@phdthesis{Haarmann2022,
  author    = {Haarmann, Stephan},
  title     = {WICKR: A Joint Semantics for Flexible Processes and Data},
  doi       = {10.25932/publishup-54613},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-546137},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xvii, 191},
  year      = {2022},
  abstract  = {Knowledge-intensive business processes are flexible and data-driven. Therefore, traditional process modeling languages do not meet their requirements: These languages focus on highly structured processes in which data plays a minor role. As a result, process-oriented information systems fail to assist knowledge workers on executing their processes. We propose a novel case management approach that combines flexible activity-centric processes with data models, and we provide a joint semantics using colored Petri nets. The approach is suited to model, verify, and enact knowledge-intensive processes and can aid the development of information systems that support knowledge work. Knowledge-intensive processes are human-centered, multi-variant, and data-driven. Typical domains include healthcare, insurances, and law. The processes cannot be fully modeled, since the underlying knowledge is too vast and changes too quickly. Thus, models for knowledge-intensive processes are necessarily underspecified. In fact, a case emerges gradually as knowledge workers make informed decisions. Knowledge work imposes special requirements on modeling and managing respective processes. They include flexibility during design and execution, ad-hoc adaption to unforeseen situations, and the integration of behavior and data. However, the predominantly used process modeling languages (e.g., BPMN) are unsuited for this task. Therefore, novel modeling languages have been proposed. Many of them focus on activities' data requirements and declarative constraints rather than imperative control flow. Fragment-Based Case Management, for example, combines activity-centric imperative process fragments with declarative data requirements. At runtime, fragments can be combined dynamically, and new ones can be added. Yet, no integrated semantics for flexible activity-centric process models and data models exists. In this thesis, Wickr, a novel case modeling approach extending fragment-based Case Management, is presented. It supports batch processing of data, sharing data among cases, and a full-fledged data model with associations and multiplicity constraints. We develop a translational semantics for Wickr targeting (colored) Petri nets. The semantics assert that a case adheres to the constraints in both the process fragments and the data models. Among other things, multiplicity constraints must not be violated. Furthermore, the semantics are extended to multiple cases that operate on shared data. Wickr shows that the data structure may reflect process behavior and vice versa. Based on its semantics, prototypes for executing and verifying case models showcase the feasibility of Wickr. Its applicability to knowledge-intensive and to data-centric processes is evaluated using well-known requirements from related work.},
  language  = {en}
}
@phdthesis{Marwecki2021,
  author    = {Marwecki, Sebastian},
  title     = {Virtualizing physical space},
  doi       = {10.25932/publishup-52033},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-520332},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xi, 128},
  year      = {2021},
  abstract  = {The true cost for virtual reality is not the hardware, but the physical space it requires, as a one-to-one mapping of physical space to virtual space allows for the most immersive way of navigating in virtual reality. Such "real-walking" requires physical space to be of the same size and the same shape of the virtual world represented. This generally prevents real-walking applications from running on any space that they were not designed for. To reduce virtual reality's demand for physical space, creators of such applications let users navigate virtual space by means of a treadmill, altered mappings of physical to virtual space, hand-held controllers, or gesture-based techniques. While all of these solutions succeed at reducing virtual reality's demand for physical space, none of them reach the same level of immersion that real-walking provides. Our approach is to virtualize physical space: instead of accessing physical space directly, we allow applications to express their need for space in an abstract way, which our software systems then map to the physical space available. We allow real-walking applications to run in spaces of different size, different shape, and in spaces containing different physical objects. We also allow users immersed in different virtual environments to share the same space. Our systems achieve this by using a tracking volume-independent representation of real-walking experiences — a graph structure that expresses the spatial and logical relationships between virtual locations, virtual elements contained within those locations, and user interactions with those elements. When run in a specific physical space, this graph representation is used to define a custom mapping of the elements of the virtual reality application and the physical space by parsing the graph using a constraint solver. To re-use space, our system splits virtual scenes and overlap virtual geometry. The system derives this split by means of hierarchically clustering of our virtual objects as nodes of our bi-partite directed graph that represents the logical ordering of events of the experience. We let applications express their demands for physical space and use pre-emptive scheduling between applications to have them share space. We present several application examples enabled by our system. They all enable real-walking, despite being mapped to physical spaces of different size and shape, containing different physical objects or other users. We see substantial real-world impact in our systems. Today's commercial virtual reality applications are generally designing to be navigated using less immersive solutions, as this allows them to be operated on any tracking volume. While this is a commercial necessity for the developers, it misses out on the higher immersion offered by real-walking. We let developers overcome this hurdle by allowing experiences to bring real-walking to any tracking volume, thus potentially bringing real-walking to consumers. Die eigentlichen Kosten f{\"u}r Virtual Reality Anwendungen entstehen nicht prim{\"a}r durch die erforderliche Hardware, sondern durch die Nutzung von physischem Raum, da die eins-zu-eins Abbildung von physischem auf virtuellem Raum die immersivste Art von Navigation erm{\"o}glicht. Dieses als „Real-Walking" bezeichnete Erlebnis erfordert hinsichtlich Gr{\"o}ße und Form eine Entsprechung von physischem Raum und virtueller Welt. Resultierend daraus k{\"o}nnen Real-Walking-Anwendungen nicht an Orten angewandt werden, f{\"u}r die sie nicht entwickelt wurden. Um den Bedarf an physischem Raum zu reduzieren, lassen Entwickler von Virtual Reality-Anwendungen ihre Nutzer auf verschiedene Arten navigieren, etwa mit Hilfe eines Laufbandes, verf{\"a}lschten Abbildungen von physischem zu virtuellem Raum, Handheld-Controllern oder gestenbasierten Techniken. All diese L{\"o}sungen reduzieren zwar den Bedarf an physischem Raum, erreichen jedoch nicht denselben Grad an Immersion, den Real-Walking bietet. Unser Ansatz zielt darauf, physischen Raum zu virtualisieren: Anstatt auf den physischen Raum direkt zuzugreifen, lassen wir Anwendungen ihren Raumbedarf auf abstrakte Weise formulieren, den unsere Softwaresysteme anschließend auf den verf{\"u}gbaren physischen Raum abbilden. Dadurch erm{\"o}glichen wir Real-Walking-Anwendungen R{\"a}ume mit unterschiedlichen Gr{\"o}ßen und Formen und R{\"a}ume, die unterschiedliche physische Objekte enthalten, zu nutzen. Wir erm{\"o}glichen auch die zeitgleiche Nutzung desselben Raums durch mehrere Nutzer verschiedener Real-Walking-Anwendungen. Unsere Systeme erreichen dieses Resultat durch eine Repr{\"a}sentation von Real-Walking-Erfahrungen, die unabh{\"a}ngig sind vom gegebenen Trackingvolumen - eine Graphenstruktur, die die r{\"a}umlichen und logischen Beziehungen zwischen virtuellen Orten, den virtuellen Elementen innerhalb dieser Orte, und Benutzerinteraktionen mit diesen Elementen, ausdr{\"u}ckt. Bei der Instanziierung der Anwendung in einem bestimmten physischen Raum wird diese Graphenstruktur und ein Constraint Solver verwendet, um eine individuelle Abbildung der virtuellen Elemente auf den physischen Raum zu erreichen. Zur mehrmaligen Verwendung des Raumes teilt unser System virtuelle Szenen und {\"u}berlagert virtuelle Geometrie. Das System leitet diese Aufteilung anhand eines hierarchischen Clusterings unserer virtuellen Objekte ab, die als Knoten unseres bi-partiten, gerichteten Graphen die logische Reihenfolge aller Ereignisse repr{\"a}sentieren. Wir verwenden pr{\"a}emptives Scheduling zwischen den Anwendungen f{\"u}r die zeitgleiche Nutzung von physischem Raum. Wir stellen mehrere Anwendungsbeispiele vor, die Real-Walking erm{\"o}glichen - in physischen R{\"a}umen mit unterschiedlicher Gr{\"o}ße und Form, die verschiedene physische Objekte oder weitere Nutzer enthalten. Wir sehen in unseren Systemen substantielles Potential. Heutige Virtual Reality-Anwendungen sind bisher zwar so konzipiert, dass sie auf einem beliebigen Trackingvolumen betrieben werden k{\"o}nnen, aber aus kommerzieller Notwendigkeit kein Real-Walking beinhalten. Damit entgeht Entwicklern die Gelegenheit eine h{\"o}here Immersion herzustellen. Indem wir es erm{\"o}glichen, Real-Walking auf jedes Trackingvolumen zu bringen, geben wir Entwicklern die M{\"o}glichkeit Real-Walking zu ihren Nutzern zu bringen.},
  language  = {en}
}
@phdthesis{Perscheid2023,
  author    = {Perscheid, Cindy},
  title     = {Integrative biomarker detection using prior knowledge on gene expression data sets},
  doi       = {10.25932/publishup-58241},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-582418},
  school      = {Universit{\"a}t Potsdam},
  pages     = {ix, 197},
  year      = {2023},
  abstract  = {Gene expression data is analyzed to identify biomarkers, e.g. relevant genes, which serve for diagnostic, predictive, or prognostic use. Traditional approaches for biomarker detection select distinctive features from the data based exclusively on the signals therein, facing multiple shortcomings in regards to overfitting, biomarker robustness, and actual biological relevance. Prior knowledge approaches are expected to address these issues by incorporating prior biological knowledge, e.g. on gene-disease associations, into the actual analysis. However, prior knowledge approaches are currently not widely applied in practice because they are often use-case specific and seldom applicable in a different scope. This leads to a lack of comparability of prior knowledge approaches, which in turn makes it currently impossible to assess their effectiveness in a broader context. Our work addresses the aforementioned issues with three contributions. Our first contribution provides formal definitions for both prior knowledge and the flexible integration thereof into the feature selection process. Central to these concepts is the automatic retrieval of prior knowledge from online knowledge bases, which allows for streamlining the retrieval process and agreeing on a uniform definition for prior knowledge. We subsequently describe novel and generalized prior knowledge approaches that are flexible regarding the used prior knowledge and applicable to varying use case domains. Our second contribution is the benchmarking platform Comprior. Comprior applies the aforementioned concepts in practice and allows for flexibly setting up comprehensive benchmarking studies for examining the performance of existing and novel prior knowledge approaches. It streamlines the retrieval of prior knowledge and allows for combining it with prior knowledge approaches. Comprior demonstrates the practical applicability of our concepts and further fosters the overall development and comparability of prior knowledge approaches. Our third contribution is a comprehensive case study on the effectiveness of prior knowledge approaches. For that, we used Comprior and tested a broad range of both traditional and prior knowledge approaches in combination with multiple knowledge bases on data sets from multiple disease domains. Ultimately, our case study constitutes a thorough assessment of a) the suitability of selected knowledge bases for integration, b) the impact of prior knowledge being applied at different integration levels, and c) the improvements in terms of classification performance, biological relevance, and overall robustness. In summary, our contributions demonstrate that generalized concepts for prior knowledge and a streamlined retrieval process improve the applicability of prior knowledge approaches. Results from our case study show that the integration of prior knowledge positively affects biomarker results, particularly regarding their robustness. Our findings provide the first in-depth insights on the effectiveness of prior knowledge approaches and build a valuable foundation for future research.},
  language  = {en}
}