TY - CHAP A1 - Desel, Jörg A1 - Opel, Simone A1 - Siegeris, Juliane A1 - Draude, Claude A1 - Weber, Gerhard A1 - Schell, Timon A1 - Schwill, Andreas A1 - Thorbrügge, Carsten A1 - Schäfer, Len Ole A1 - Netzer, Cajus Marian A1 - Gerstenberger, Dietrich A1 - Winkelnkemper, Felix A1 - Schulte, Carsten A1 - Böttcher, Axel A1 - Thurner, Veronika A1 - Häfner, Tanja A1 - Ottinger, Sarah A1 - Große-Bölting, Gregor A1 - Scheppach, Lukas A1 - Mühling, Andreas A1 - Baberowski, David A1 - Leonhardt, Thiemo A1 - Rentsch, Susanne A1 - Bergner, Nadine A1 - Bonorden, Leif A1 - Stemme, Jonas A1 - Hoppe, Uwe A1 - Weicker, Karsten A1 - Bender, Esther A1 - Barbas, Helena A1 - Hamann, Fabian A1 - Soll, Marcus A1 - Sitzmann, Daniel ED - Desel, Jörg ED - Opel, Simone ED - Siegeris, Juliane T1 - Hochschuldidaktik Informatik HDI 2021 BT - 9. Fachtagung des GI-Fachbereichs Informatik und Ausbildung/Didaktik der Informatik 15.–16. September 2021 in Dortmund T2 - Commentarii informaticae didacticae N2 - Die Fachtagungen HDI (Hochschuldidaktik Informatik) beschäftigen sich mit den unterschiedlichen Aspekten informatischer Bildung im Hochschulbereich. Neben den allgemeinen Themen wie verschiedenen Lehr- und Lernformen, dem Einsatz von Informatiksystemen in der Hochschullehre oder Fragen der Gewinnung von geeigneten Studierenden, deren Kompetenzerwerb oder auch der Betreuung der Studierenden widmet sich die HDI immer auch einem Schwerpunktthema. Im Jahr 2021 war dies die Berücksichtigung von Diversität in der Lehre. Diskutiert wurden beispielsweise die Einbeziehung von besonderen fachlichen und überfachlichen Kompetenzen Studierender, der Unterstützung von Durchlässigkeit aus nichtakademischen Berufen, aber auch die Gestaltung inklusiver Lehr- und Lernszenarios, Aspekte des Lebenslangen Lernens oder sich an die Diversität von Studierenden adaptierte oder adaptierende Lehrsysteme. Dieser Band enthält ausgewählte Beiträge der 9. Fachtagung 2021, die in besonderer Weise die Konferenz und die dort diskutierten Themen repräsentieren. T3 - Commentarii informaticae didacticae (CID) - 13 KW - Hochschuldidaktik KW - Informatikdidaktik KW - HDI KW - Hochschullehre KW - digitale Hochschullehre KW - Diversität KW - Heterogenität KW - Lebenslanges Lernen KW - Informatikstudium KW - Didaktische Konzepte KW - Assessment Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-565070 SN - 978-3-86956-548-4 SN - 1868-0844 SN - 2191-1940 IS - 13 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Prasse, Paul A1 - Iversen, Pascal A1 - Lienhard, Matthias A1 - Thedinga, Kristina A1 - Herwig, Ralf A1 - Scheffer, Tobias T1 - Pre-Training on In Vitro and Fine-Tuning on Patient-Derived Data Improves Deep Neural Networks for Anti-Cancer Drug-Sensitivity Prediction JF - MDPI N2 - Large-scale databases that report the inhibitory capacities of many combinations of candidate drug compounds and cultivated cancer cell lines have driven the development of preclinical drug-sensitivity models based on machine learning. However, cultivated cell lines have devolved from human cancer cells over years or even decades under selective pressure in culture conditions. Moreover, models that have been trained on in vitro data cannot account for interactions with other types of cells. Drug-response data that are based on patient-derived cell cultures, xenografts, and organoids, on the other hand, are not available in the quantities that are needed to train high-capacity machine-learning models. We found that pre-training deep neural network models of drug sensitivity on in vitro drug-sensitivity databases before fine-tuning the model parameters on patient-derived data improves the models’ accuracy and improves the biological plausibility of the features, compared to training only on patient-derived data. From our experiments, we can conclude that pre-trained models outperform models that have been trained on the target domains in the vast majority of cases. KW - deep neural networks KW - drug-sensitivity prediction KW - anti-cancer drugs Y1 - 2022 U6 - https://doi.org/10.3390/cancers14163950 SN - 2072-6694 VL - 14 SP - 1 EP - 14 PB - MDPI CY - Basel, Schweiz ET - 16 ER - TY - CHAP A1 - Curzon, Paul A1 - Kalas, Ivan A1 - Schubert, Sigrid A1 - Schaper, Niclas A1 - Barnes, Jan A1 - Kennewell, Steve A1 - Bröker, Kathrin A1 - Kastens, Uwe A1 - Magenheim, Johannes A1 - Dagiene, Valentina A1 - Stupuriene, Gabriele A1 - Ellis, Jason Brent A1 - Abreu-Ellis, Carla Reis A1 - Grillenberger, Andreas A1 - Romeike, Ralf A1 - Haugsbakken, Halvdan A1 - Jones, Anthony A1 - Lewin, Cathy A1 - McNicol, Sarah A1 - Nelles, Wolfgang A1 - Neugebauer, Jonas A1 - Ohrndorf, Laura A1 - Schaper, Niclas A1 - Schubert, Sigrid A1 - Opel, Simone A1 - Kramer, Matthias A1 - Trommen, Michael A1 - Pottbäcker, Florian A1 - Ilaghef, Youssef A1 - Passig, David A1 - Tzuriel, David A1 - Kedmi, Ganit Eshel A1 - Saito, Toshinori A1 - Webb, Mary A1 - Weigend, Michael A1 - Bottino, Rosa A1 - Chioccariello, Augusto A1 - Christensen, Rhonda A1 - Knezek, Gerald A1 - Gioko, Anthony Maina A1 - Angondi, Enos Kiforo A1 - Waga, Rosemary A1 - Ohrndorf, Laura A1 - Or-Bach, Rachel A1 - Preston, Christina A1 - Younie, Sarah A1 - Przybylla, Mareen A1 - Romeike, Ralf A1 - Reynolds, Nicholas A1 - Swainston, Andrew A1 - Bendrups, Faye A1 - Sysło, Maciej M. A1 - Kwiatkowska, Anna Beata A1 - Zieris, Holger A1 - Gerstberger, Herbert A1 - Müller, Wolfgang A1 - Büchner, Steffen A1 - Opel, Simone A1 - Schiller, Thomas A1 - Wegner, Christian A1 - Zender, Raphael A1 - Lucke, Ulrike A1 - Diethelm, Ira A1 - Syrbe, Jörn A1 - Lai, Kwok-Wing A1 - Davis, Niki A1 - Eickelmann, Birgit A1 - Erstad, Ola A1 - Fisser, Petra A1 - Gibson, David A1 - Khaddage, Ferial A1 - Knezek, Gerald A1 - Micheuz, Peter A1 - Kloos, Carlos Delgado ED - Brinda, Torsten ED - Reynolds, Nicholas ED - Romeike, Ralf ED - Schwill, Andreas T1 - KEYCIT 2014 BT - key competencies in informatics and ICT N2 - In our rapidly changing world it is increasingly important not only to be an expert in a chosen field of study but also to be able to respond to developments, master new approaches to solving problems, and fulfil changing requirements in the modern world and in the job market. In response to these needs key competencies in understanding, developing and using new digital technologies are being brought into focus in school and university programmes. The IFIP TC3 conference "KEYCIT – Key Competences in Informatics and ICT (KEYCIT 2014)" was held at the University of Potsdam in Germany from July 1st to 4th, 2014 and addressed the combination of key competencies, Informatics and ICT in detail. The conference was organized into strands focusing on secondary education, university education and teacher education (organized by IFIP WGs 3.1 and 3.3) and provided a forum to present and to discuss research, case studies, positions, and national perspectives in this field. T3 - Commentarii informaticae didacticae (CID) - 7 KW - Schlüsselkompetenzen KW - Informatik KW - Bildung KW - ICT KW - Informatikdidaktik KW - Key Competencies KW - Informatics KW - education KW - ICT KW - Computer Science Education Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-70325 SN - 978-3-86956-292-6 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - THES A1 - Videla, Santiago T1 - Reasoning on the response of logical signaling networks with answer set programming T1 - Modellierung Logischer Signalnetzwerke mittels Antwortmengenprogrammierung N2 - Deciphering the functioning of biological networks is one of the central tasks in systems biology. In particular, signal transduction networks are crucial for the understanding of the cellular response to external and internal perturbations. Importantly, in order to cope with the complexity of these networks, mathematical and computational modeling is required. We propose a computational modeling framework in order to achieve more robust discoveries in the context of logical signaling networks. More precisely, we focus on modeling the response of logical signaling networks by means of automated reasoning using Answer Set Programming (ASP). ASP provides a declarative language for modeling various knowledge representation and reasoning problems. Moreover, available ASP solvers provide several reasoning modes for assessing the multitude of answer sets. Therefore, leveraging its rich modeling language and its highly efficient solving capacities, we use ASP to address three challenging problems in the context of logical signaling networks: learning of (Boolean) logical networks, experimental design, and identification of intervention strategies. Overall, the contribution of this thesis is three-fold. Firstly, we introduce a mathematical framework for characterizing and reasoning on the response of logical signaling networks. Secondly, we contribute to a growing list of successful applications of ASP in systems biology. Thirdly, we present a software providing a complete pipeline for automated reasoning on the response of logical signaling networks. N2 - Deciphering the functioning of biological networks is one of the central tasks in systems biology. In particular, signal transduction networks are crucial for the understanding of the cellular response to external and internal perturbations. Importantly, in order to cope with the complexity of these networks, mathematical and computational modeling is required. We propose a computational modeling framework in order to achieve more robust discoveries in the context of logical signaling networks. More precisely, we focus on modeling the response of logical signaling networks by means of automated reasoning using Answer Set Programming (ASP). ASP provides a declarative language for modeling various knowledge representation and reasoning problems. Moreover, available ASP solvers provide several reasoning modes for assessing the multitude of answer sets. Therefore, leveraging its rich modeling language and its highly efficient solving capacities, we use ASP to address three challenging problems in the context of logical signaling networks: learning of (Boolean) logical networks, experimental design, and identification of intervention strategies. Overall, the contribution of this thesis is three-fold. Firstly, we introduce a mathematical framework for characterizing and reasoning on the response of logical signaling networks. Secondly, we contribute to a growing list of successful applications of ASP in systems biology. Thirdly, we present a software providing a complete pipeline for automated reasoning on the response of logical signaling networks. KW - Systembiologie KW - logische Signalnetzwerke KW - Antwortmengenprogrammierung KW - systems biology KW - logical signaling networks KW - answer set programming Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-71890 ER - TY - CHAP A1 - Gebser, Martin A1 - Hinrichs, Henrik A1 - Schaub, Torsten H. A1 - Thiele, Sven T1 - xpanda: a (simple) preprocessor for adding multi-valued propositions to ASP N2 - We introduce a simple approach extending the input language of Answer Set Programming (ASP) systems by multi-valued propositions. Our approach is implemented as a (prototypical) preprocessor translating logic programs with multi-valued propositions into logic programs with Boolean propositions only. Our translation is modular and heavily benefits from the expressive input language of ASP. The resulting approach, along with its implementation, allows for solving interesting constraint satisfaction problems in ASP, showing a good performance. Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-41466 ER - TY - CHAP A1 - Geske, Ulrich A1 - Wolf, Armin T1 - Preface N2 - The workshops on (constraint) logic programming (WLP) are the annual meeting of the Society of Logic Programming (GLP e.V.) and bring together researchers interested in logic programming, constraint programming, and related areas like databases, artificial intelligence and operations research. In this decade, previous workshops took place in Dresden (2008), Würzburg (2007), Vienna (2006), Ulm (2005), Potsdam (2004), Dresden (2002), Kiel (2001), and Würzburg (2000). Contributions to workshops deal with all theoretical, experimental, and application aspects of constraint programming (CP) and logic programming (LP), including foundations of constraint/ logic programming. Some of the special topics are constraint solving and optimization, extensions of functional logic programming, deductive databases, data mining, nonmonotonic reasoning, , interaction of CP/LP with other formalisms like agents, XML, JAVA, program analysis, program transformation, program verification, meta programming, parallelism and concurrency, answer set programming, implementation and software techniques (e.g., types, modularity, design patterns), applications (e.g., in production, environment, education, internet), constraint/logic programming for semantic web systems and applications, reasoning on the semantic web, data modelling for the web, semistructured data, and web query languages. KW - Logic Programming KW - Constraint Solving KW - Logics KW - Deduction KW - Planing KW - Optimization Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-41401 ER - TY - THES A1 - Jiang, Chunyan T1 - Multi-visualization and hybrid segmentation approaches within telemedicine framework T1 - Multi-Visualisierung und hybride Segmentierungsansätze auf dem Gebiet der Telemedizin N2 - The innovation of information techniques has changed many aspects of our life. In health care field, we can obtain, manage and communicate high-quality large volumetric image data by computer integrated devices, to support medical care. In this dissertation I propose several promising methods that could assist physicians in processing, observing and communicating the image data. They are included in my three research aspects: telemedicine integration, medical image visualization and image segmentation. And these methods are also demonstrated by the demo software that I developed. One of my research point focuses on medical information storage standard in telemedicine, for example DICOM, which is the predominant standard for the storage and communication of medical images. I propose a novel 3D image data storage method, which was lacking in current DICOM standard. I also created a mechanism to make use of the non-standard or private DICOM files. In this thesis I present several rendering techniques on medical image visualization to offer different display manners, both 2D and 3D, for example, cut through data volume in arbitrary degree, rendering the surface shell of the data, and rendering the semi-transparent volume of the data. A hybrid segmentation approach, designed for semi-automated segmentation of radiological image, such as CT, MRI, etc, is proposed in this thesis to get the organ or interested area from the image. This approach takes advantage of the region-based method and boundary-based methods. Three steps compose the hybrid approach: the first step gets coarse segmentation by fuzzy affinity and generates homogeneity operator; the second step divides the image by Voronoi Diagram and reclassifies the regions by the operator to refine segmentation from the previous step; the third step handles vague boundary by level set model. Topics for future research are mentioned in the end, including new supplement for DICOM standard for segmentation information storage, visualization of multimodal image information, and improvement of the segmentation approach to higher dimension. N2 - Innovative Informationstechnologien haben viele Bereiche unseres Lebens verändert. Im Gesundheitsbereich ist es mittels Computer möglich, qualitativ hochwertige und große volumetrische Bilddaten zu verwalten, zu verarbeiten und dadurch die medizinische Betreuung zu unterstützen. In dieser Dissertation stelle ich verschiedene Methoden vor, die Mediziner beim Prozess der Beobachtung, Verarbeitung und Nutzung von Bilddaten verstärkt unterstützten können. Meine Forschungsarbeit befasst sich mit drei Schwerpunktthemen: Telemedizinintegration, Visualisierung von medizinischen Bildern und Bildsegmentierung. Zur Demonstration der Machbarkeit der vorgeschlagenen Methoden implementierte ich zudem eine Anwendungssoftware. Das entwickelte System kann in punkto Telemedizinintegration nicht nur Dateien im DICOM Format lesen und schreiben, sondern auch nicht-standardisierte Dateien reparieren. In meiner Arbeit gebe ich außerdem einen Vorschlag für eine Erweiterung des DICOM Standards für die Speicherung von 3D Bildinformationen. Zur Darstellung der Bilddaten wurden in dem entwickelten System drei verschiedene Ansichten implementiert: Volumen Ansicht, Oberflächen Ansicht sowie Querschnitt Ansicht. Ein Großteil meiner Arbeit ist der Vorschlag eines neuen hybriden Bildsegmentierungsansatzes. Durch das neu vorgeschlagene Verfahren können komplexe neurale MRI Daten effizient und präzise segmentiert werden. Zusätzlich wird der manuelle Arbeitsaufwand der Experten drastisch verringert. KW - medizinisch KW - bild KW - Segmentierung KW - medical KW - image KW - segmentation Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-12829 ER -