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  • 251.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Perjons, Erik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Preparing for the era of cloud computing: Towards a framework for selecting business process support services2012In: Enterprise, Business-Process and Information Systems Modeling: 13th International Conference, BPMDS 2012, 17th International Conference, EMMSAD 2012, and 5th EuroSymposium, held at CAiSE 2012, Gdańsk, Poland, June 25-26, 2012. Proceedings, Springer Berlin/Heidelberg, 2012, p. 16-30Conference paper (Refereed)
    Abstract [en]

    The shift to the cloud computing creates new opportunities for the IT usage in business. New standard and customizable services that do not require high initial investment allow business people to choose services to support their business activities without involving technicians. Business process solutions providers are already moving their products to the cloud offering them as services. The question arises of how a business person, e.g. a department manager, can decide on which service suits best his/her needs. The paper investigates this issue in respect to the services that provide fully customizable operational support to business processes. The paper suggests a practical framework for defining requirements based on characteristics of the process to be supported by the service. The framework determines the needs of such capabilities as process flow support, shared spaces, team collaboration, etc., based on the high-level analysis of a process in question. The framework is aimed at serving as a basis for designing a practical methodology for selecting business process support services.

  • 252.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Perjons, Erik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Reviving Language/Action Perspective in the Era of Social Software: Research in Progress2012In: Emerging Topics in the Practice of Enterprise Modeling: 5th IFIP WG 8.1Working Conference, PoEM 2012 / [ed] Kurt Sandkuhl, Ulf Seigerroth, Janis Stirna, 2012Conference paper (Refereed)
    Abstract [en]

    Language/Action perspective (LAP) was introduced by Flores and Winograd and their associates in the 1980th. This perspective, which is based on the speech act theory, has been originally suggested as guidelines for designing information systems. Though LAP had some success in designing commercial systems, it had never become widespread as a basis for systems design. This paper suggests reviving LAP, however, not as a tool for system design, but as a tool for analysis of communication models of systems designed on some other principles than LAP. The paper is focused on modern systems of social software type in which communication is based on the usage of shared spaces. The paper is a research in progress report that presents the main ideas, a research plan, and preliminary results achieved in its first two steps: (1) testing LAP for analysis of one system with shared spaces architecture, and (2) classification of atomic communication acts typical for business processes. The long term goal of the research is to create practical recommendations for choosing an appropriate communication model for particular business needs.

  • 253.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Perjons, Erik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Towards a Business Process Modeling Technique for Agile Development of Case Management Systems2017In: Complex Systems Informatics and Modeling Quarterly, E-ISSN 2255-9922, no 13, p. 73-113Article in journal (Refereed)
    Abstract [en]

    A modern organization needs to adapt its behavior to changes in the business environment by changing its Business Processes (BP) and corresponding Business Process Support (BPS) systems. One way of achieving such adaptability is via separation of the system code from the process description/model by applying the concept of executable process models. Furthermore, to ease introduction of changes, such process model should separate different perspectives, for example, control-flow, human resources, and data perspectives, from each other. In addition, for developing a completely new process, it should be possible to start with a reduced process model to get a BPS system quickly running, and then continue to develop it in an agile manner. This article consists of two parts, the first sets requirements on modeling techniques that could be used in the tools that supports agile development of BPs and BPS systems. The second part suggests a business process modeling technique that allows to start modeling with the data/information perspective which would be appropriate for processes supported by Case or Adaptive Case Management (CM/ACM) systems. In a model produced by this technique, called data-centric business process model, a process instance/case is defined as sequence of states in a specially designed instance database, while the process model is defined as a set of rules that set restrictions on allowed states and transitions between them. The article details the background for the project of developing the data-centric process modeling technique, presents the outline of the structure of the model, and gives formal definitions for a substantial part of the model

  • 254.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Perjons, Erik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Using a Fractal Enterprise Model for Business Model Innovation2017In: RADAR+EMISA 2017 BPMDS 2017 RADAR, EMMSAD 2017 RADAR, and EMISA 2017 Workshop: Joint Proceedings / [ed] Jens Gulden, Selmin Nurcan, Iris Reinhartz-Berger, Wided Guédria, Palash Bera, Sérgio Guerreiro, Michael Fellmann, Matthias Weidlich, CEUR-WS.org , 2017, p. 20-29Conference paper (Refereed)
    Abstract [en]

    In their previous work, the authors have developed a new kind of enterprise model, called fractal enterprise model, that connects enterprise processes via assets used for running these processes. One of the possible usages of this model is facilitating innovation, more exactly, changing or extending a business model used in the enterprise. This research-in-progress paper presents the idea of how such facilitation could be arranged, and lists the problems that need to be solved in order to convert the idea into a practical methodology. The discussionis based on a hypothetical example.

  • 255.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Perjons, Erik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Using Fractal Enterprise Model for Business Model Innovation2018In: Advanced Information Systems Engineering: Proceedings / [ed] John Krogstie, Hajo A. Reijers, Springer, 2018, p. 627-628Conference paper (Refereed)
    Abstract [en]

    The pace of changes in the business environment in which a modern enterprise operates requires the enterprise to constantly review its business models in order to survive and prosper in the dynamic world. The tutorial introduces an approach to Business Model Innovation (BMI) based on a new type of enterprise models called Fractal Enterprise Model (FEM). The model express the relationship between the enterprise assets and its business processes. The innovation consists of finding a new way of using enterprise assets to produce value for a new group of customers. The tutorial introduces FEM and shows how it could be used for BMI. The introduction is followed by an exercise in which the participants will apply the approach and invent a new business model for their own organizations.

  • 256.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Perjons, Erik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Using Fractal Enterprise Model to Assist Complexity Management2018In: BIR-WS 2018: BIR Short Papers, Workshops and Doctoral Consortium / [ed] Jelena Zdravkovic, Jānis Grabis, Selmin Nurcan, Janis Stirna, CEUR-WS.org , 2018, p. 233-238Conference paper (Refereed)
    Abstract [en]

    This paper deals with the problems of a complex organizational system in which not each of its parts is directly connected to all other parts. For such a system, it is important to identify which parts/sub-systems need to be directly connected to each other, and which could be left without such connections. The paper puts forward a hypothesis that a suitable enterprise model could be used for this end, and investigates the suitability for this end of one particular enterprise modeling technique called Fractal Enterprise Model.

  • 257.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Perjons, Erik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Using Structural Coupling Approach for Defining and Maintaining Identity of an Educational Institution. Experience Report2018In: 4th International Workshop on Socio-Technical Perspective in IS development (STPIS'18): Proceedings / [ed] Stewart Kowalski, Peter Bednar, Ilia Bider, CEUR-WS.org , 2018, p. 24-39Conference paper (Refereed)
    Abstract [en]

    This paper presents an ongoing study on defining and maintaining organizational identity of an institution of higher education, such as a department or school. The theoretical background used in the study is the concept of structural coupling that comes from biological cybernetics. The study concerns the authors own department. The paper presents proposals of to which elements of the environment such an institution is structurally coupled and how the identity maintenance is arranged. The paper provides examples of how maintaining identity works or not works in practice based on reflections on the authors' experience of working in their own department. It also shows that maintaining identity may requires changes in different components of the socio-technical system, e.g. methods, people, technology.

  • 258.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Perjons, Erik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Elias, Mturi
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Untangling the Dynamic Structure of an Enterprise by Applying a Fractal Approach to Business Processes2012In: The Practice of Enterprise Modeling: Proceedings / [ed] Kurt Sandkuhl, Ulf Seigerroth, Janis Stirna, Berlin/Heidelberg: Springer Berlin/Heidelberg, 2012, p. 61-75Conference paper (Refereed)
    Abstract [en]

    A promising approach for analyzing and designing an enterprise is to consider it as a complex adaptive system (CAS) able to self-adjust to the changes in the environment. An important part of designing a CAS model is to untangle the dynamic structure of an enterprise. This paper presents a procedure for identifying all processes that exist in an enterprise as well as their interconnections. The procedure makes use of a number of process-assets and asset-processes archetypes. The first ones help to find out what assets are needed for a particular process, the second ones help to find out supporting processes that are needed to have each type of assets ready available for deployment. The procedure is based on the ideas of fractal organization where the same pattern is repeated on different levels. The uncovered dynamic structure of an enterprise can support strategic planning, change management, as well as discovering and preventing misbalances between its business processes. The paper also presents an example of applying the procedure to research activities of a university.

  • 259.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Perjons, Erik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Elias, Mturi
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Johannesson, Paul
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    A fractal enterprise model and its application for business development2017In: Software and Systems Modeling, ISSN 1619-1366, E-ISSN 1619-1374, Vol. 16, no 3, p. 663-689Article in journal (Refereed)
    Abstract [en]

    This paper suggests a new type of enterprise models called fractal enterprise models (FEM), with accompanying methodological support for their design. FEM shows interconnections between the business processes in an enterprise by connecting them to the assets they use and manage. Assets considered in the model could be tangible (buildings, heavy machinery, etc.) and intangible (employees, business process definitions, etc.). A FEM model is built by using two types of patterns called archetypes: a process-assets archetype that connects a process with assets used in it, and an asset-processes archetype that connects an asset with processes aimed to manage this asset (e.g., hiring people, or servicing machinery). Alternating these patterns creates a fractal structure that makes relationships between various parts of the enterprise explicit. FEM can be used for different purposes, including finding a majority of the processes in an enterprise and planning business change or radical transformation. Besides discussing FEM and areas of its usage, the paper presents results from a completed project in order to test the practical usefulness of FEM and its related methodological support.

  • 260.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Perjons, Erik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Riaz Dar, Zakria
    Using Data-Centric Business Process Modeling for Discovering Requirements for Business Process Support Systems: Experience Report2013In: Enterprise, Business-Process and Information Systems Modeling BPMDS 2013: Proceedings / [ed] Selmin Nurcan et al., Springer Berlin/Heidelberg, 2013, p. 63-77Conference paper (Refereed)
    Abstract [en]

    Building a process model is a natural part of the requirements engineering (RE) when creating requirements for a computerized system/service to support a business process. When the process in question is workflowable (i.e. a process in which the order and the flow of tasks/ operations/activities can be predefined), there are plenty of modeling techniques, notations and tools that can help in this undertaking. These techniques, however, are of little use for discovering requirements for support of non-workflowable processes in which the information artifacts created in the process (e.g. reports, lecture slides, budget documents) are of more importance than the flow of tasks/operations/activities. Other types of techniques, notations and tools are required in this case. This paper reports on a project of using a data-centric modeling approach supported by a computerized tool in RE. The goal of the project was to test whether the approach could be useful for the task of discovering requirements on a computerized system/service supporting the process, and which and how much of requirements could be captured using it. The process used in the test is a process of course preparation in the authors’ own department. The paper reports on the environment in which the project has been conducted, results achieved, and lessons learned.

  • 261.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Rogers, David
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    YASQLT – Yet Another SQL Tutor: A Pragmatic Approach2016In: Advances in Conceptual Modeling: ER 2016 Workshops, AHA, MoBiD, MORE-BI, MReBA, QMMQ, SCME, and WM2SP, Gifu, Japan, November 14–17, 2016, Proceedings / [ed] Sebastian Link, Juan C. Trujillo, Springer, 2016, p. 197-206Conference paper (Refereed)
    Abstract [en]

    The paper describes an ongoing project of creating an automated assessment tool to help novice students learning SQL in a frame of an introductory database course. In difference to other tools of this kind, the project has chosen a pragmatic approach of focusing on catching common semantic errors, leaving syntax control to professional DBMS. Using agile system development, the project successfully completed two iterations, both of which were tested in practice with satisfactory results. The students appreciated the tool and would like to have similar tools for other subjects, including Relational Algebra, and Conceptual Modeling. The latter is planned for implementation in the near future. The tool is considered to be appropriate for Learning by Failure in the situation of large size classes and short courses.

  • 262.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Schmidt, Rainer
    Preface2016In: Enterprise, Business-Process and Information Systems Modeling: 17th International Conference, BPMDS 2016, 21st International Conference, EMMSAD 2016, Held at CAiSE 2016, Ljubljana, Slovenia, June 13-14,2016, Proceedings / [ed] Rainer Schmidt, Wided Guédria, Ilia Bider, Sérgio Guerreiro, 2016, p. V-VIConference paper (Other academic)
  • 263.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Söderberg, Oscar
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Becoming Agile in a Non-disruptive Way: Is It Possible?2016In: Proceedings of the 18th International Conference on Enterprise Information Systems / [ed] Slimane Hammoudi, Leszek Maciaszek, Michele M. Missikoff, Olivier Camp, José Cordeiro, SciTePress, 2016, Vol. 1, p. 294-305Conference paper (Refereed)
    Abstract [en]

    Due to the increasing popularity of Agile Software Development (ASD), more software development teams are planning to transit to ASD. As ASD substantially differs from the traditional Software Development (TSD), there are a number of issues and challenges that needs to be overcome when transiting to ASD. One of the most difficult challenges here is acquiring an agile “mindset”. The question arises whether it is possible to acquire this mindset with the minimum disruption of an already established TSD process. The paper tries to answer this question by developing a non-disruptive method of transition to ASD, while using a knowledge transformation perspective to identify the main features of ASD mindset and how it differs from the one of TSD. To map the current mindset and plan the movement to the mindset that is more agile, the paper suggests using a process modelling technique that considers the development process as a socio-technical system with components that correspond to the pha ses of the development process. The method suggested in the paper has been designed in connection to a business case of a development team interested to transit to agility in a non-disruptive manner.

  • 264.
    Bider, Ilia
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Söderberg, Oscar
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Moving towards Agility in an Ordered Fashion2017In: Enterprise Information Systems: Revised Selected Papers / [ed] Slimane Hammoudi, Leszek A. Maciaszek, Michele M. Missikoff, Olivier Camp, José Cordeiro, Springer, 2017, p. 175-199Conference paper (Refereed)
    Abstract [en]

    The paper suggests a new method of transiting from Traditional Software Development (TSD) to Agile Software Development (ASD) called non-disruptive transition. The novelty of the method consists of allowing to complete the major transition steps to the agile “mindset” while remaining in the frame of an already established TSD process. The method is being developed using a knowledge transformation perspective to identify the main features of ASD mindset and how it differs from the one of TSD. More specifically, it uses a version of Nonako’s SECI model to represent software development. To analyze the current mindset and plan the movement to the mindset that is more agile, the paper suggests using a process modelling technique that considers the software development process as a complex socio-technical system. The paper also discusses external conditions that might hinder going all the way to becoming agile and require the transition to stop, and how to become agile while developing complex systems.

  • 265.
    Bigün, Elizabeth, Saers
    Stockholm University, Faculty of Social Sciences, Department of Statistics.
    Bayesian risk analysis of rare events, such as catastrophes, by means of expert assessments1997Doctoral thesis, comprehensive summary (Other academic)
  • 266.
    Bin, Xiao
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Self-evolvable Knowledge-enhanced IoT Data Mobility for Smart EnvironmentsArticle in journal (Refereed)
  • 267.
    Bin, Xiao
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Rahim, Rahmani
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Yuhong, Li
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Kanter, Theo
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Edge-based Interoperable Service-driven Information Distribution for Intelligent Pervasive ServicesIn: Pervasive and Mobile Computing, ISSN 1574-1192, E-ISSN 1873-1589Article in journal (Refereed)
  • 268.
    Bjelkmar, Pär
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Modeling of voltage-gated ion channels2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The recent determination of several crystal structures of voltage-gated ion channels has catalyzed computational efforts of studying these remarkable molecular machines that are able to conduct ions across biological membranes at extremely high rates without compromising the ion selectivity.

    Starting from the open crystal structures, we have studied the gating mechanism of these channels by molecular modeling techniques. Firstly, by applying a membrane potential, initial stages of the closing of the channel were captured, manifested in a secondary-structure change in the voltage-sensor. In a follow-up study, we found that the energetic cost of translocating this 310-helix conformation was significantly lower than in the original conformation. Thirdly, collaborators of ours identified new molecular constraints for different states along the gating pathway. We used those to build new protein models that were evaluated by simulations. All these results point to a gating mechanism where the S4 helix undergoes a secondary structure transformation during gating.

    These simulations also provide information about how the protein interacts with the surrounding membrane. In particular, we found that lipid molecules close to the protein diffuse together with it, forming a large dynamic lipid-protein cluster. This has important consequences for the understanding of protein-membrane interactions and for the theories of lateral diffusion of membrane proteins.

    Further, simulations of the simple ion channel antiamoebin were performed where different molecular models of the channel were evaluated by calculating ion conduction rates, which were compared to experimentally measured values. One of the models had a conductance consistent with the experimental data and was proposed to represent the biological active state of the channel.

    Finally, the underlying methods for simulating molecular systems were probed by implementing the CHARMM force field into the GROMACS simulation package. The implementation was verified and specific GROMACS-features were combined with CHARMM and evaluated on long timescales. The CHARMM interaction potential was found to sample relevant protein conformations indifferently of the model of solvent used.

  • 269.
    Bjerva, Johannes
    et al.
    University of Groningen.
    Grigonyte, Gintare
    Stockholm University, Faculty of Humanities, Department of Linguistics, Computational Linguistics.
    Östling, Robert
    Stockholm University, Faculty of Humanities, Department of Linguistics, Computational Linguistics.
    Plank, Barbara
    University of Groningen.
    Neural Networks and Spelling Features for Native Language Identification2017In: Proceedings of the 12th Workshop on Innovative Use of NLP for Building Educational Applications, Association for Computational Linguistics, 2017, p. 235-239Conference paper (Refereed)
    Abstract [en]

    We present the RUG-SU team's submission at the Native Language Identification Shared Task 2017. We combine several approaches into an ensemble, based on spelling error features, a simple neural network using word representations, a deep residual network using word and character features, and a system based on a recurrent neural network. Our best system is an ensemble of neural networks, reaching an F1 score of 0.8323. Although our system is not the highest ranking one, we do outperform the baseline by far.

  • 270. Bjerva, Johannes
    et al.
    Östling, Robert
    Stockholm University, Faculty of Humanities, Department of Linguistics, Computational Linguistics.
    Cross-lingual Learning of Semantic Textual Similarity with Multilingual Word Representations2017In: Proceedings of the 21st Nordic Conference on Computational Linguistics / [ed] Jörg Tiedemann, Linköping: Linköping University Electronic Press, 2017, p. 211-215, article id 024Conference paper (Refereed)
    Abstract [en]

    Assessing the semantic similarity between sentences in different languages is challenging. We approach this problem by leveraging multilingual distributional word representations, where similar words in different languages are close to each other. The availability of parallel data allows us to train such representations on a large amount of languages. This allows us to leverage semantic similarity data for languages for which no such data exists. We train and evaluate on five language pairs, including English, Spanish, and Arabic. We are able to train wellperforming systems for several language pairs, without any labelled data for that language pair.

  • 271.
    Björck, Fredrik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Discovering Information Security Management2005Doctoral thesis, monograph (Other academic)
    Abstract [en]

    This thesis is concerned with issues relating to the management of information security in organisations, motivated by the need for cost-efficient information security.

    It is based on the assumption that: in order to achieve cost-efficient information security, the point of departure must be knowledge about the empirical reality in which the management of information security takes place.

    The data gathering instruments employed are questionnaires with open-ended questions and unstructured research interviews. The empirical material is analysed, and conclusions are drawn following the principles of Grounded Theory. Data sources are professionals in the area of information security management, including information security consultants (n=13), certification auditors (n=8), and information security managers (n=8).

    The main contributions are: an integrated model illustrating the experts’ perceptions concerning the objectives, actors, resources, threats, and countermeasures of information security management; a framework for the evaluation, formation, and implementation of information security management systems; a new approach for the evaluation of information security in organisations; a set of success factors concerning the formation of information security management systems; and a problem inventory concerning the value and assessment of information security education and training.

  • 272.
    Björck, Fredrik
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Henkel, Martin
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Stirna, Janis
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Zdravkovic, Jelena
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Cyber Resilience – Fundamentals for a Definition2015In: New Contributions in Information Systems and Technologies: Volume 1 / [ed] Alvaro Rocha, Ana Maria Correia, Sandor Costanzo, Luis Paulo Reis., Springer, 2015, p. 311-316Conference paper (Refereed)
    Abstract [en]

    This short paper examines the concept of cyber resilience from an organizational perspective. Cyber resilience is defined as “the ability to continuously deliver the intended outcome despite adverse cyber events”, and this definition is systematically described and justified. The fundamental building blocks of cyber resilience are identified and analyzed through the contrasting of cyber resilience against cybersecurity with regards to five central characteristics.

  • 273.
    Björkholm, Patrik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Protein Interactions from the Molecular to the Domain Level2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The basic unit of life is the cell, from single-cell bacteria to the largest creatures on the planet. All cells have DNA, which contains the blueprint for proteins. This information is transported in the form of messenger RNA from the genome to ribosomes where proteins are produced. Proteins are the main functional constituents of the cell, they usually have one or several functions and are the main actors in almost all essential biological processes. Proteins are what make the cell alive. Proteins are found as solitary units or as part of large complexes. Proteins can be found in all parts of the cell, the most common place being the cytoplasm, a central space in all cells. They are also commonly found integrated into or attached to various membranes.

    Membranes define the cell architecture. Proteins integrated into the membrane have a wide number of responsibilities: they are the gatekeepers of the cell, they secrete cellular waste products, and many of them are receptors and enzymes.

    The main focus of this thesis is the study of protein interactions, from the molecular level up to the protein domain level.

    In paper I use reoccurring local protein structures to try and predict what sections of a protein interacts with another part using only sequence information. In papers II and III we use a randomization approach on a membrane protein motif that we know interacts with a sphingomyelin lipid to find other candidate proteins that interact with sphingolipids. These are then experimentally verified as sphingolipid-binding. In the last paper, paper IV, we look at how protein domain interaction networks overlap and can be evaluated.

  • 274.
    Björkholm, Patrik
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Ernst, Andreas
    Hacke, Moritz
    Wieland, Felix
    Brügger, Britta
    von Heijne, Gunnar
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Identification of novel sphingolipid-binding motifs in mammalian membrane proteinsManuscript (preprint) (Other academic)
    Abstract [en]

    Specific interactions between transmembrane proteins and sphingolipids is a poorly understood phenomenon, and only a couple of instances have been identified. The best characterized example is the sphingolipid-binding motif VXXTLXXIY found in the transmembrane helix of the vesicular transport protein p24. Here, we have used a simple motif- probability algorithm (MOPRO) to identify proteins that contain putative sphingolipid-binding motifs in a dataset comprising full proteomes from mammalian organisms. Four selected candidate proteins all tested positive for sphingolipid binding in a photoaffinity assay. The putative sphingolipid-binding motifs are noticeably enriched in the 7TM family of G-protein coupled receptors, predominantly in transmembrane helix 6. 

  • 275. Björkqvist, Olof
    et al.
    Larsson, Aron
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Idefeldt, Jim
    Risk Assessment of New Pricing Strategies in the District Heating Market: A Case Study at Sundsvall Energi AB2010In: Energy Policy, ISSN 0301-4215, E-ISSN 1873-6777, Vol. 38, no 5, p. 2171-2178Article in journal (Refereed)
    Abstract [en]

    The price structure of district heating has been no major scientific issue for the last decades in energy-related research. However, today trends in district heating pricing tend to move towards a more customer-oriented approach with predetermined prices under a longer periods, leading to a more complex price structure. If a district heating supplier offers district heating with predetermined prices in order to compete with similar electricity offers, the financial risk of the new price structure is significantly higher than the risk of an ordinary variable cost offer based on short-run marginal cost. In contrary to an electricity seller, the district heating company cannot transfer all of the risk of predetermined prices to the financial market, instead the company is thrown upon its own ability to handle the risk by, e.g., hedging its own energy purchase. However, all uncertainties cannot be coped with in this manner. Thus, there is a need for a methodology that can be used to estimate the financial risk of different price structures and to value different opportunities to reduce the risk. In this article, we propose a methodology, implemented in prototype software, to evaluate the risk associated with new price structures in district heating.

  • 276. Bloom, Bard
    et al.
    Field, John
    Nystrom, Nathaniel
    Oestlund, Johan
    Richards, Gregor
    Strnisa, Rok
    Vitek, Jan
    Wrigstad, Tobias
    Stockholm University, Faculty of Humanities, Department of Scandinavian Languages.
    Thorn-Robust, Concurrent, Extensible Scripting on the JVM2009In: SIGPLAN notices, ISSN 0362-1340, E-ISSN 1558-1160, Vol. 44, no 10, p. 117-136Article in journal (Refereed)
    Abstract [en]

    Scripting languages enjoy great popularity due to their support for rapid and exploratory development. They typically have lightweight syntax, weak data privacy, dynamic typing, powerful aggregate data types, and allow execution of the completed parts of incomplete programs. The price of these features comes later in the software life cycle. Scripts are hard to evolve and compose, and often slow. An additional weakness of most scripting languages is lack of support for concurrency-though concurrency is required for scalability and interacting with remote services. This paper reports on the design and implementation of Thorn, a novel programming language targeting the JVM. Our principal contributions are a careful selection of features that support the evolution of scripts into industrial grade programs-e.g., an expressive module system, an optional type annotation facility for declarations, and support for concurrency based on message passing between lightweight, isolated processes. On the implementation side, Thorn has been designed to accommodate the evolution of the language itself through a compiler plugin mechanism and target the Java virtual machine.

  • 277.
    Blåsjö, Mona
    et al.
    Stockholm University, Faculty of Humanities, Department of Scandinavian Languages.
    Knutsson, Ola
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Cerratto-Pargman, Teresa
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Exploring the Design Space of Genre Pedagogy and Virtual Learning Environments2012In: Designs for Learning 2012: 3rd International Conference Exploring Learning Environments. Conference Proceedings, 2012, p. 75-77Conference paper (Refereed)
    Abstract [en]

    This paper explores the design space of genre pedagogy and virtual learning environments. This is done by examining the cornerstones of genre pedagogy and the main activities they give raise to, and how the activities are transformed when they are partly or completely moved from the classroom to virtual learning environments, and what implications for interaction design they give raise to.

  • 278. Boella, Guido
    et al.
    Noriega, Pablo
    Pigozzi, Gabriella
    Verhagen, Harko
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Introduction to the special issue on NorMAS 20092013In: Journal of logic and computation (Print), ISSN 0955-792X, E-ISSN 1465-363X, Vol. 23, no 2, p. 307-308Article in journal (Other academic)
  • 279. Boella, Guido
    et al.
    Pigozzi, Gabriella
    Singh, Munindar
    Verhagen, Harko
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Normative Multiagent Systems: Guest Editors’ Introduction2010In: Logic journal of the IGPL (Print), ISSN 1367-0751, E-ISSN 1368-9894, Vol. 18, no 1, p. 1-3Article in journal (Refereed)
  • 280. Boella, Guido
    et al.
    van der Torre, Leendert
    Verhagen, Harko
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Introduction to Normative Multiagent Systems2006In: Computational and mathematical organization theory, ISSN 1381-298X, E-ISSN 1572-9346, Vol. 12, no 2-3, p. 71-79Article in journal (Refereed)
    Abstract [en]

    This article introduces the research issues related to and definition of normative multiagent systems. It also describes the papers selected from NorMAS05 that are part of this double special issue and relates the papers to each other.

  • 281.
    Boella, Guido
    et al.
    Universita di Torino, , Dipartimento di Informatica.
    van der Torre, Leendert
    University of Luxembourg, , Computer Science and Communication Research Unit.
    Verhagen, Harko
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Ten Challenges for Normative Multiagent Systems2008In: Programming Multi-Agent Systems, Programming Multi-Agent Systems , 2008Conference paper (Refereed)
    Abstract [en]

    In this paper we discuss the shift from a legal to an interactionist view on normative multiagent systems, examples, and ten new challenges in this more dynamic setting.

  • 282.
    Boeva, Veselka
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Ekenberg, Love
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    A transition logic for schemata conflicts2004In: Data & Knowledge Engineering, ISSN 0169-023X, E-ISSN 1872-6933, Vol. 51, no 3, p. 277-294Article in journal (Refereed)
    Abstract [en]

    Conflict detection and analysis are of high importance, e.g., when integrating conceptual schemata, such as UML-Specifications, or analysing goal-fulfilment of sets of autonomous agents. In general, models for this introduce unnecessarily complicated frameworks with several disadvantages regarding semantics as well as complexity. This paper demonstrates that an important set of static and dynamic conflicts between specifications can be diagnosed using ordinary first-order modal logic. Furthermore, we show how the framework can be extended for handling situations when there are convex sets of probability measures over a state-space. Thus, representing specifications as conceptual schemata and using standard Kripke models of modal logic, augmented with an interval-valued probability measure, we propose instrumental definitions and procedures for conflict detection.

  • 283.
    Bohman, Samuel
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Civic Participation and Empowerment through Visualization2015In: Proceedings of SIGRAD 2015, June 1st and 2nd, Stockholm, Sweden / [ed] Christopher E. Peters and Lars Kjelldahl, Linköping: Linköping University Electronic Press, 2015, p. 20-23Conference paper (Refereed)
    Abstract [en]

    This article elaborates on the use of data visualization to promote civic participation and democratic engagement. The power and potential of data visualization is examined through a brief historical overview and four interconnected themes that provide new opportunities for electronic participation research: data storytelling, infographics, data physicalization, and quantified self. The goal is to call attention to this space and encourage a larger community of researchers to explore the possibilities that data visualization can bring.

  • 284.
    Bohman, Samuel
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Data Visualization: An Untapped Potential for Political Participation and Civic Engagement2015In: Electronic Government and the Information Systems Perspective: 4th International Conference, EGOVIS 2015, Valencia, Spain, September 1-3, 2015, Proceedings / [ed] Andrea Kö, Enrico Francesconi, Springer, 2015, p. 302-315Conference paper (Refereed)
    Abstract [en]

    This article elaborates on the use of data visualization to promote a more informed and engaged participation in civic and democratic life. First, it outlines the main constraints and challenges in electronic participation research and concludes that the conventional deliberative approach to political participation has been impeding civic engagement. Then, through a couple of recent examples and a brief historical overview, it examines the power of data visualization. Following this, it explores the democratization of data visualization through four interconnected themes that provide new opportunities for political participation and civic engagement research: data storytelling, infographics, data physicalisation, and the quantified self. The goal is to call attention to this space and encourage a larger community of researchers to explore the possibilities that data visualization can bring.

  • 285.
    Bohman, Samuel
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Information Technology in eParticipation Research: A Word Frequency Analysis2014In: Electronic Participation: Proceedings, Springer Berlin/Heidelberg, 2014, p. 78-89Conference paper (Refereed)
    Abstract [en]

    Recent literature and project reviews suggest information technology is inadequately reflected in eParticipation research. This study uses text search queries to investigate the occurrence of 60 technology categories in a bibliographic database consisting of over a thousand research articles. The results show that eParticipation research have overwhelmingly focused on websites and discussion forums as the main technologies under study. Many other technologies that are frequently mentioned in overview articles as being part of eParticipation have received relatively scant attention in actual research. This article presents findings that may be useful in broadening and deepening the field’s treatment of technology.

  • 286.
    Bohman, Samuel
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Hansson, Henrik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Mobini, Pooyeh
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Online participation in higher education decision-making: a mixed methods study of the MyUniversity EU-project2014In: eJournal of eDemocracy and Open Government, ISSN 2075-9517, Vol. 6, p. 267-285Article in journal (Refereed)
    Abstract [en]

    This article considers online participation in higher education decision-making using the MyUniversity EU project as a case study. MyUniversity was a pilot designed to provide European universities with a web-based system to empower and involve students and other members of the academic community in the Bologna Process. Thirteen universities in Spain, Slovakia, Bulgaria, and Lithuania participated in trials. The study uses data collection methods from across the quantitative and qualitative spectrum: web analytics, online surveys, key performance indicators, interviews, focus groups, participant observation, document studies, and usability evaluations. The results are represented by 10 themes: project design, participation, functionality and usability, impact on decision-making, privacy and trust, institutional resistance, motivational factors, the political, economic, and sociocultural context, language barriers, and moderation and framing. The article ends with a discussion based on the results, including recommendations for future research.

  • 287.
    Bohman, Samuel
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Kalinina, Maria
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Larsson, Aron
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Trade-off in statistical design process2012Conference paper (Other academic)
    Abstract [en]

    The design and planning of a statistical survey can be regarded as a complex decision process involving multiple stakeholders and a diverse set of users. The process involves finding a balance between statistical quality, burden on respondents and costs. Our research is aimed towards developing a prototype system consisting of computational core based on the combination of multi-objective optimization, multi-criteria analysis, and a user-friendly interface. The overall objective of the research is to maximize statistical quality while minimizing the burden on respondents and costs.

  • 288. Bolelli, K.
    et al.
    Musdal, Yaman
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Aki-Yalcin, E.
    Mannervik, Bengt
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Yalcin, I.
    Synthesis and activity mechanism of some novel 2-substituted benzothiazoles as hGSTP1-1 enzyme inhibitors2017In: SAR and QSAR in environmental research (Print), ISSN 1062-936X, E-ISSN 1029-046X, Vol. 28, no 11, p. 927-940Article in journal (Refereed)
    Abstract [en]

    Human GSTP1-1 is one of the most important proteins, which overexpresses in a large number of human tumours and is involved in the development of resistance to several anticancer drugs. So, it has become an important target in cancer treatment. In this study, 12 benzothiazole derivatives were synthesized and screened for their in vitro inhibitory activity for hGSTP1-1. Among these compounds, two of them (compounds #2 and #5) have been found to be the leads when compared with the reference drug etoposide. In order to analyse the structure-activity relationships (SARs) and to investigate the binding side interactions of the observed lead compounds, a HipHop pharmacophore model was generated and the molecular docking studies were performed by using CDocker method. In conclusion, it is observed that the lead compounds #2 and #5 possessed inhibitory activity on the hGSTP1-1 by binding to the H-site as a substrate in which the para position of the phenyl ring of the benzamide moiety on the benzothiazole ring is important. Substitution at this position with a hydrophobic group that reduces the electron density at the phenyl ring is required for the interaction with the H side active residue Tyr108.

  • 289.
    Boman, Magnus
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Holm, Einar
    Multi-agent systems, time geography, and microsimulations2004In: Systems Approaches and their Application / [ed] Olsson, M-O. and Sjöstedt, G., Boston: Kluwer Academic , 2004Chapter in book (Other academic)
  • 290. Bonnay, Denis
    et al.
    Westerståhl, Dag
    Stockholm University, Faculty of Humanities, Department of Philosophy.
    Dynamic Versus Classical Consequence2014In: Johan van Benthem on Logic and Information Dynamics / [ed] Baltag, A.; Smets, S., Dordrecht: Springer, 2014, Vol. 5, p. 837-854Chapter in book (Refereed)
    Abstract [en]

    The shift of interest in logic from just reasoning to all forms of information flow has considerably widened the scope of the discipline, as amply illustrated in Johan van Benthem's recent book Logical Dynamics of Information and Interaction. But how much does this change when it comes to the study of traditional logical notions such as logical consequence? We propose a systematic comparison between classical consequence, explicated in terms of truth preservation, and a dynamic notion of consequence, explicated in terms of information flow. After a brief overview of logical consequence relations and the distinctive features of classical consequence, we define classical and dynamic consequence over abstract information frames. We study the properties of information under which the two notions prove to be equivalent, both in the abstract setting of information frames and in the concrete setting of Public Announcement Logic. The main lesson is that dynamic consequence diverges from classical consequence when information is not persistent, which is in particular the case of epistemic information about what we do not yet know. We end by comparing our results with recent work by Rothschild and Yalcin on the conditions under which the dynamics of information updates can be classically represented. We show that classicality for consequence is strictly less demanding than classicality for updates. Johan van Benthem's recent book Logical Dynamics of Information and Interaction [8] can be seen as a passionate plea for a radically new view of logic. To be sure, the book is not a philosophical discussion of what logic is but rather an impressive series of illustrations of what logic can be, with presentations of numerous logical languages and a wealth of meta-logical results about them. The view is called simply Logical Dynamics, and contrasted with more traditional views of logic, and also with the earlier view from e.g. [5], now called Pluralism, in which logic was seen as the study of consequence relations. According to Logical Dynamics, logic is not only about reasoning, about what follows from what, but about all aspects of information flow among rational agents. Not just proof and inference, but observations, questions, announcements, communication, plans, strategies, etc. are first-class citizens in the land of Logic. And not only the output of these activities belong to logic, but also the processes leading up to it. This is a fascinating and inspiring view of logic. But how different is it from a more standard view? In particular, what does it change for the analysis of logical consequence, which had been the focus of traditional logical enquiry? This paper attempts some answers to the latter question, with a view to get clearer about the former.

  • 291. Boonman, Hettie J.
    et al.
    Siddiqui, Afzal S.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences. University College London, UK; HEC Montréal, Canada.
    Capacity optimization under uncertainty: The impact of operational time lags2017In: European Journal of Operational Research, ISSN 0377-2217, E-ISSN 1872-6860, Vol. 262, no 2, p. 660-672Article in journal (Refereed)
    Abstract [en]

    Time lags in switching operational modes are typical in the manufacturing and power sectors but are not treated in most real options models. In this paper, we consider a firm that has the opportunity to suspend and to resume production infinitely many times subject to a time lag after each startup decision. We contribute to the literature by allowing the firm to determine its level of installed capacity in conjunction with its optimal investment timing. We find that an increase in the length of the time lag results in an increase in the optimal capacity level. Capacity optimization also interacts with the length of the time lag to affect investment timing and the triggers to suspend and resume production, thereby weakening the result about hysteresis from a standard real options model. Under the assumption of a fixed level of capacity, a longer lag speeds up the decision to resume operations due to a positive upside to the revenue but delays the suspension of operations. By contrast, with capacity optimization, a longer time lag results in a larger capacity choice, which can indirectly delay the investment decision and the timing to resume operations. This indirect effect dominates when the level of market uncertainty is low and the time lag is initially small.

  • 292.
    Borg Gyllenbäck, Katarina
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Boman, Magnus
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Narrative Bridging2011In: Design Computing and Cognition ’10 / [ed] John S. Gero, Berlin: Springer Verlag , 2011, p. 525-544Conference paper (Refereed)
    Abstract [en]

    In the design of interactive media, various forms of intuitive practice come into play. It might prove tempting to use templates and strong narrative structures instead of developing the narrative directly for interactive media. This leads towards computer implementation too swiftly. The narrative bridging method focuses on the initial design phase, in which the conceptual modeling takes place. The purpose is to provide designers with a non-intrusive method that supports the design process without interfering with its creative elements. The method supports the sentient construction of digital games with a narrative, with the ultimate goal of enhancing the player’s experience. A prototype test served as a first evaluation, and two games from that test are showcased here for the purpose of illustrating the hands-on use of narrative bridging. The test demonstrated that the method could aid time-constrained design, and in the process detect inconsistencies that could prevent the design team from making improvements. The method also provided teams with a shared vocabulary and outlook.

  • 293. Borking, Kjell
    et al.
    Danielson, Mats
    Davies, Guy
    Ekenberg, Love
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Idefeldt, Jim
    Larsson, Aron
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Transcending Business Intelligence2011Book (Other academic)
  • 294. Borking, Kjell
    et al.
    Danielson, Mats
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Ekenberg, Love
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Idefeldt, Jim
    Larsson, Aron
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Bortom Business Intelligence2009 (ed. 1)Book (Other academic)
  • 295. Bornemann, Leon
    et al.
    Lecerf, Jason
    Papapetrou, Panagiotis
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    STIFE: A Framework for Feature-based Classification of Sequences of Temporal Intervals2016In: Discovery Science: 19th International Conference, DS 2016, Bari, Italy, October 19–21, 2016, Proceedings / [ed] Toon Calders, Michelangelo Ceci, Donato Malerba, Springer, 2016, p. 85-100Conference paper (Refereed)
    Abstract [en]

    In this paper, we study the problem of classification of sequences of temporal intervals. Our main contribution is the STIFE framework for extracting relevant features from interval sequences to build feature-based classifiers. STIFE uses a combination of basic static metrics, shapelet discovery and selection, as well as distance-based approaches. Additionally, we propose an improved way of computing the state of the art IBSM distance measure between two interval sequences, that reduces both runtime and memory needs from pseudo-polynomial to fully polynomial, which greatly reduces the runtime of distance based classification approaches. Our empirical evaluation not only shows that STIFE provides a very fast classification time in all evaluated scenarios but also reveals that a random forests using STIFE achieves similar or better accuracy than the state of the art k-NN classifier.

  • 296. Bornoe, Nis
    et al.
    Barkhuus, Louise
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    TagPad: Supporting Field Interviews and Analysis2013In: iConference 2013 Proceedings / [ed] Linda Schamber, iShools , 2013, p. 316-325Conference paper (Refereed)
    Abstract [en]

    The area of cyberinfrastructures has looked extensively at research within the natural sciences, however, the social sciences have been largely overlooked in terms of novel data collection and analysis systems. We developed a probe tool, TagPad, to look at the process for social science data collection through interviews and surveys. Our research participants found that TagPad facilitated structuring of interviews but we also found that the setting in which the interview takes place is essential to the success of using this particular tool. We conclude suggesting future designs of social science research tools.

  • 297.
    Boström, Henrik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Concurrent Learning of Large-Scale Random Forests2011In: Scandinavian Conference on Artificial Intelligence, IOS Press , 2011Conference paper (Refereed)
  • 298.
    Boström, Henrik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Estimating Class Probabilities in Random Forests2007In: Proceedings of the Sixth International Conference on Machine Learning and Applications, IEEE , 2007, p. 211-216Conference paper (Refereed)
    Abstract [en]

    For both single probability estimation trees (PETs) and ensembles of such trees, commonly employed class probability estimates correct the observed relative class frequencies in each leaf to avoid anomalies caused by small sample sizes. The effect of such corrections in random forests of PETs is investigated, and the use of the relative class frequency is compared to using two corrected estimates, the Laplace estimate and the m-estimate. An experiment with 34 datasets from the UCI repository shows that estimating class probabilities using relative class frequency clearly outperforms both using the Laplace estimate and the m-estimate with respect to accuracy, area under the ROC curve (AUC) and Brier score. Hence, in contrast to what is commonly employed for PETs and ensembles of PETs, these results strongly suggest that a non-corrected probability estimate should be used in random forests of PETs. The experiment further shows that learning random forests of PETs using relative class frequency significantly outperforms learning random forests of classification trees (i.e., trees for which only an unweighted vote on the most probable class is counted) with respect to both accuracy and AUC, but that the latter is clearly ahead of the former with respect to Brier score.

  • 299.
    Boström, Henrik
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Feature vs. Classifier Fusion for Predictive Data - a Case Study in Pesticide Classification2007In: Proceedings of the 10th International Conference on Information Fusion, IEEE , 2007, p. 1-7Conference paper (Refereed)
    Abstract [en]

    Two strategies for fusing information from multiple sources when generating predictive models in the domain of pesticide classification are investigated: i) fusing different sets of features (molecular descriptors) before building a model and ii) fusing the classifiers built from the individual descriptor sets. An empirical investigation demonstrates that the choice of strategy can have a significant impact on the predictive performance. Furthermore, the experiment shows that the best strategy is dependent on the type of predictive model considered. When generating a decision tree for pesticide classification, a statistically significant difference in accuracy is observed in favor of combining predictions from the individual models compared to generating a single model from the fused set of molecular descriptors. On the other hand, when the model consists of an ensemble of decision trees, a statistically significant difference in accuracy is observed in favor of building the model from the fused set of descriptors compared to fusing ensemble models built from the individual sources.

  • 300. Boström, Henrik
    et al.
    Asker, Lars
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Gurung, Ram
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Karlsson, Isak
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Lindgren, Tony
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Papapetrou, Panagiotis
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Conformal prediction using random survival forests2017In: 16th IEEE International Conference on Machine Learning and Applications: Proceedings / [ed] Xuewen Chen, Bo Luo, Feng Luo, Vasile Palade, M. Arif Wani, Institute of Electrical and Electronics Engineers (IEEE), 2017, p. 812-817Conference paper (Refereed)
    Abstract [en]

    Random survival forests constitute a robust approach to survival modeling, i.e., predicting the probability that an event will occur before or on a given point in time. Similar to most standard predictive models, no guarantee for the prediction error is provided for this model, which instead typically is empirically evaluated. Conformal prediction is a rather recent framework, which allows the error of a model to be determined by a user specified confidence level, something which is achieved by considering set rather than point predictions. The framework, which has been applied to some of the most popular classification and regression techniques, is here for the first time applied to survival modeling, through random survival forests. An empirical investigation is presented where the technique is evaluated on datasets from two real-world applications; predicting component failure in trucks using operational data and predicting survival and treatment of heart failure patients from administrative healthcare data. The experimental results show that the error levels indeed are very close to the provided confidence levels, as guaranteed by the conformal prediction framework, and that the error for predicting each outcome, i.e., event or no-event, can be controlled separately. The latter may, however, lead to less informative predictions, i.e., larger prediction sets, in case the class distribution is heavily imbalanced.

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