulics computer applications are used to simulate the behavior of the plants. The computer applications must be validated before they can be used reliably. The simulation results are compared against the experimental results. In this thesis a model of the PWR PACTEL steam generator was prepared with the TRAC/RELAP Advanced Computational Engine computer application. The simulation results can be compared against the results of the Advanced Process Simulator analysis software in future. Development of the model of the PWR PACTEL vertical steam generator is introduced in this thesis. Loss of feedwater transient simulation examples were carried out with the model.

Pienen metallituotteita valmistavan yrityksen kustannuslaskentamallin kehittäminen

Tämän diplomityön tavoitteena oli rakentaa pienelle metallituotteita valmistavalle yritykselle kustannuslaskentamalli, joka olisi helppo käyttää ja ylläpitää ja joka huomioisi käytettävissä olevat resurssit ja jossa hyödynnettäisiin mahdollisimman paljon yrityksen olemassa olevia tietokoneohjelmia. Tavoitteena oli erityisesti kustannusten kohdistettavuuden parantaminen eri tuotteille ja yrityksen kustannuslaskentakäytännön dokumentointi. Kehitettävän kustannuslaskentamallin perustaksi valittiin nykytila-analyysin, valmistettavien tuotteiden, tuotantomenetelmien, yrityksen kustannusrakenteen, käytettävien resurssien ja yrityksen käytössä olevien tietokoneohjemien perusteella lisäyslaskenta. Työssä kuvattiin kustannuslaskentamallin rakentamisvaiheita ja konetuntihintojen määrittelyä. Valmista laskentamallia testattiin laskemalla viidelle erilaiselle tuotteelle omakustannushinnat. Lopuksi pohdittiin jatkokehitystarpeita.

Loviisan ydinvoimalaitoksen todennäköisyyspohjaisen riskianalyysin tason 2 epävarmuustarkastelut

Diplomityössä tarkastellaan Loviisan ydinvoimalaitoksen todennäköisyyspohjaisen riskianalyysin tason 2 epävarmuuksia. Tason 2 riskitutkimuksissa tutkitaan ydinvoimalaitosonnettomuuksia, joiden seurauksena osa reaktorin radioaktiivisista aineista vapautuu ympäristöön. Näiden tutkimuksien päätulos on suuren päästön vuotuinen taajuus ja se on pääosin todelliseen laitoshistoriaan perustuva tilastollinen odotusarvo. Tämän odotusarvon uskottavuutta voidaan parantaa huomioimalla merkittävimmät laskentaan liittyvät epävarmuudet. Epävarmuuksia laskentaan aiheutuu muiden muassa vakavan reaktorionnettomuuden ilmiöistä, turvallisuusjärjestelmien laitteista, inhimillisistä toiminnoista sekä luotettavuusmallin määrittelemättömistä osista. Diplomityössä kuvataan, kuinka epävarmuustarkastelut integroidaan osaksi Loviisan ydinvoimalaitoksen todennäköisyyspohjaisia riskianalyysejä. Tämä toteutetaan diplomityössä kehitetyillä apuohjelmilla PRALA:lla ja PRATU:lla, joiden avulla voidaan lisätä laitoshistorian perusteella muodostetut epävarmuusparametrit osaksi riskianalyysien luotettavuusdataa. Lisäksi diplomityössä on laskettu laskentaesimerkkinä Loviisan ydinvoimalaitoksen suuren päästön vuotuisen taajuuden vaihtelua kuvaava luottamusväli. Tämä laskentaesimerkki pohjautuu pääosin konservatiivisiin epävarmuusarvioihin, ei todellisiin tilastollisiin epävarmuuksiin. Laskentaesimerkin tulosten perusteella Loviisan suuren päästön taajuudella on laaja vaihteluväli; virhekertoimeksi saatiin 8,4 nykyisillä epävarmuusparametreilla. Suuren päästön taajuuden luottamusväliä voidaan kuitenkin tulevaisuudessa supistaa, kun hyödynnetään todelliseen laitoshistoriaan perustuvia epävarmuusparametreja.

Scaling up stepwise feature introduction to construction of large software systems

Developing software is a difficult and error-prone activity. Furthermore, the complexity of modern computer applications is significant. Hence,an organised approach to software construction is crucial. Stepwise Feature Introduction – created by R.-J. Back – is a development paradigm, in which software is constructed by adding functionality in small increments. The resulting code has an organised, layered structure and can be easily reused. Moreover, the interaction with the users of the software and the correctness concerns are essential elements of the development process, contributing to high quality and functionality of the final product. The paradigm of Stepwise Feature Introduction has been successfully applied in an academic environment, to a number of small-scale developments. The thesis examines the paradigm and its suitability to construction of large and complex software systems by focusing on the development of two software systems of significant complexity. Throughout the thesis we propose a number of improvements and modifications that should be applied to the paradigm when developing or reengineering large and complex software systems. The discussion in the thesis covers various aspects of software development that relate to Stepwise Feature Introduction. More specifically, we evaluate the paradigm based on the common practices of object-oriented programming and design and agile development methodologies. We also outline the strategy to testing systems built with the paradigm of Stepwise Feature Introduction.

Design of an Embedded Computer Board for Networking Applications

Tämä diplomityö tehtiin Convergens Oy:lle. Convergens on elektroniikan suunnittelutoimisto, joka on erikoistunut sulautettuihin järjestelmiin sekä tietoliikennetekniikkaan. Diplomityön tavoitteena oli suunnitella tietokonekortti tietoliikennesovelluksia varten asiakkaalle, jolta vaatimusmäärittelyt tulivat. Työ on rajattu koskemaan laitteen prototyypin suunnittelua. Työssä suunnitellaan pääasiassa WLAN-tukiaseman tietokone. Tukiasema onasennettavissa toimistoihin, varastoihin, kauppoihin sekä myös liikkuvaan ajoneuvoon. Suunnittelussa on otettu nämä asiat huomioon, ja laitteen akun pystyy lataamaan muun muassa auton akulla. Langattomat tekniikat ovat voimakkaasti yleistymässä, ja tämän työn tukiasema tarjoaakin varteenotettavan vaihtoehdon lukuisilla ominaisuuksillaan. Mukana on mm. GPS, Bluetooth sekä Ethernet-valmius. Langattomien tekniikoiden lisäksi myös sulautetut järjestelmät ovat voimakkaasti yleistymässä, ja nykyään mikroprosessoreita löytääkin lähesmistä vain. Tässä projektissa käytetty prosessori on nopeutensa puolesta kilpailukykyinen, ja siitä löytyy useita eri rajapintoja. Jatkossa tietokonekortille on myös tulossa WiMAX-tuki, joka lisää tukiaseman tulevaisuuden arvoa asiakkaalle. Projektiin valittu Freescalen MPC8321E-prosessori on PowerPC-arkkitehtuuriin perustuva ja juuri markkinoille ilmestynyt. Tämä toi mukanaan lisähaasteen, sillä kyseisestä prosessorista ei ollut vielä kaikkea tietoa saatavilla. Mekaniikka toi omat haasteensa mukanaan, sillä se rajoitti piirilevyn koonniin, että ylimääräistä piirilevytilaa ei juurikaan jäänyt. Tämän takia esimerkiksi DDR-muistit olivat haastavia reitittää, sillä muistivetojen on oltava melko samanpituisia keskenään. Käyttöjärjestelmänä projektissa käytetään Linuxia. Suunnittelu alkoi keväällä 2007 ja toimiva prototyyppi oli valmis alkusyksystä. Prototyypin testaus osoitti, että tietokonekortti kykenee täyttämään kaikki asiakkaan vaatimukset. Prototyypin testauksessa löytyneet viat ja optimoinnit on tarkoitus korjata tuotantomalliin, joten se antaa hyvän pohjan jatkosuunnittelua varten.

Patent claims in certain geographical regions

Työn tavoitteena oli käsitellä mahdollisuutta laatia patenttihakemuksen vaatimuksia siten, että patenttihakemukset toimisivat eri oikeusalueilla, jotka ovat tässä Eurooppa, Suomi ja USA. Aluksi käsiteltiin patentointia ja eri patenttijärjestelmiä yleisesti, jonka jälkeen käsiteltiin lähemmin patenttivaatimuksia, niiden muotoja ja eri vaatimusten edellytyksiä, joita vaaditaan Euroopan patenttisopimuksessa, suomalaisessa ja USA:laisessa patenttijärjestelmässä. Vaikka uutuus, keksinnöllisyys ja teollinen käyttökelpoisuus ovat tärkeimmät edellytykset kun määritetään patenttivaatimuksia, niitä ei käsitelty työn empiirisessä osassa. Työn empiirinen osuus osoittaa selvästi, että erilaiset muodolliset vaatimukset Euroopan patenttisopimuksessa, suomalaisessa ja USA:laisessa patenttijärjestelmässä hankaloittavat patenttivaatimusten laatimista siten että ne toimisivat yhdessä patenttihakemuksessa yllä mainituissa patenttijärjestelmissä. Empiirisen tutkimuksen ja eri oikeusalueilla patenttivaatimusten edellytysten perusteella, ei ole yksinkertaista ratkaisua laatia patenttivaatimuksia (ja myös patenttiselostuksia), jotka toimisivat monilla oikeusalueilla. Eräs ratkaisu ongelmaan on laatia yksi sarja patenttivaatimuksia, jotka täyttävät Euroopan patenttisopimuksen käytännön mukaiset edellytykset (täyttävät myös Suomalaisen patenttijärjestelmän edellytykset) ja toinen sarja patenttivaatimuksia, jotka täyttävät USA:laisen patenttijärjestelmän edellytykset samassa patenttihakemuksessa. Hakemuksen käsittelyvaiheessa hakija voi pudottaa patenttivaatimukset, jotka eivät täytä kansallisen patenttijärjestelmän edellytyksiä patenttihakemuksesta.

Adaptive MCMC methods with applications in environmental and geophysical models

This work presents new, efficient Markov chain Monte Carlo (MCMC) simulation methods for statistical analysis in various modelling applications. When using MCMC methods, the model is simulated repeatedly to explore the probability distribution describing the uncertainties in model parameters and predictions. In adaptive MCMC methods based on the Metropolis-Hastings algorithm, the proposal distribution needed by the algorithm learns from the target distribution as the simulation proceeds. Adaptive MCMC methods have been subject of intensive research lately, as they open a way for essentially easier use of the methodology. The lack of user-friendly computer programs has been a main obstacle for wider acceptance of the methods. This work provides two new adaptive MCMC methods: DRAM and AARJ. The DRAM method has been built especially to work in high dimensional and non-linear problems. The AARJ method is an extension to DRAM for model selection problems, where the mathematical formulation of the model is uncertain and we want simultaneously to fit several different models to the same observations. The methods were developed while keeping in mind the needs of modelling applications typical in environmental sciences. The development work has been pursued while working with several application projects. The applications presented in this work are: a winter time oxygen concentration model for Lake Tuusulanjärvi and adaptive control of the aerator; a nutrition model for Lake Pyhäjärvi and lake management planning; validation of the algorithms of the GOMOS ozone remote sensing instrument on board the Envisat satellite of European Space Agency and the study of the effects of aerosol model selection on the GOMOS algorithm.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Economic Geographical Analysis of The Finnish Paper Industry

The purpose of this academic economic geographical dissertation is to study and describe how competitiveness in the Finnish paper industry has developed during 2001–2008. During these years, the Finnish paper industry has faced economically challenging times. This dissertation attempts to fill the existing gap between theoretical and empirical discussions concerning economic geographical issues in the paper industry. The main research questions are: How have the supply chain costs and margins developed during 2001–2008? How do sales prices, transportation, and fixed and variable costs correlate with gross margins in a spatial context? The research object for this case study is a typical large Finnish paper mill that exports over 90 % of its production. The economic longitudinal research data were obtained from the case mill’s controlled economic system and, correlation (R2) analysis was used as the main research method. The time series data cover monthly economic and manufacturing observations from the mill from 2001 to 2008. The study reveals the development of prices, costs and transportation in the case mill, and it shows how economic variables correlate with the paper mills’ gross margins in various markets in Europe. The research methods of economic geography offer perspectives that pay attention to the spatial (market) heterogeneity. This type of research has been quite scarce in the research tradition of Finnish economic geography and supply chain management. This case study gives new insight into the research tradition of Finnish economic geography and supply chain management and its applications. As a concrete empirical result, this dissertation states that the competitive advantages of the Finnish paper industry were significantly weakened during 2001–2008 by low paper prices, costly manufacturing and expensive transportation. Statistical analysis expose that, in several important markets, transport costs lower gross margins as much as decreasing paper prices, which was a new finding. Paper companies should continuously pay attention to lowering manufacturing and transporting costs to achieve more profitable economic performance. The location of a mill being far from markets clearly has an economic impact on paper manufacturing, as paper demand is decreasing and oversupply is pressuring paper prices down. Therefore, market and economic forecasting in the paper industry is advantageous at the country and product levels while simultaneously taking into account the economic geographically specific dimensions.

Novel Interaction Techniques for Mobile Augmented Reality applications. A Systematic Literature Review

This study reviews the research on interaction techniques and methods that could be applied in mobile augmented reality scenarios. The review is focused on themost recent advances and considers especially the use of head-mounted displays. Inthe review process, we have followed a systematic approach, which makes the reviewtransparent, repeatable, and less prone to human errors than if it was conducted in amore traditional manner. The main research subjects covered in the review are headorientation and gaze-tracking, gestures and body part-tracking, and multimodality– as far as the subjects are related to human-computer interaction. Besides these,also a number of other areas of interest will be discussed.

Usability and Security in Medication Administration Applications

The traditional process of filling the medicine trays and dispensing the medicines to the patients in the hospitals is manually done by reading the printed paper medicine chart. This process can be very strenuous and error-prone, given the number of sub-tasks involved in the entire workflow and the dynamic nature of the work environment. Therefore, efforts are being made to digitalise the medication dispensation process by introducing a mobile application called Smart Dosing application. The introduction of the Smart Dosing application into hospital workflow raises security concerns and calls for security requirement analysis. This thesis is written as a part of the smart medication management project at Embedded Systems Laboratory, A° bo Akademi University. The project aims at digitising the medicine dispensation process by integrating information from various health systems, and making them available through the Smart Dosing application. This application is intended to be used on a tablet computer which will be incorporated on the medicine tray. The smart medication management system include the medicine tray, the tablet device, and the medicine cups with the cup holders. Introducing the Smart Dosing application should not interfere with the existing process carried out by the nurses, and it should result in minimum modifications to the tray design and the workflow. The re-designing of the tray would include integrating the device running the application into the tray in a manner that the users find it convenient and make less errors while using it. The main objective of this thesis is to enhance the security of the hospital medicine dispensation process by ensuring the security of the Smart Dosing application at various levels. The methods used for writing this thesis was to analyse how the tray design, and the application user interface design can help prevent errors and what secure technology choices have to be made before starting the development of the next prototype of the Smart Dosing application. The thesis first understands the context of the use of the application, the end-users and their needs, and the errors made in everyday medication dispensation workflow by continuous discussions with the nursing researchers. The thesis then gains insight to the vulnerabilities, threats and risks of using mobile application in hospital medication dispensation process. The resulting list of security requirements was made by analysing the previously built prototype of the Smart Dosing application, continuous interactive discussions with the nursing researchers, and an exhaustive stateof- the-art study on security risks of using mobile applications in hospital context. The thesis also uses Octave Allegro method to make the readers understand the likelihood and impact of threats, and what steps should be taken to prevent or fix them. The security requirements obtained, as a result, are a starting point for the developers of the next iteration of the prototype for the Smart Dosing application.

Usability and Security in Medication. Administration Applications

The traditional process of filling the medicine trays and dispensing the medicines to the patients in the hospitals is manually done by reading the printed paper medicinechart. This process can be very strenuous and error-prone, given the number of sub-tasksinvolved in the entire workflow and the dynamic nature of the work environment.Therefore, efforts are being made to digitalise the medication dispensation process byintroducing a mobile application called Smart Dosing application. The introduction ofthe Smart Dosing application into hospital workflow raises security concerns and callsfor security requirement analysis. This thesis is written as a part of the smart medication management project at EmbeddedSystems Laboratory, A˚bo Akademi University. The project aims at digitising the medicine dispensation process by integrating information from various health systems, and making them available through the Smart Dosing application. This application is intended to be used on a tablet computer which will be incorporated on the medicine tray. The smart medication management system include the medicine tray, the tablet device, and the medicine cups with the cup holders. Introducing the Smart Dosing application should not interfere with the existing process carried out by the nurses, and it should result in minimum modifications to the tray design and the workflow. The re-designing of the tray would include integrating the device running the application into the tray in a manner that the users find it convenient and make less errors while using it. The main objective of this thesis is to enhance the security of the hospital medicine dispensation process by ensuring the security of the Smart Dosing application at various levels. The methods used for writing this thesis was to analyse how the tray design, and the application user interface design can help prevent errors and what secure technology choices have to be made before starting the development of the next prototype of the Smart Dosing application. The thesis first understands the context of the use of the application, the end-users and their needs, and the errors made in everyday medication dispensation workflow by continuous discussions with the nursing researchers. The thesis then gains insight to the vulnerabilities, threats and risks of using mobile application in hospital medication dispensation process. The resulting list of security requirements was made by analysing the previously built prototype of the Smart Dosing application, continuous interactive discussions with the nursing researchers, and an exhaustive state-of-the-art study on security risks of using mobile applications in hospital context. The thesis also uses Octave Allegro method to make the readers understand the likelihood and impact of threats, and what steps should be taken to prevent or fix them. The security requirements obtained, as a result, are a starting point for the developers of the next iteration of the prototype for the Smart Dosing application.