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).

Management of Customer Co-development in Business-to-Business Markets

Management of customer co-development means involving customers in the development of new products and services, and coordinating the process. In business-tobusiness markets, customer co-development enables the development of innovations that better match customer needs and strengthens customer relationships. However, close collaboration with customers can hamper the innovativeness of new products and lead to overly customized solutions. Therefore, the management of co-development is crucial to its success. Yet the existing research on management of co-development has mainly focused on selecting the right collaboration partners, and the field lacks understanding on how to manage the tensions inherent in customer co-development. The purpose of this thesis is to increase understanding on the management of the codevelopment. The thesis is divided into two parts. The first comprises the literature review and conclusions for the whole study, and the second presents four publications. From the methodological perspective, the research papers follow exploratory qualitative research design. The empirical data comprise interviews with 60 persons, representing 25 different organizations, and a group of 11 end users. The study conceptualizes management of customer co-development in three dimensions 1) relational co-development processes, 2) co-development challenges and paradoxes, and 3) internal customer involvement processes. The findings contribute to the customersupplier relationship, innovation, and marketing management literatures by providing a framework on supplier-customer co-development, addressing co-development paradoxes and their management processes, and suggesting practices for customer involvement. For practitioners, the findings provide tools to manage the challenges related to codevelopment with customers.

Käytettävyyssuunnittelun teoria ja käytäntö: Tapaustutkimus huonekalujen verkkokaupasta

Käytettävien ohjelmistojen suunnittelu tuo hyötyjä loppukäyttäjälle sekä muille sidosryhmille. Verkkokaupassa käytettävyys on elintärkeää, koska asiakkaat vaihtavat helposti seuraavalle sivustolle, mikäli he eivät löydä etsimäänsä. Tutkimusten mukaan käytettävyys vaikuttaa ostopäätöksen tekemiseen. Lisäksi käytettävyydellä on merkitystä asiakastyytyväisyyteen, joka taas vaikuttaa asiakasuskollisuuteen. Tässä tutkielmassa tutkittiin, miten käytettävyyttä suunnitellaan käytännössä verrattuna teoreettisiin suosituksiin. Tapaustutkimuksen kohteena oli huonekaluja myyvän kansainvälisen yrityksen verkkokaupan uudistamiseen tähtäävä projekti. Uudistamistarve nousi aikaisemman verkkokauppaversion puutteellisesta käytettävyydestä. Projekti toteutettiin ketterällä Scrum-menetelmällä. Empiirinen aineisto kerättiin puolistrukturoitujen haastattelujen avulla. Haastateltavat olivat käyttökokemuksen suunnitteluun osallistuvia henkilöitä. Haastattelujen teemat laadittiin teoreettisen aineiston pohjalta. Teoreettisessa osuudessa tutkittiin käytettävyyden suunnitteluun liittyviä periaatteita, prosessia ja menetelmiä. Aikaisemmasta tutkimuksesta löydettiin 12 periaatetta, jotka tukevat ja luonnehtivat käyttäjäkeskeistä suunnittelua. Käytettävyyttä suunnitellaan käyttäjäkeskeisen prosessin avulla. Eri prosessimallit pitivät keskeisinä asioina käyttökontekstin määrittelyä ja ymmärtämistä, mitattavia käytettävyysvaatimuksia, suunnitteluratkaisujen empiiristä arviointia sekä suunnitteluprosessin iteratiivisuutta. Lisäksi tarkasteltiin, mitä suunnittelumenetelmiä tutkijat ehdottavat käytettävyyden suunnitteluun ja mitä kyselytutkimusten perusteella todellisuudessa käytetään. Verkkokauppaprojektissa käytettävyyden suunnittelu erosi osittain teoreettisista suosituksista. Käyttökontekstitietoa ei ollut kaikilla projektiin osallistuvilla, eikä käytettävyysvaatimuksia ollut asetettu teorian tarkoittamalla tavalla. Yhtäläisyyksiäkin löytyi. Verkkokauppaprojektissa suunnitteluratkaisuja arvioitiin empiirisesti todellisten käyttäjien edustajien avulla. Suunnitteluprosessi oli iteratiivinen eli suunnitteluratkaisuja oltiin valmiita muuttamaan arvioinnin tuloksena. Tutkimuksen perusteella suositellaan, että verkkokauppaprojektissa parannettaisiin kommunikointia, koska käyttökontekstitieto ei saavuttanut kaikkia projektissa työskenteleviä. Teorian tulisi entisestään korostaa kommunikoinnin tärkeyttä. Tutkimuksen perusteella esitetään myös, että teoria ohjaisi paremmin vaatimusmäärittelyjen tekemiseen käytännössä. Avainsanat: Käytettävyys, käyttäjäkeskeinen suunnittelu, käytettävyyden periaatteet, käytettävyyden suunnittelumenetelmät, ketterä ohjelmistokehitys, tapaustutkimus

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.

Specification of a smart meter/actuator description mechanism & development of a mobile application

Home Automation holds the potential of realizing cost savings for end users while reducing the carbon footprint of domestic energy consumption. Yet, adoption is still very low. High cost of vendor-supplied home automation systems is a major prohibiting factor. Open source systems such as FHEM, Domoticz, OpenHAB etc. are a cheaper alternative and can drive the adoption of home automation. Moreover, they have the advantage of not being limited to a single vendor or communication technology which gives end users flexibility in the choice of devices to include in their installation. However, interaction with devices having diverse communication technologies can be inconvenient for users thus limiting the utility they derive from it. For application developers, creating applications which interact with the several technologies in the home automation systems is not a consistent process. Hence, there is the need for a common description mechanism that makes interaction smooth for end users and which enables application developers to make home automation applications in a consistent and uniform way. This thesis proposes such a description mechanism within the context of an open source home automation system – FHEM, together with a system concept for its application. A mobile application was developed as a proof of concept of the proposed description mechanism and the results of the implementation are reflected upon.

Towards sustainable transport: A comparison of demographic and behavioural characteristics of Finnish and international car sharing users

Strong evidence suggests that the climate is changing and that these changes are largely caused by human activities. A consensus exists among researchers that human activity is causing global warming and that actions to mitigate global warming need to be taken swiftly. The transportation sector, which relies heavily on fossil fuel burning and primarily oil, is one of the big contributors to air pollution problems at local, regional and global levels. It is the fastest growing source of greenhouse gas emissions and is estimated to be responsible for nearly a quarter of global energyrelated carbon dioxide emissions. Car sharing is a mobility solution encouraging its users to decrease private car usage in favour of communal transit and environmental goals. The idea of car sharing originates from the aspiration to decrease personal car ownership and to reduce vehicle distance travelled. This thesis seeks to complement the understanding of Finnish car sharing users and their usage through better categorization. Through better categorization and segmentation of Finnish car sharing users the thesis seeks to provide information for improved marketing insight. Research is done on the demographic and behavioural characteristics of Finnish car sharing users and they are compared with international findings about the characteristics of International car sharing users. The main research problem is Are Finnish car sharing users similar to international ones? A theoretical research framework on the determinants of individual car sharing usage is built based on international research about demographic and behaviouristic characteristics. After this a quantitative survey is performed to the customers of a Finnish car sharing organization. The data analysed in the thesis consist out of 532 answers received from the car sharing organizations customers. The data is analysed with descriptive and other exploratory methods, which create an understanding of Finnish car sharing users. At the end of the analysis the demographic and behavioural characteristics of Finnish car sharing users are compared with international ones. The research findings of the thesis indicate that the demographic and behavioural characteristics of Finnish car sharing usage largely follow those of their international counterparts. Thanks to the thesis results the car sharing organization is able to better target their customers through improved marketing insight.

Front end development for building automation systems using JavaScript Frameworks

Automation technologies are widely acclaimed to have the potential to significantly reduce energy consumption and energy-related costs in buildings. However, despite the abundance of commercially available technologies, automation in domestic environments keep on meeting commercial failures. The main reason for this is the development process that is used to build the automation applications, which tend to focus more on technical aspects rather than on the needs and limitations of the users. An instance of this problem is the complex and poorly designed home automation front-ends that deter customers from investing in a home automation product. On the other hand, developing a usable and interactive interface is a complicated task for developers due to the multidisciplinary challenges that need to be identified and solved. In this context, the current research work investigates the different design problems associated with developing a home automation interface as well as the existing design solutions that are applied to these problems. The Qualitative Data Analysis approach was used for collecting data from research papers and the open coding process was used to cluster the findings. From the analysis of the data collected, requirements for designing the interface were derived. A home energy management functionality for a Web-based home automation front-end was developed as a proof-of-concept and a user evaluation was used to assess the usability of the interface. The results of the evaluation showed that this holistic approach to designing interfaces improved its usability which increases the chances of its commercial success.