@book{MeinelDoellnerWeskeetal.2021,
  author    = {Meinel, Christoph and D{\"o}llner, J{\"u}rgen Roland Friedrich and Weske, Mathias and Polze, Andreas and Hirschfeld, Robert and Naumann, Felix and Giese, Holger and Baudisch, Patrick and Friedrich, Tobias and B{\"o}ttinger, Erwin and Lippert, Christoph and D{\"o}rr, Christian and Lehmann, Anja and Renard, Bernhard and Rabl, Tilmann and Uebernickel, Falk and Arnrich, Bert and H{\"o}lzle, Katharina},
  title     = {Proceedings of the HPI Research School on Service-oriented Systems Engineering 2020 Fall Retreat},
  number    = {138},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-513-2},
  issn      = {1613-5652},
  doi       = {10.25932/publishup-50413},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-504132},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {vi, 144},
  year      = {2021},
  abstract  = {Design and Implementation of service-oriented architectures imposes a huge number of research questions from the fields of software engineering, system analysis and modeling, adaptability, and application integration. Component orientation and web services are two approaches for design and realization of complex web-based system. Both approaches allow for dynamic application adaptation as well as integration of enterprise application. Service-Oriented Systems Engineering represents a symbiosis of best practices in object-orientation, component-based development, distributed computing, and business process management. It provides integration of business and IT concerns. The annual Ph.D. Retreat of the Research School provides each member the opportunity to present his/her current state of their research and to give an outline of a prospective Ph.D. thesis. Due to the interdisciplinary structure of the research school, this technical report covers a wide range of topics. These include but are not limited to: Human Computer Interaction and Computer Vision as Service; Service-oriented Geovisualization Systems; Algorithm Engineering for Service-oriented Systems; Modeling and Verification of Self-adaptive Service-oriented Systems; Tools and Methods for Software Engineering in Service-oriented Systems; Security Engineering of Service-based IT Systems; Service-oriented Information Systems; Evolutionary Transition of Enterprise Applications to Service Orientation; Operating System Abstractions for Service-oriented Computing; and Services Specification, Composition, and Enactment.},
  language  = {en}
}
@article{RezaeiNaeppiLippertetal.2020,
  author    = {Rezaei, Mina and N{\"a}ppi, Janne J. and Lippert, Christoph and Meinel, Christoph and Yoshida, Hiroyuki},
  title     = {Generative multi-adversarial network for striking the right balance in abdominal image segmentation},
  series = {International journal of computer assisted radiology and surgery},
  volume    = {15},
  journal   = {International journal of computer assisted radiology and surgery},
  number    = {11},
  publisher = {Springer},
  address   = {Berlin},
  issn      = {1861-6410},
  doi       = {10.1007/s11548-020-02254-4},
  pages     = {1847 -- 1858},
  year      = {2020},
  abstract  = {Purpose: The identification of abnormalities that are relatively rare within otherwise normal anatomy is a major challenge for deep learning in the semantic segmentation of medical images. The small number of samples of the minority classes in the training data makes the learning of optimal classification challenging, while the more frequently occurring samples of the majority class hamper the generalization of the classification boundary between infrequently occurring target objects and classes. In this paper, we developed a novel generative multi-adversarial network, called Ensemble-GAN, for mitigating this class imbalance problem in the semantic segmentation of abdominal images. Method: The Ensemble-GAN framework is composed of a single-generator and a multi-discriminator variant for handling the class imbalance problem to provide a better generalization than existing approaches. The ensemble model aggregates the estimates of multiple models by training from different initializations and losses from various subsets of the training data. The single generator network analyzes the input image as a condition to predict a corresponding semantic segmentation image by use of feedback from the ensemble of discriminator networks. To evaluate the framework, we trained our framework on two public datasets, with different imbalance ratios and imaging modalities: the Chaos 2019 and the LiTS 2017. Result: In terms of the F1 score, the accuracies of the semantic segmentation of healthy spleen, liver, and left and right kidneys were 0.93, 0.96, 0.90 and 0.94, respectively. The overall F1 scores for simultaneous segmentation of the lesions and liver were 0.83 and 0.94, respectively. Conclusion: The proposed Ensemble-GAN framework demonstrated outstanding performance in the semantic segmentation of medical images in comparison with other approaches on popular abdominal imaging benchmarks. The Ensemble-GAN has the potential to segment abdominal images more accurately than human experts.},
  language  = {en}
}
@techreport{DoellnerFriedrichArnrichetal.2022,
  author    = {D{\"o}llner, J{\"u}rgen Roland Friedrich and Friedrich, Tobias and Arnrich, Bert and Hirschfeld, Robert and Lippert, Christoph and Meinel, Christoph},
  title     = {Abschlussbericht KI-Labor ITSE},
  doi       = {10.25932/publishup-57860},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-578604},
  pages     = {60},
  year      = {2022},
  abstract  = {Der Abschlussbericht beschreibt Aufgaben und Ergebnisse des KI-Labors "ITSE". Gegenstand des KI-Labors bildeten Methodik, Technik und Ausbildung in der IT-Systemtechnik zur Analyse, Planung und Konstruktion KI-basierter, komplexer IT-Systeme.},
  language  = {de}
}
@article{FehrJaramilloGutierrezOalaetal.2022,
  author    = {Fehr, Jana and Jaramillo-Gutierrez, Giovanna and Oala, Luis and Gr{\"o}schel, Matthias I. and Bierwirth, Manuel and Balachandran, Pradeep and Werneck-Leite, Alixandro and Lippert, Christoph},
  title     = {Piloting a Survey-Based Assessment of Transparency and Trustworthiness with Three Medical AI Tools},
  series = {Healthcare},
  volume    = {10},
  journal   = {Healthcare},
  number    = {10},
  publisher = {MDPI},
  address   = {Basel, Schweiz},
  issn      = {2227-9032},
  doi       = {10.3390/healthcare10101923},
  pages     = {30},
  year      = {2022},
  abstract  = {Artificial intelligence (AI) offers the potential to support healthcare delivery, but poorly trained or validated algorithms bear risks of harm. Ethical guidelines stated transparency about model development and validation as a requirement for trustworthy AI. Abundant guidance exists to provide transparency through reporting, but poorly reported medical AI tools are common. To close this transparency gap, we developed and piloted a framework to quantify the transparency of medical AI tools with three use cases. Our framework comprises a survey to report on the intended use, training and validation data and processes, ethical considerations, and deployment recommendations. The transparency of each response was scored with either 0, 0.5, or 1 to reflect if the requested information was not, partially, or fully provided. Additionally, we assessed on an analogous three-point scale if the provided responses fulfilled the transparency requirement for a set of trustworthiness criteria from ethical guidelines. The degree of transparency and trustworthiness was calculated on a scale from 0\% to 100\%. Our assessment of three medical AI use cases pin-pointed reporting gaps and resulted in transparency scores of 67\% for two use cases and one with 59\%. We report anecdotal evidence that business constraints and limited information from external datasets were major obstacles to providing transparency for the three use cases. The observed transparency gaps also lowered the degree of trustworthiness, indicating compliance gaps with ethical guidelines. All three pilot use cases faced challenges to provide transparency about medical AI tools, but more studies are needed to investigate those in the wider medical AI sector. Applying this framework for an external assessment of transparency may be infeasible if business constraints prevent the disclosure of information. New strategies may be necessary to enable audits of medical AI tools while preserving business secrets.},
  language  = {en}
}
@misc{FehrJaramilloGutierrezOalaetal.2022,
  author    = {Fehr, Jana and Jaramillo-Gutierrez, Giovanna and Oala, Luis and Gr{\"o}schel, Matthias I. and Bierwirth, Manuel and Balachandran, Pradeep and Werneck-Leite, Alixandro and Lippert, Christoph},
  title     = {Piloting a Survey-Based Assessment of Transparency and Trustworthiness with Three Medical AI Tools},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Reihe der Digital Engineering Fakult{\"a}t},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Reihe der Digital Engineering Fakult{\"a}t},
  number    = {15},
  doi       = {10.25932/publishup-58328},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-583281},
  pages     = {30},
  year      = {2022},
  abstract  = {Artificial intelligence (AI) offers the potential to support healthcare delivery, but poorly trained or validated algorithms bear risks of harm. Ethical guidelines stated transparency about model development and validation as a requirement for trustworthy AI. Abundant guidance exists to provide transparency through reporting, but poorly reported medical AI tools are common. To close this transparency gap, we developed and piloted a framework to quantify the transparency of medical AI tools with three use cases. Our framework comprises a survey to report on the intended use, training and validation data and processes, ethical considerations, and deployment recommendations. The transparency of each response was scored with either 0, 0.5, or 1 to reflect if the requested information was not, partially, or fully provided. Additionally, we assessed on an analogous three-point scale if the provided responses fulfilled the transparency requirement for a set of trustworthiness criteria from ethical guidelines. The degree of transparency and trustworthiness was calculated on a scale from 0\% to 100\%. Our assessment of three medical AI use cases pin-pointed reporting gaps and resulted in transparency scores of 67\% for two use cases and one with 59\%. We report anecdotal evidence that business constraints and limited information from external datasets were major obstacles to providing transparency for the three use cases. The observed transparency gaps also lowered the degree of trustworthiness, indicating compliance gaps with ethical guidelines. All three pilot use cases faced challenges to provide transparency about medical AI tools, but more studies are needed to investigate those in the wider medical AI sector. Applying this framework for an external assessment of transparency may be infeasible if business constraints prevent the disclosure of information. New strategies may be necessary to enable audits of medical AI tools while preserving business secrets.},
  language  = {en}
}
@misc{MontiRautenstrauchGhanbarietal.2022,
  author    = {Monti, Remo and Rautenstrauch, Pia and Ghanbari, Mahsa and Rani James, Alva and Kirchler, Matthias and Ohler, Uwe and Konigorski, Stefan and Lippert, Christoph},
  title     = {Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Reihe der Digital Engineering Fakult{\"a}t},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Reihe der Digital Engineering Fakult{\"a}t},
  number    = {16},
  doi       = {10.25932/publishup-58607},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-586078},
  pages     = {16},
  year      = {2022},
  abstract  = {Here we present an exome-wide rare genetic variant association study for 30 blood biomarkers in 191,971 individuals in the UK Biobank. We compare gene- based association tests for separate functional variant categories to increase interpretability and identify 193 significant gene-biomarker associations. Genes associated with biomarkers were ~ 4.5-fold enriched for conferring Mendelian disorders. In addition to performing weighted gene-based variant collapsing tests, we design and apply variant-category-specific kernel-based tests that integrate quantitative functional variant effect predictions for mis- sense variants, splicing and the binding of RNA-binding proteins. For these tests, we present a computationally efficient combination of the likelihood- ratio and score tests that found 36\% more associations than the score test alone while also controlling the type-1 error. Kernel-based tests identified 13\% more associations than their gene-based collapsing counterparts and had advantages in the presence of gain of function missense variants. We introduce local collapsing by amino acid position for missense variants and use it to interpret associations and identify potential novel gain of function variants in PIEZO1. Our results show the benefits of investigating different functional mechanisms when performing rare-variant association tests, and demonstrate pervasive rare-variant contribution to biomarker variability.},
  language  = {en}
}
@article{MontiRautenstrauchGhanbarietal.2022,
  author    = {Monti, Remo and Rautenstrauch, Pia and Ghanbari, Mahsa and Rani James, Alva and Kirchler, Matthias and Ohler, Uwe and Konigorski, Stefan and Lippert, Christoph},
  title     = {Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes},
  series = {Nature Communications},
  volume    = {13},
  journal   = {Nature Communications},
  publisher = {Nature Publishing Group UK},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-022-32864-2},
  pages     = {16},
  year      = {2022},
  abstract  = {Here we present an exome-wide rare genetic variant association study for 30 blood biomarkers in 191,971 individuals in the UK Biobank. We compare gene- based association tests for separate functional variant categories to increase interpretability and identify 193 significant gene-biomarker associations. Genes associated with biomarkers were ~ 4.5-fold enriched for conferring Mendelian disorders. In addition to performing weighted gene-based variant collapsing tests, we design and apply variant-category-specific kernel-based tests that integrate quantitative functional variant effect predictions for mis- sense variants, splicing and the binding of RNA-binding proteins. For these tests, we present a computationally efficient combination of the likelihood- ratio and score tests that found 36\% more associations than the score test alone while also controlling the type-1 error. Kernel-based tests identified 13\% more associations than their gene-based collapsing counterparts and had advantages in the presence of gain of function missense variants. We introduce local collapsing by amino acid position for missense variants and use it to interpret associations and identify potential novel gain of function variants in PIEZO1. Our results show the benefits of investigating different functional mechanisms when performing rare-variant association tests, and demonstrate pervasive rare-variant contribution to biomarker variability.},
  language  = {en}
}