Optimization and Applications of Large-Scale Biomedical Event Networks

The overwhelming amount and unprecedented speed of publication in the biomedical domain make it difficult for life science researchers to acquire and maintain a broad view of the field and gather all information that would be relevant for their research. As a response to this problem, the BioNLP (Biomedical Natural Language Processing) community of researches has emerged and strives to assist life science researchers by developing modern natural language processing (NLP), information extraction (IE) and information retrieval (IR) methods that can be applied at large-scale, to scan the whole publicly available biomedical literature and extract and aggregate the information found within, while automatically normalizing the variability of natural language statements. Among different tasks, biomedical event extraction has received much attention within BioNLP community recently. Biomedical event extraction constitutes the identification of biological processes and interactions described in biomedical literature, and their representation as a set of recursive event structures. The 2009–2013 series of BioNLP Shared Tasks on Event Extraction have given raise to a number of event extraction systems, several of which have been applied at a large scale (the full set of PubMed abstracts and PubMed Central Open Access full text articles), leading to creation of massive biomedical event databases, each of which containing millions of events. Sinece top-ranking event extraction systems are based on machine-learning approach and are trained on the narrow-domain, carefully selected Shared Task training data, their performance drops when being faced with the topically highly varied PubMed and PubMed Central documents. Specifically, false-positive predictions by these systems lead to generation of incorrect biomolecular events which are spotted by the end-users. This thesis proposes a novel post-processing approach, utilizing a combination of supervised and unsupervised learning techniques, that can automatically identify and filter out a considerable proportion of incorrect events from large-scale event databases, thus increasing the general credibility of those databases. The second part of this thesis is dedicated to a system we developed for hypothesis generation from large-scale event databases, which is able to discover novel biomolecular interactions among genes/gene-products. We cast the hypothesis generation problem as a supervised network topology prediction, i.e predicting new edges in the network, as well as types and directions for these edges, utilizing a set of features that can be extracted from large biomedical event networks. Routine machine learning evaluation results, as well as manual evaluation results suggest that the problem is indeed learnable. This work won the Best Paper Award in The 5th International Symposium on Languages in Biology and Medicine (LBM 2013).

Integrated environmental research and networking of economy and information in rural areas of Finland

Selostus: Kestävän kehityksen integroidun tutkimuksen ja verkostotalouden teorian tutkimusmenetelmälliset ongelmat

Monitoring and information reporting through regulation : an inter-jurisdictional comparison of forestry-related hard laws

[Abstract]

Social capital, coping and information behaviour of long-term unemployed people in Finland

Avhandlingen studerar hur långtidsarbetslösa klarar av sin situation, hurdant socialt kapital och informationsbeteende de har, samt granskar hur de ovannämnda faktorerna är relaterade till varandra. Därtill undersöks om det finns skillnader mellan finsk- och svenskspråkiga långtidsarbetslösa på de här tre livsområdena. I undersökningen består socialt kapital av sociala relationer, deltagande i organisatoriska aktiviteter samt känslan av tillhörighet med olika grupper och samfund. Gällande informationsbeteende är fokus på vardaglig informationssökning, vilka källor som används, och hurdana problem man stöter på när man söker information. Som mest påfrestande upplevdes arbetslösheten av män, som var i början eller mitten av sin arbetskarriär. De äldre (över 55 år) verkade på många sätt klara av arbetslöshetssituationen bättre än de yngre, som drabbades hårdare av ekonomiska problem och stress. Kvinnor kunde bättre än män bibehålla en positiv inställning, de hade t.ex. starkare sociala nätverk som stöd, medan mäns sociala relationer i högre grad verkade vila på en arbetsgemenskap, som blev allt svagare i och med utdragen arbetslöshet. Yngre män upplevde också ofta att deras hälsa hade försämrats, när den för kvinnor och äldre arbetslösa i genomsnitt blev bättre. När arbetslösas bemästring av arbetslöshetssituationen, sociala relationer och informationssökning granskades, framgick att människor som var aktiva på ett livsområde också var aktiva på andra livsområden. I de flesta fall framkom inte några större skillnader mellan finsk- och svenskspråkiga arbetslösa. Beträffande informationssökning var de upplevda problemen ändå av diametralt motsatt karaktär – för svenskspråkiga åsamkade för lite tillgänglig information ofta problem, medan problemet för de finskspråkiga var att hitta det väsentliga i informationsflödet. Finskspråkiga kände sig också mera fast anknutna till sin boendemiljö och det finska samhället i stort, svenskspråkiga hade däremot i genomsnitt bredare och tätare sociala nätverk.

Customer satisfaction data utilization: identifying value drivers and information use practices

The objective of this master’s thesis was twofold: first to examine the concept of customer value and its drivers and second to identify information use practices. The first part of the study represents explorative research that was carried out by examining a case company’s customer satisfaction data that was used to identify sales and technical customer service related value drivers on a detailed attribute level. This was followed by an examination of whether these attributes had been commented on in a positive or a negative light and what were the reasons why the case company had received higher or lower ratings than its competitor. As a result a classification of different sales and technical customer service related attributes was created. The results indicated that the case company has performed well, but that the results varied on the company’s business segment level. The case company’s staff, service and the benefits from a long-lasting relationship came up in a positive light whereas attitude, flexibility and reaction time came up in a negative light. The reasons for a higher or lower score in comparison to competitor varied. The results indicated that a customer’s satisfaction with the company’s performance did not always mean that the company was outperforming the competition. The second part of the study focused on customer satisfaction information use from the viewpoints of information access, dissemination and reaction. The study was conducted by running an internal survey among the case company’s staff. The results showed that information use practices varied across the company and some units or teams had taken a more proactive approach to the information use than others.

Immediate Decision-Making and Information Needs in Intensive Care Coordination

The aim of this study was to develop a theoretical model for information integration to support the deci¬sion making of intensive care charge nurses, and physicians in charge – that is, ICU shift leaders. The study focused on the ad hoc decision-making and immediate information needs of shift leaders during the management of an intensive care unit’s (ICU) daily activities. The term ‘ad hoc decision-making’ was defined as critical judgements that are needed for a specific purpose at a precise moment with the goal of ensuring instant and adequate patient care and a fluent flow of ICU activities. Data collection and research analysis methods were tested in the identification of ICU shift leaders’ ad hoc decision-making. Decision-making of ICU charge nurses (n = 12) and physicians in charge (n = 8) was observed using a think-aloud technique in two university-affiliated Finnish ICUs for adults. The ad hoc decisions of ICU shift leaders were identified using an application of protocol analysis. In the next phase, a structured online question¬naire was developed to evaluate the immediate information needs of ICU shift leaders. A national survey was conducted in all Finnish, university-affiliated hospital ICUs for adults (n = 17). The questionnaire was sent to all charge nurses (n = 515) and physicians in charge (n = 223). Altogether, 257 charge nurses (50%) and 96 physicians in charge (43%) responded to the survey. The survey was also tested internationally in 16 Greek ICUs. From Greece, 50 charge nurses out of 240 (21%) responded to the survey. A think-aloud technique and protocol analysis were found to be applicable for the identification of the ad hoc decision-making of ICU shift leaders. During one day shift leaders made over 200 ad hoc decisions. Ad hoc decisions were made horizontally, related to the whole intensive care process, and vertically, concerning single intensive care incidents. Most of the ICU shift leaders’ ad hoc decisions were related to human resources and know-how, patient information and vital signs, and special treatments. Commonly, this ad hoc decision-making involved several multiprofessional decisions that constituted a bundle of immediate decisions and various information needs. Some of these immediate information needs were shared between the charge nurses and the physicians in charge. The majority of which concerned patient admission, the organisation and management of work, and staff allocation. In general, the information needs of charge nurses were more varied than those of physicians. It was found that many ad hoc deci-sions made by the physicians in charge produced several information needs for ICU charge nurses. This meant that before the task at hand was completed, various kinds of information was sought by the charge nurses to support the decision-making process. Most of the immediate information needs of charge nurses were related to the organisation and management of work and human resources, whereas the information needs of the physicians in charge mainly concerned direct patient care. Thus, information needs differ between professionals even if the goal of decision-making is the same. The results of the international survey confirmed these study results for charge nurses. Both in Finland and in Greece the information needs of charge nurses focused on the organisation and management of work and human resources. Many of the most crucial information needs of Finnish and Greek ICU charge nurses were common. In conclusion, it was found that ICU shift leaders make hundreds of ad hoc decisions during the course of a day related to the allocation of resources and organisation of patient care. The ad hoc decision-making of ICU shift leaders is a complex multi-professional process, which requires a lot of immediate information. Real-time support for information related to patient admission, the organisation and man¬agement of work, and allocation of staff resources is especially needed. The preliminary information integration model can be applied when real-time enterprise resource planning systems are developed for intensive care daily management

Utilisation of Statistics in Intelligent Web Applications

Web-portaalien aiheenmukaista luokittelua voidaan hyödyntää tunnistamaan käyttäjän kiinnostuksen kohteet keräämällä tilastotietoa hänen selaustottumuksistaan eri kategorioissa. Tämä diplomityö käsittelee web-sovelluksien osa-alueita, joissa kerättyä tilastotietoa voidaan hyödyntää personalisoinnissa. Yleisperiaatteet sisällön personalisoinnista, Internet-mainostamisesta ja tiedonhausta selitetään matemaattisia malleja käyttäen. Lisäksi työssä kuvaillaan yleisluontoiset ominaisuudet web-portaaleista sekä tilastotiedon keräämiseen liittyvät seikat.

A systematic mapping study of web services discovery mechanisms

Context: Web services have been gaining popularity due to the success of service oriented architecture and cloud computing. Web services offer tremendous opportunity for service developers to publish their services and applications over the boundaries of the organization or company. However, to fully exploit these opportunities it is necessary to find efficient discovery mechanism thus, Web services discovering mechanism has attracted a considerable attention in Semantic Web research, however, there have been no literature surveys that systematically map the present research result thus overall impact of these research efforts and level of maturity of their results are still unclear. This thesis aims at providing an overview of the current state of research into Web services discovering mechanism using systematic mapping. The work is based on the papers published 2004 to 2013, and attempts to elaborate various aspects of the analyzed literature including classifying them in terms of the architecture, frameworks and methods used for web services discovery mechanism. Objective: The objective if this work is to summarize the current knowledge that is available as regards to Web service discovery mechanisms as well as to systematically identify and analyze the current published research works in order to identify different approaches presented. Method: A systematic mapping study has been employed to assess the various Web Services discovery approaches presented in the literature. Systematic mapping studies are useful for categorizing and summarizing the level of maturity research area. Results: The result indicates that there are numerous approaches that are consistently being researched and published in this field. In terms of where these researches are published, conferences are major contributing publishing arena as 48% of the selected papers were conference published papers illustrating the level of maturity of the research topic. Additionally selected 52 papers are categorized into two broad segments namely functional and non-functional based approaches taking into consideration architectural aspects and information retrieval approaches, semantic matching, syntactic matching, behavior based matching as well as QOS and other constraints.

Patents in the Information and Communications Technology Sector - Development Trends, Problem Areas and Pressures for Change

The patent system was created for the purpose of promoting innovation by granting the inventors a legally defined right to exclude others in return for public disclosure. Today, patents are being applied and granted in greater numbers than ever, particularly in new areas such as biotechnology and information andcommunications technology (ICT), in which research and development (R&D) investments are also high. At the same time, the patent system has been heavily criticized. It has been claimed that it discourages rather than encourages the introduction of new products and processes, particularly in areas that develop quickly, lack one-product-one-patent correlation, and in which theemergence of patent thickets is characteristic. A further concern, which is particularly acute in the U.S., is the granting of so-called 'bad patents', i.e. patents that do not factually fulfil the patentability criteria. From the perspective of technology-intensive companies, patents could,irrespective of the above, be described as the most significant intellectual property right (IPR), having the potential of being used to protect products and processes from imitation, to limit competitors' freedom-to-operate, to provide such freedom to the company in question, and to exchange ideas with others. In fact, patents define the boundaries of ownership in relation to certain technologies. They may be sold or licensed on their ownor they may be components of all sorts of technology acquisition and licensing arrangements. Moreover, with the possibility of patenting business-method inventions in the U.S., patents are becoming increasingly important for companies basing their businesses on services. The value of patents is dependent on the value of the invention it claims, and how it is commercialized. Thus, most of them are worth very little, and most inventions are not worth patenting: it may be possible to protect them in other ways, and the costs of protection may exceed the benefits. Moreover, instead of making all inventions proprietary and seeking to appropriate as highreturns on investments as possible through patent enforcement, it is sometimes better to allow some of them to be disseminated freely in order to maximize market penetration. In fact, the ideology of openness is well established in the software sector, which has been the breeding ground for the open-source movement, for instance. Furthermore, industries, such as ICT, that benefit from network effects do not shun the idea of setting open standards or opening up their proprietary interfaces to allow everyone todesign products and services that are interoperable with theirs. The problem is that even though patents do not, strictly speaking, prevent access to protected technologies, they have the potential of doing so, and conflicts of interest are not rare. The primary aim of this dissertation is to increase understanding of the dynamics and controversies of the U.S. and European patent systems, with the focus on the ICT sector. The study consists of three parts. The first part introduces the research topic and the overall results of the dissertation. The second part comprises a publication in which academic, political, legal and business developments that concern software and business-method patents are investigated, and contentiousareas are identified. The third part examines the problems with patents and open standards both of which carry significant economic weight inthe ICT sector. Here, the focus is on so-called submarine patents, i.e. patentsthat remain unnoticed during the standardization process and then emerge after the standard has been set. The factors that contribute to the problems are documented and the practical and juridical options for alleviating them are assessed. In total, the dissertation provides a good overview of the challenges and pressures for change the patent system is facing,and of how these challenges are reflected in standard setting.

Information integration and its impacts on logistics performance - Using information technology and systems to facilitate information integration

Fast changing environment sets pressure on firms to share large amount of information with their customers and suppliers. The terms information integration and information sharing are essential for facilitating a smooth flow of information throughout the supply chain, and the terms are used interchangeably in research literature. By integrating and sharing information, firms want to improve their logistics performance. Firms share information with their suppliers and customers by using traditional communication methods (telephone, fax, Email, written and face-to-face contacts) and by using advanced or modern communication methods such as electronic data interchange (EDI), enterprise resource planning (ERP), web-based procurement systems, electronic trading systems and web portals. Adopting new ways of using IT is one important resource for staying competitive on the rapidly changing market (Saeed et al. 2005, 387), and an information system that provides people the information they need for performing their work, will support company performance (Boddy et al. 2005, 26). The purpose of this research has been to test and understand the relationship between information integration with key suppliers and/or customers and a firm’s logistics performance, especially when information technology (IT) and information systems (IS) are used for integrating information. Quantitative and qualitative research methods have been used to perform the research. Special attention has been paid to the scope, level and direction of information integration (Van Donk & van der Vaart 2005a). In addition, the four elements of integration (Jahre & Fabbe-Costes 2008) are closely tied to the frame of reference. The elements are integration of flows, integration of processes and activities, integration of information technologies and systems and integration of actors. The study found that information integration has a low positive relationship to operational performance and a medium positive relationship to strategic performance. The potential performance improvements found in this study vary from efficiency, delivery and quality improvements (operational) to profit, profitability or customer satisfaction improvements (strategic). The results indicate that although information integration has an impact on a firm’s logistics performance, all performance improvements have not been achieved. This study also found that the use of IT and IS have a mediocre positive relationship to information integration. Almost all case companies agreed on that the use of IT and IS could facilitate information integration and improve their logistics performance. The case companies felt that an implementation of a web portal or a data bank would benefit them - enhance their performance and increase information integration.

Possibilities and challenges in utilization of information provided by Industrial Internet applications

Global digitalization has affected also industrial sector. A trend called Industrial Internet has been present for some years and established relatively steady position in businesses. Industrial Internet is also referred with the terminology Industry 4.0 and in consumer businesses IoT (Internet of Things). Eventually, trend consists of many traditionally proven technologies and concepts, such as condition monitoring, remote services, predictive maintenance and Internet customer portals. All these technologies and information related to them are estimated to change the rules of business in industrial sector. This may result even a new industrial revolution. This research has its focus on Industrial Internet products, services and applications. The study analyses four case companies and their digital service offerings. According to this analysis the comparison of these services is done to find out if there is still space for companies to gain competitive advantage through differentiation with these state of the art solutions. One of the case companies, Case Company Ltd., is working as a primary case company and a subscriber of this particular research. The research and results are analyzed primarily from this company’s perspective and need. In empirical part, the research clarifies how Case Company Ltd. has allocated its development resources through last five years. These allocations in certain categories are then compared to other case companies’ current customer offering and conclusions are made how the approach of different companies differ from each other. Existing theoretical knowledge of Industrial Internet is about to find its shape. In this research we take a look how the case company analysis and findings correlate with the existing knowledge and literature of the topic.

Value added logistics in supply and demand chains. Smile. Part 1. eBusiness between global company and itslocal sme supplier network

VALOSADE (Value Added Logistics in Supply and Demand Chains) is the research project of Anita Lukka's VALORE (Value Added Logistics Research) research team inLappeenranta University of Technology. VALOSADE is included in ELO (Ebusiness logistics) technology program of Tekes (Finnish Technology Agency). SMILE (SME-sector, Internet applications and Logistical Efficiency) is one of four subprojects of VALOSADE. SMILE research focuses on case network that is composed of small and medium sized mechanical maintenance service providers and global wood processing customers. Basic principle of SMILE study is communication and ebusiness insupply and demand network. This first phase of research concentrates on creating backgrounds for SMILE study and for ebusiness solutions of maintenance case network. The focus is on general trends of ebusiness in supply chains and networksof different industries; total ebusiness system architecture of company networks; ebusiness strategy of company network; information value chain; different factors, which influence on ebusiness solution of company network; and the correlation between ebusiness and competitive advantage. Literature, interviews and benchmarking were used as research methods in this qualitative case study. Networks and end-to-end supply chains are the organizational structures, which can add value for end customer. Information is one of the key factors in these decentralized structures. Because of decentralization of business, information is produced and used in different companies and in different information systems. Information refinement services are needed to manage information flows in company networksbetween different systems. Furthermore, some new solutions like network information systems are utilised in optimising network performance and in standardizingnetwork common processes. Some cases have however indicated, that utilization of ebusiness in decentralized business model is not always a necessity, but value-add of ICT must be defined case-specifically. In the theory part of report, different ebusiness and architecture models are introduced. These models are compared to empirical case data in research results. The biggest difference between theory and empirical data is that models are mainly developed for large-scale companies - not for SMEs. This is due to that implemented network ebusiness solutions are mainly large company centered. Genuine SME network centred ebusiness models are quite rare, and the study in that area has been few in number. Business relationships between customer and their SME suppliers are nowadays concentrated more on collaborative tactical and strategic initiatives besides transaction based operational initiatives. However, ebusiness systems are further mainly based on exchange of operational transactional data. Collaborative ebusiness solutions are in planning or pilot phase in most case companies. Furthermore, many ebusiness solutions are nowadays between two participants, but network and end-to-end supply chain transparency and information systems are quite rare. Transaction volumes, data formats, the types of exchanged information, information criticality,type and duration of business relationship, internal information systems of partners, processes and operation models (e.g. different ordering models) differ among network companies, and furthermore companies are at different stages on networking and ebusiness readiness. Because of former factors, different customer-supplier combinations in network must utilise totally different ebusiness architectures, technologies, systems and standards.

Wireless Authentication and Authorization, case Wireless Access Control System

Lyhyen kantaman radiotekniikoiden hyödyntäminen mahdollistaa uudenlaisten paikallisten palveluiden käytön ja vanhojen palveluiden kehittämisen. Kulunvalvonta on päivittäisenä palveluna valittu työn esimerkkisovellukseksi. Useita tunnistus- ja valtuutustapoja tutkitaan, ja julkisen avaimen infrastruktuuri on esitellään tarkemmin. Langattomat tekniikat Bluetooth, Zigbee, RFID ja IrDA esitellän yleisellä tasolla langattomat tekniikat –luvussa. Bluetooth-tekniikan rakennetta, mukaan lukien sen tietoturva-arkkitehtuuria, tutkitaan tarkemmin. Bluetooth-tekniikkaa käytetään työssä suunnitellun langattoman kulunvalvontajärjestelmän tietojen siirtoon. Kannettava päätelaite toimii käyttäjän henkilökohtaisena luotettuna laitteena, jota voi käyttää avaimena. Käyttäjän tunnistaminen ja valtuuttaminen perustuu julkisen avaimen infrastruktuuriin. Ylläpidon allekirjoittamat varmenteet sisältävät käyttäjän julkisen avaimen lisäksi tietoa hänestä ja hänen oikeuksistaan. Käyttäjän tunnistaminen kulunvalvontapisteissä tehdään julkisen ja salaisen avaimen käyttöön perustuvalla haaste-vastaus-menetelmällä. Lyhyesti, järjestelmässä käytetään Bluetooth-päätelaitteita langattomina avaimina.

Text Classification and Indexing in IP Networks

Internet on elektronisen postin perusrakenne ja ollut tärkeä tiedonlähde akateemisille käyttäjille jo pitkään. Siitä on tullut merkittävä tietolähde kaupallisille yrityksille niiden pyrkiessä pitämään yhteyttä asiakkaisiinsa ja seuraamaan kilpailijoitansa. WWW:n kasvu sekä määrällisesti että sen moninaisuus on luonut kasvavan kysynnän kehittyneille tiedonhallintapalveluille. Tällaisia palveluja ovet ryhmittely ja luokittelu, tiedon löytäminen ja suodattaminen sekä lähteiden käytön personointi ja seuranta. Vaikka WWW:stä saatavan tieteellisen ja kaupallisesti arvokkaan tiedon määrä on huomattavasti kasvanut viime vuosina sen etsiminen ja löytyminen on edelleen tavanomaisen Internet hakukoneen varassa. Tietojen hakuun kohdistuvien kasvavien ja muuttuvien tarpeiden tyydyttämisestä on tullut monimutkainen tehtävä Internet hakukoneille. Luokittelu ja indeksointi ovat merkittävä osa luotettavan ja täsmällisen tiedon etsimisessä ja löytämisessä. Tämä diplomityö esittelee luokittelussa ja indeksoinnissa käytettävät yleisimmät menetelmät ja niitä käyttäviä sovelluksia ja projekteja, joissa tiedon hakuun liittyvät ongelmat on pyritty ratkaisemaan.