@article{BorchertMockTomczaketal.2021,
  author    = {Borchert, Florian and Mock, Andreas and Tomczak, Aurelie and H{\"u}gel, Jonas and Alkarkoukly, Samer and Knurr, Alexander and Volckmar, Anna-Lena and Stenzinger, Albrecht and Schirmacher, Peter and Debus, J{\"u}rgen and J{\"a}ger, Dirk and Longerich, Thomas and Fr{\"o}hling, Stefan and Eils, Roland and Bougatf, Nina and Sax, Ulrich and Schapranow, Matthieu-Patrick},
  title     = {Knowledge bases and software support for variant interpretation in precision oncology},
  series = {Briefings in bioinformatics},
  volume    = {22},
  journal   = {Briefings in bioinformatics},
  number    = {6},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1467-5463},
  doi       = {10.1093/bib/bbab134},
  pages     = {17},
  year      = {2021},
  abstract  = {Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and molecularly informed treatment recommendations. A wealth of mainly academia-driven knowledge bases calls for software tools supporting the multi-step diagnostic process. We derive a comprehensive list of knowledge bases relevant for variant interpretation by a review of existing literature followed by a survey among medical experts from university hospitals in Germany. In addition, we review cancer variant interpretation tools, which integrate multiple knowledge bases. We categorize the knowledge bases along the diagnostic process in precision oncology and analyze programmatic access options as well as the integration of knowledge bases into software tools. The most commonly used knowledge bases provide good programmatic access options and have been integrated into a range of software tools. For the wider set of knowledge bases, access options vary across different parts of the diagnostic process. Programmatic access is limited for information regarding clinical classifications of variants and for therapy recommendations. The main issue for databases used for biological classification of pathogenic variants and pathway context information is the lack of standardized interfaces. There is no single cancer variant interpretation tool that integrates all identified knowledge bases. Specialized tools are available and need to be further developed for different steps in the diagnostic process.},
  language  = {en}
}
@misc{DellepianeVaidJaladankietal.2021,
  author    = {Dellepiane, Sergio and Vaid, Akhil and Jaladanki, Suraj K. and Coca, Steven and Fayad, Zahi A. and Charney, Alexander W. and B{\"o}ttinger, Erwin and He, John Cijiang and Glicksberg, Benjamin S. and Chan, Lili and Nadkarni, Girish},
  title     = {Acute kidney injury in patients hospitalized with COVID-19 in New York City},
  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    = {5},
  issn      = {2590-0595},
  doi       = {10.25932/publishup-58541},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-585415},
  pages     = {5},
  year      = {2021},
  language  = {en}
}
@article{DellepianeVaidJaladankietal.2021,
  author    = {Dellepiane, Sergio and Vaid, Akhil and Jaladanki, Suraj K. and Coca, Steven and Fayad, Zahi A. and Charney, Alexander W. and B{\"o}ttinger, Erwin and He, John Cijiang and Glicksberg, Benjamin S. and Chan, Lili and Nadkarni, Girish},
  title     = {Acute kidney injury in patients hospitalized with COVID-19 in New York City},
  series = {Kidney medicine},
  volume    = {3},
  journal   = {Kidney medicine},
  number    = {5},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {2590-0595},
  doi       = {10.1016/j.xkme.2021.06.008},
  pages     = {877 -- 879},
  year      = {2021},
  language  = {en}
}
@article{ZhouFischerBrahmsetal.2023,
  author    = {Zhou, Lin and Fischer, Eric and Brahms, Clemens Markus and Granacher, Urs and Arnrich, Bert},
  title     = {DUO-GAIT},
  series = {Scientific data},
  volume    = {10},
  journal   = {Scientific data},
  number    = {1},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2052-4463},
  doi       = {10.1038/s41597-023-02391-w},
  pages     = {10},
  year      = {2023},
  abstract  = {In recent years, there has been a growing interest in developing and evaluating gait analysis algorithms based on inertial measurement unit (IMU) data, which has important implications, including sports, assessment of diseases, and rehabilitation. Multi-tasking and physical fatigue are two relevant aspects of daily life gait monitoring, but there is a lack of publicly available datasets to support the development and testing of methods using a mobile IMU setup. We present a dataset consisting of 6-minute walks under single- (only walking) and dual-task (walking while performing a cognitive task) conditions in unfatigued and fatigued states from sixteen healthy adults. Especially, nine IMUs were placed on the head, chest, lower back, wrists, legs, and feet to record under each of the above-mentioned conditions. The dataset also includes a rich set of spatio-temporal gait parameters that capture the aspects of pace, symmetry, and variability, as well as additional study-related information to support further analysis. This dataset can serve as a foundation for future research on gait monitoring in free-living environments.},
  language  = {en}
}
@article{AndersArnrich2022,
  author    = {Anders, Christoph and Arnrich, Bert},
  title     = {Wearable electroencephalography and multi-modal mental state classification: a systematic literature review},
  series = {Computers in biology and medicine : an international journal},
  volume    = {150},
  journal   = {Computers in biology and medicine : an international journal},
  publisher = {Elsevier Science},
  address   = {Amsterdam [u.a.]},
  issn      = {0010-4825},
  doi       = {10.1016/j.compbiomed.2022.106088},
  pages     = {18},
  year      = {2022},
  abstract  = {Background: Wearable multi-modal time-series classification applications outperform their best uni-modal counterparts and hold great promise. A modality that directly measures electrical correlates from the brain is electroencephalography. Due to varying noise sources, different key brain regions, key frequency bands, and signal characteristics like non-stationarity, techniques for data pre-processing and classification algorithms are task-dependent. Method: Here, a systematic literature review on mental state classification for wearable electroencephalog-raphy is presented. Four search terms in different combinations were used for an in-title search. The search was executed on the 29th of June 2022, across Google Scholar, PubMed, IEEEXplore, and ScienceDirect. 76 most relevant publications were set into context as the current state-of-the-art in mental state time-series classification. Results: Pre-processing techniques, features, and time-series classification models were analyzed. Across publications, a window length of one second was mainly chosen for classification and spectral features were utilized the most. The achieved performance per time-series classification model is analyzed, finding linear discriminant analysis, decision trees, and k-nearest neighbors models outperform support-vector machines by a factor of up to 1.5. A historical analysis depicts future trends while under-reported aspects relevant to practical applications are discussed. Conclusions: Five main conclusions are given, covering utilization of available area for electrode placement on the head, most often or scarcely utilized features and time-series classification model architectures, baseline reporting practices, as well as explainability and interpretability of Deep Learning. The importance of a 'test battery' assessing the influence of data pre-processing and multi-modality on time-series classification performance is emphasized.},
  language  = {en}
}
@article{GoebelLagodzinskiSeidel2021,
  author    = {G{\"o}bel, Andreas and Lagodzinski, Julius Albert Gregor and Seidel, Karen},
  title     = {Counting homomorphisms to trees modulo a prime},
  series = {ACM transactions on computation theory : TOCT / Association for Computing Machinery},
  volume    = {13},
  journal   = {ACM transactions on computation theory : TOCT / Association for Computing Machinery},
  number    = {3},
  publisher = {Association for Computing Machinery},
  address   = {New York},
  issn      = {1942-3454},
  doi       = {10.1145/3460958},
  pages     = {1 -- 33},
  year      = {2021},
  abstract  = {Many important graph-theoretic notions can be encoded as counting graph homomorphism problems, such as partition functions in statistical physics, in particular independent sets and colourings. In this article, we study the complexity of \#(p) HOMSTOH, the problem of counting graph homomorphisms from an input graph to a graph H modulo a prime number p. Dyer and Greenhill proved a dichotomy stating that the tractability of non-modular counting graph homomorphisms depends on the structure of the target graph. Many intractable cases in non-modular counting become tractable in modular counting due to the common phenomenon of cancellation. In subsequent studies on counting modulo 2, however, the influence of the structure of H on the tractability was shown to persist, which yields similar dichotomies. <br /> Our main result states that for every tree H and every prime p the problem \#pHOMSTOH is either polynomial time computable or \#P-p-complete. This relates to the conjecture of Faben and Jerrum stating that this dichotomy holds for every graph H when counting modulo 2. In contrast to previous results on modular counting, the tractable cases of \#pHOMSTOH are essentially the same for all values of the modulo when H is a tree. To prove this result, we study the structural properties of a homomorphism. As an important interim result, our study yields a dichotomy for the problem of counting weighted independent sets in a bipartite graph modulo some prime p. These results are the first suggesting that such dichotomies hold not only for the modulo 2 case but also for the modular counting functions of all primes p.},
  language  = {en}
}
@article{TalebRohrerBergneretal.2022,
  author    = {Taleb, Aiham and Rohrer, Csaba and Bergner, Benjamin and De Leon, Guilherme and Rodrigues, Jonas Almeida and Schwendicke, Falk and Lippert, Christoph and Krois, Joachim},
  title     = {Self-supervised learning methods for label-efficient dental caries classification},
  series = {Diagnostics : open access journal},
  volume    = {12},
  journal   = {Diagnostics : open access journal},
  number    = {5},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2075-4418},
  doi       = {10.3390/diagnostics12051237},
  pages     = {15},
  year      = {2022},
  abstract  = {High annotation costs are a substantial bottleneck in applying deep learning architectures to clinically relevant use cases, substantiating the need for algorithms to learn from unlabeled data. In this work, we propose employing self-supervised methods. To that end, we trained with three self-supervised algorithms on a large corpus of unlabeled dental images, which contained 38K bitewing radiographs (BWRs). We then applied the learned neural network representations on tooth-level dental caries classification, for which we utilized labels extracted from electronic health records (EHRs). Finally, a holdout test-set was established, which consisted of 343 BWRs and was annotated by three dental professionals and approved by a senior dentist. This test-set was used to evaluate the fine-tuned caries classification models. Our experimental results demonstrate the obtained gains by pretraining models using self-supervised algorithms. These include improved caries classification performance (6 p.p. increase in sensitivity) and, most importantly, improved label-efficiency. In other words, the resulting models can be fine-tuned using few labels (annotations). Our results show that using as few as 18 annotations can produce >= 45\% sensitivity, which is comparable to human-level diagnostic performance. This study shows that self-supervision can provide gains in medical image analysis, particularly when obtaining labels is costly and expensive.},
  language  = {en}
}
@article{KonakvandeWaterDoeringetal.2023,
  author    = {Konak, Orhan and van de Water, Robin and D{\"o}ring, Valentin and Fiedler, Tobias and Liebe, Lucas and Masopust, Leander and Postnov, Kirill and Sauerwald, Franz and Treykorn, Felix and Wischmann, Alexander and Gjoreski, Hristijan and Luštrek, Mitja and Arnrich, Bert},
  title     = {HARE},
  series = {Sensors},
  volume    = {23},
  journal   = {Sensors},
  number    = {23},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1424-8220},
  doi       = {10.3390/s23239571},
  pages     = {23},
  year      = {2023},
  abstract  = {Sensor-based human activity recognition is becoming ever more prevalent. The increasing importance of distinguishing human movements, particularly in healthcare, coincides with the advent of increasingly compact sensors. A complex sequence of individual steps currently characterizes the activity recognition pipeline. It involves separate data collection, preparation, and processing steps, resulting in a heterogeneous and fragmented process. To address these challenges, we present a comprehensive framework, HARE, which seamlessly integrates all necessary steps. HARE offers synchronized data collection and labeling, integrated pose estimation for data anonymization, a multimodal classification approach, and a novel method for determining optimal sensor placement to enhance classification results. Additionally, our framework incorporates real-time activity recognition with on-device model adaptation capabilities. To validate the effectiveness of our framework, we conducted extensive evaluations using diverse datasets, including our own collected dataset focusing on nursing activities. Our results show that HARE's multimodal and on-device trained model outperforms conventional single-modal and offline variants. Furthermore, our vision-based approach for optimal sensor placement yields comparable results to the trained model. Our work advances the field of sensor-based human activity recognition by introducing a comprehensive framework that streamlines data collection and classification while offering a novel method for determining optimal sensor placement.},
  language  = {en}
}
@article{DoerrKoetzingLagodzinskietal.2020,
  author    = {Doerr, Benjamin and K{\"o}tzing, Timo and Lagodzinski, Julius Albert Gregor and Lengler, Johannes},
  title     = {The impact of lexicographic parsimony pressure for ORDER/MAJORITY on the run time},
  series = {Theoretical computer science : the journal of the EATCS},
  volume    = {816},
  journal   = {Theoretical computer science : the journal of the EATCS},
  publisher = {Elsevier},
  address   = {Amsterdam [u.a.]},
  issn      = {0304-3975},
  doi       = {10.1016/j.tcs.2020.01.011},
  pages     = {144 -- 168},
  year      = {2020},
  abstract  = {While many optimization problems work with a fixed number of decision variables and thus a fixed-length representation of possible solutions, genetic programming (GP) works on variable-length representations. A naturally occurring problem is that of bloat, that is, the unnecessary growth of solution lengths, which may slow down the optimization process. So far, the mathematical runtime analysis could not deal well with bloat and required explicit assumptions limiting bloat. In this paper, we provide the first mathematical runtime analysis of a GP algorithm that does not require any assumptions on the bloat. Previous performance guarantees were only proven conditionally for runs in which no strong bloat occurs. Together with improved analyses for the case with bloat restrictions our results show that such assumptions on the bloat are not necessary and that the algorithm is efficient without explicit bloat control mechanism. More specifically, we analyzed the performance of the (1 + 1) GP on the two benchmark functions ORDER and MAJORITY. When using lexicographic parsimony pressure as bloat control, we show a tight runtime estimate of O(T-init + nlogn) iterations both for ORDER and MAJORITY. For the case without bloat control, the bounds O(T-init logT(i)(nit) + n(logn)(3)) and Omega(T-init + nlogn) (and Omega(T-init log T-init) for n = 1) hold for MAJORITY(1).},
  language  = {en}
}
@article{KoetzingLagodzinskiLengleretal.2020,
  author    = {K{\"o}tzing, Timo and Lagodzinski, Julius Albert Gregor and Lengler, Johannes and Melnichenko, Anna},
  title     = {Destructiveness of lexicographic parsimony pressure and alleviation by a concatenation crossover in genetic programming},
  series = {Theoretical computer science},
  volume    = {816},
  journal   = {Theoretical computer science},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0304-3975},
  doi       = {10.1016/j.tcs.2019.11.036},
  pages     = {96 -- 113},
  year      = {2020},
  abstract  = {For theoretical analyses there are two specifics distinguishing GP from many other areas of evolutionary computation: the variable size representations, in particular yielding a possible bloat (i.e. the growth of individuals with redundant parts); and also the role and the realization of crossover, which is particularly central in GP due to the tree-based representation. Whereas some theoretical work on GP has studied the effects of bloat, crossover had surprisingly little share in this work. <br /> We analyze a simple crossover operator in combination with randomized local search, where a preference for small solutions minimizes bloat (lexicographic parsimony pressure); we denote the resulting algorithm Concatenation Crossover GP. We consider three variants of the well-studied MAJORITY test function, adding large plateaus in different ways to the fitness landscape and thus giving a test bed for analyzing the interplay of variation operators and bloat control mechanisms in a setting with local optima. We show that the Concatenation Crossover GP can efficiently optimize these test functions, while local search cannot be efficient for all three variants independent of employing bloat control. (C) 2019 Elsevier B.V. All rights reserved.},
  language  = {en}
}