@phdthesis{Hecher2021,
  author    = {Hecher, Markus},
  title     = {Advanced tools and methods for treewidth-based problem solving},
  doi       = {10.25932/publishup-51251},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-512519},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xv, 184},
  year      = {2021},
  abstract  = {In the last decades, there was a notable progress in solving the well-known Boolean satisfiability (Sat) problem, which can be witnessed by powerful Sat solvers. One of the reasons why these solvers are so fast are structural properties of instances that are utilized by the solver's interna. This thesis deals with the well-studied structural property treewidth, which measures the closeness of an instance to being a tree. In fact, there are many problems parameterized by treewidth that are solvable in polynomial time in the instance size when parameterized by treewidth. In this work, we study advanced treewidth-based methods and tools for problems in knowledge representation and reasoning (KR). Thereby, we provide means to establish precise runtime results (upper bounds) for canonical problems relevant to KR. Then, we present a new type of problem reduction, which we call decomposition-guided (DG) that allows us to precisely monitor the treewidth when reducing from one problem to another problem. This new reduction type will be the basis for a long-open lower bound result for quantified Boolean formulas and allows us to design a new methodology for establishing runtime lower bounds for problems parameterized by treewidth. Finally, despite these lower bounds, we provide an efficient implementation of algorithms that adhere to treewidth. Our approach finds suitable abstractions of instances, which are subsequently refined in a recursive fashion, and it uses Sat solvers for solving subproblems. It turns out that our resulting solver is quite competitive for two canonical counting problems related to Sat.},
  language  = {en}
}
@article{HaarmannHolfterPufahletal.2021,
  author    = {Haarmann, Stephan and Holfter, Adrian and Pufahl, Luise and Weske, Mathias},
  title     = {Formal framework for checking compliance of data-driven case management},
  series = {Journal on data semantics : JoDS},
  volume    = {10},
  journal   = {Journal on data semantics : JoDS},
  number    = {1-2},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {1861-2032},
  doi       = {10.1007/s13740-021-00120-3},
  pages     = {143 -- 163},
  year      = {2021},
  abstract  = {Business processes are often specified in descriptive or normative models. Both types of models should adhere to internal and external regulations, such as company guidelines or laws. Employing compliance checking techniques, it is possible to verify process models against rules. While traditionally compliance checking focuses on well-structured processes, we address case management scenarios. In case management, knowledge workers drive multi-variant and adaptive processes. Our contribution is based on the fragment-based case management approach, which splits a process into a set of fragments. The fragments are synchronized through shared data but can, otherwise, be dynamically instantiated and executed. We formalize case models using Petri nets. We demonstrate the formalization for design-time and run-time compliance checking and present a proof-of-concept implementation. The application of the implemented compliance checking approach to a use case exemplifies its effectiveness while designing a case model. The empirical evaluation on a set of case models for measuring the performance of the approach shows that rules can often be checked in less than a second.},
  language  = {en}
}
@article{GoebelLagodzinskiSeidel2021,
  author    = {G{\"o}bel, Andreas and Lagodzinski, Gregor J. A. 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{GruenerMuehleMeinel2021,
  author    = {Gr{\"u}ner, Andreas and M{\"u}hle, Alexander and Meinel, Christoph},
  title     = {ATIB},
  series = {IEEE access : practical research, open solutions / Institute of Electrical and Electronics Engineers},
  volume    = {9},
  journal   = {IEEE access : practical research, open solutions / Institute of Electrical and Electronics Engineers},
  publisher = {Institute of Electrical and Electronics Engineers},
  address   = {New York, NY},
  issn      = {2169-3536},
  doi       = {10.1109/ACCESS.2021.3116095},
  pages     = {138553 -- 138570},
  year      = {2021},
  abstract  = {Identity management is a principle component of securing online services. In the advancement of traditional identity management patterns, the identity provider remained a Trusted Third Party (TTP). The service provider and the user need to trust a particular identity provider for correct attributes amongst other demands. This paradigm changed with the invention of blockchain-based Self-Sovereign Identity (SSI) solutions that primarily focus on the users. SSI reduces the functional scope of the identity provider to an attribute provider while enabling attribute aggregation. Besides that, the development of new protocols, disregarding established protocols and a significantly fragmented landscape of SSI solutions pose considerable challenges for an adoption by service providers. We propose an Attribute Trust-enhancing Identity Broker (ATIB) to leverage the potential of SSI for trust-enhancing attribute aggregation. Furthermore, ATIB abstracts from a dedicated SSI solution and offers standard protocols. Therefore, it facilitates the adoption by service providers. Despite the brokered integration approach, we show that ATIB provides a high security posture. Additionally, ATIB does not compromise the ten foundational SSI principles for the users.},
  language  = {en}
}
@article{GautamZhangLandwehretal.2021,
  author    = {Gautam, Khem Raj and Zhang, Guoqiang and Landwehr, Niels and Adolphs, Julian},
  title     = {Machine learning for improvement of thermal conditions inside a hybrid ventilated animal building},
  series = {Computers and electronics in agriculture : COMPAG online ; an international journal},
  volume    = {187},
  journal   = {Computers and electronics in agriculture : COMPAG online ; an international journal},
  publisher = {Elsevier Science},
  address   = {Amsterdam [u.a.]},
  issn      = {0168-1699},
  doi       = {10.1016/j.compag.2021.106259},
  pages     = {10},
  year      = {2021},
  abstract  = {In buildings with hybrid ventilation, natural ventilation opening positions (windows), mechanical ventilation rates, heating, and cooling are manipulated to maintain desired thermal conditions. The indoor temperature is regulated solely by ventilation (natural and mechanical) when the external conditions are favorable to save external heating and cooling energy. The ventilation parameters are determined by a rule-based control scheme, which is not optimal. This study proposes a methodology to enable real-time optimum control of ventilation parameters. We developed offline prediction models to estimate future thermal conditions from the data collected from building in operation. The developed offline model is then used to find the optimal controllable ventilation parameters in real-time to minimize the setpoint deviation in the building. With the proposed methodology, the experimental building's setpoint deviation improved for 87\% of time, on average, by 0.53 degrees C compared to the current deviations.},
  language  = {en}
}
@article{FreitasdaCruzPfahringerMartensenetal.2021,
  author    = {Freitas da Cruz, Harry and Pfahringer, Boris and Martensen, Tom and Schneider, Frederic and Meyer, Alexander and B{\"o}ttinger, Erwin and Schapranow, Matthieu-Patrick},
  title     = {Using interpretability approaches to update "black-box" clinical prediction models},
  series = {Artificial intelligence in medicine : AIM},
  volume    = {111},
  journal   = {Artificial intelligence in medicine : AIM},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0933-3657},
  doi       = {10.1016/j.artmed.2020.101982},
  pages     = {13},
  year      = {2021},
  abstract  = {Despite advances in machine learning-based clinical prediction models, only few of such models are actually deployed in clinical contexts. Among other reasons, this is due to a lack of validation studies. In this paper, we present and discuss the validation results of a machine learning model for the prediction of acute kidney injury in cardiac surgery patients initially developed on the MIMIC-III dataset when applied to an external cohort of an American research hospital. To help account for the performance differences observed, we utilized interpretability methods based on feature importance, which allowed experts to scrutinize model behavior both at the global and local level, making it possible to gain further insights into why it did not behave as expected on the validation cohort. The knowledge gleaned upon derivation can be potentially useful to assist model update during validation for more generalizable and simpler models. We argue that interpretability methods should be considered by practitioners as a further tool to help explain performance differences and inform model update in validation studies.},
  language  = {en}
}
@article{FandinoLaferriereRomeroetal.2021,
  author    = {Fandi{\~n}o, Jorge and Laferriere, Francois and Romero, Javier and Schaub, Torsten H. and Son, Tran Cao},
  title     = {Planning with incomplete information in quantified answer set programming},
  series = {Theory and practice of logic programming},
  volume    = {21},
  journal   = {Theory and practice of logic programming},
  number    = {5},
  publisher = {Cambridge University Press},
  address   = {Cambridge},
  issn      = {1471-0684},
  doi       = {10.1017/S1471068421000259},
  pages     = {663 -- 679},
  year      = {2021},
  abstract  = {We present a general approach to planning with incomplete information in Answer Set Programming (ASP). More precisely, we consider the problems of conformant and conditional planning with sensing actions and assumptions. We represent planning problems using a simple formalism where logic programs describe the transition function between states, the initial states and the goal states. For solving planning problems, we use Quantified Answer Set Programming (QASP), an extension of ASP with existential and universal quantifiers over atoms that is analogous to Quantified Boolean Formulas (QBFs). We define the language of quantified logic programs and use it to represent the solutions different variants of conformant and conditional planning. On the practical side, we present a translation-based QASP solver that converts quantified logic programs into QBFs and then executes a QBF solver, and we evaluate experimentally the approach on conformant and conditional planning benchmarks.},
  language  = {en}
}
@article{DoerrKrejca2021,
  author    = {Doerr, Benjamin and Krejca, Martin Stefan},
  title     = {A simplified run time analysis of the univariate marginal distribution algorithm on LeadingOnes},
  series = {Theoretical computer science},
  volume    = {851},
  journal   = {Theoretical computer science},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0304-3975},
  doi       = {10.1016/j.tcs.2020.11.028},
  pages     = {121 -- 128},
  year      = {2021},
  abstract  = {With elementary means, we prove a stronger run time guarantee for the univariate marginal distribution algorithm (UMDA) optimizing the LEADINGONES benchmark function in the desirable regime with low genetic drift. If the population size is at least quasilinear, then, with high probability, the UMDA samples the optimum in a number of iterations that is linear in the problem size divided by the logarithm of the UMDA's selection rate. This improves over the previous guarantee, obtained by Dang and Lehre (2015) via the deep level-based population method, both in terms of the run time and by demonstrating further run time gains from small selection rates. Under similar assumptions, we prove a lower bound that matches our upper bound up to constant factors.},
  language  = {en}
}
@article{DeFreitasJohnsonGoldenetal.2021,
  author    = {De Freitas, Jessica K. and Johnson, Kipp W. and Golden, Eddye and Nadkarni, Girish N. and Dudley, Joel T. and B{\"o}ttinger, Erwin and Glicksberg, Benjamin S. and Miotto, Riccardo},
  title     = {Phe2vec},
  series = {Patterns},
  volume    = {2},
  journal   = {Patterns},
  number    = {9},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {2666-3899},
  doi       = {10.1016/j.patter.2021.100337},
  pages     = {9},
  year      = {2021},
  abstract  = {Robust phenotyping of patients from electronic health records (EHRs) at scale is a challenge in clinical informatics. Here, we introduce Phe2vec, an automated framework for disease phenotyping from EHRs based on unsupervised learning and assess its effectiveness against standard rule-based algorithms from Phenotype KnowledgeBase (PheKB). Phe2vec is based on pre-computing embeddings of medical concepts and patients' clinical history. Disease phenotypes are then derived from a seed concept and its neighbors in the embedding space. Patients are linked to a disease if their embedded representation is close to the disease phenotype. Comparing Phe2vec and PheKB cohorts head-to-head using chart review, Phe2vec performed on par or better in nine out of ten diseases. Differently from other approaches, it can scale to any condition and was validated against widely adopted expert-based standards. Phe2vec aims to optimize clinical informatics research by augmenting current frameworks to characterize patients by condition and derive reliable disease cohorts.},
  language  = {en}
}
@article{CsehKavitha2021,
  author    = {Cseh, {\´A}gnes and Kavitha, Telikepalli},
  title     = {Popular matchings in complete graphs},
  series = {Algorithmica : an international journal in computer science},
  volume    = {83},
  journal   = {Algorithmica : an international journal in computer science},
  number    = {5},
  publisher = {Springer},
  address   = {New York},
  issn      = {0178-4617},
  doi       = {10.1007/s00453-020-00791-7},
  pages     = {1493 -- 1523},
  year      = {2021},
  abstract  = {Our input is a complete graph G on n vertices where each vertex has a strict ranking of all other vertices in G. The goal is to construct a matching in G that is popular. A matching M is popular if M does not lose a head-to-head election against any matching M ': here each vertex casts a vote for the matching in {M,M '} in which it gets a better assignment. Popular matchings need not exist in the given instance G and the popular matching problem is to decide whether one exists or not. The popular matching problem in G is easy to solve for odd n. Surprisingly, the problem becomes NP-complete for even n, as we show here. This is one of the few graph theoretic problems efficiently solvable when n has one parity and NP-complete when n has the other parity.},
  language  = {en}
}
@article{CsehJuhos2021,
  author    = {Cseh, {\´A}gnes and Juhos, Attila},
  title     = {Pairwise preferences in the stable marriage problem},
  series = {ACM Transactions on Economics and Computation / Association for Computing Machinery},
  volume    = {9},
  journal   = {ACM Transactions on Economics and Computation / Association for Computing Machinery},
  number    = {1},
  publisher = {Association for Computing Machinery},
  address   = {New York},
  issn      = {2167-8375},
  doi       = {10.1145/3434427},
  pages     = {28},
  year      = {2021},
  abstract  = {We study the classical, two-sided stable marriage problem under pairwise preferences. In the most general setting, agents are allowed to express their preferences as comparisons of any two of their edges, and they also have the right to declare a draw or even withdraw from such a comparison. This freedom is then gradually restricted as we specify six stages of orderedness in the preferences, ending with the classical case of strictly ordered lists. We study all cases occurring when combining the three known notions of stability-weak, strong, and super-stability-under the assumption that each side of the bipartite market obtains one of the six degrees of orderedness. By designing three polynomial algorithms and two NP-completeness proofs, we determine the complexity of all cases not yet known and thus give an exact boundary in terms of preference structure between tractable and intractable cases.},
  language  = {en}
}
@article{CombiOliboniWeskeetal.2021,
  author    = {Combi, Carlo and Oliboni, Barbara and Weske, Mathias and Zerbato, Francesca},
  title     = {Seamless conceptual modeling of processes with transactional and analytical data},
  series = {Data \& knowledge engineering},
  volume    = {134},
  journal   = {Data \& knowledge engineering},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0169-023X},
  doi       = {10.1016/j.datak.2021.101895},
  pages     = {14},
  year      = {2021},
  abstract  = {In the field of Business Process Management (BPM), modeling business processes and related data is a critical issue since process activities need to manage data stored in databases. The connection between processes and data is usually handled at the implementation level, even if modeling both processes and data at the conceptual level should help designers in improving business process models and identifying requirements for implementation. Especially in data -and decision-intensive contexts, business process activities need to access data stored both in databases and data warehouses. In this paper, we complete our approach for defining a novel conceptual view that bridges process activities and data. The proposed approach allows the designer to model the connection between business processes and database models and define the operations to perform, providing interesting insights on the overall connected perspective and hints for identifying activities that are crucial for decision support.},
  language  = {en}
}
@article{CabalarFandinoFarinasdelCerro2021,
  author    = {Cabalar, Pedro and Fandi{\~n}o, Jorge and Fari{\~n}as del Cerro, Luis},
  title     = {Splitting epistemic logic programs},
  series = {Theory and practice of logic programming / publ. for the Association for Logic Programming},
  volume    = {21},
  journal   = {Theory and practice of logic programming / publ. for the Association for Logic Programming},
  number    = {3},
  publisher = {Cambridge Univ. Press},
  address   = {Cambridge [u.a.]},
  issn      = {1471-0684},
  doi       = {10.1017/S1471068420000058},
  pages     = {296 -- 316},
  year      = {2021},
  abstract  = {Epistemic logic programs constitute an extension of the stable model semantics to deal with new constructs called subjective literals. Informally speaking, a subjective literal allows checking whether some objective literal is true in all or some stable models. As it can be imagined, the associated semantics has proved to be non-trivial, since the truth of subjective literals may interfere with the set of stable models it is supposed to query. As a consequence, no clear agreement has been reached and different semantic proposals have been made in the literature. Unfortunately, comparison among these proposals has been limited to a study of their effect on individual examples, rather than identifying general properties to be checked. In this paper, we propose an extension of the well-known splitting property for logic programs to the epistemic case. We formally define when an arbitrary semantics satisfies the epistemic splitting property and examine some of the consequences that can be derived from that, including its relation to conformant planning and to epistemic constraints. Interestingly, we prove (through counterexamples) that most of the existing approaches fail to fulfill the epistemic splitting property, except the original semantics proposed by Gelfond 1991 and a recent proposal by the authors, called Founded Autoepistemic Equilibrium Logic.},
  language  = {en}
}
@article{BredeBotta2021,
  author    = {Brede, Nuria and Botta, Nicola},
  title     = {On the correctness of monadic backward induction},
  series = {Journal of functional programming},
  volume    = {31},
  journal   = {Journal of functional programming},
  publisher = {Cambridge University Press},
  address   = {Cambridge},
  issn      = {1469-7653},
  doi       = {10.1017/S0956796821000228},
  pages     = {39},
  year      = {2021},
  abstract  = {In control theory, to solve a finite-horizon sequential decision problem (SDP) commonly means to find a list of decision rules that result in an optimal expected total reward (or cost) when taking a given number of decision steps. SDPs are routinely solved using Bellman's backward induction. Textbook authors (e.g. Bertsekas or Puterman) typically give more or less formal proofs to show that the backward induction algorithm is correct as solution method for deterministic and stochastic SDPs. Botta, Jansson and Ionescu propose a generic framework for finite horizon, monadic SDPs together with a monadic version of backward induction for solving such SDPs. In monadic SDPs, the monad captures a generic notion of uncertainty, while a generic measure function aggregates rewards. In the present paper, we define a notion of correctness for monadic SDPs and identify three conditions that allow us to prove a correctness result for monadic backward induction that is comparable to textbook correctness proofs for ordinary backward induction. The conditions that we impose are fairly general and can be cast in category-theoretical terms using the notion of Eilenberg-Moore algebra. They hold in familiar settings like those of deterministic or stochastic SDPs, but we also give examples in which they fail. Our results show that backward induction can safely be employed for a broader class of SDPs than usually treated in textbooks. However, they also rule out certain instances that were considered admissible in the context of Botta et al. 's generic framework. Our development is formalised in Idris as an extension of the Botta et al. framework and the sources are available as supplementary material.},
  language  = {en}
}
@article{BordihnVaszil2021,
  author    = {Bordihn, Henning and Vaszil, Gy{\"o}rgy},
  title     = {Reversible parallel communicating finite automata systems},
  series = {Acta informatica},
  volume    = {58},
  journal   = {Acta informatica},
  number    = {4},
  publisher = {Springer},
  address   = {Berlin ; Heidelberg ; New York, NY},
  issn      = {0001-5903},
  doi       = {10.1007/s00236-021-00396-9},
  pages     = {263 -- 279},
  year      = {2021},
  abstract  = {We study the concept of reversibility in connection with parallel communicating systems of finite automata (PCFA in short). We define the notion of reversibility in the case of PCFA (also covering the non-deterministic case) and discuss the relationship of the reversibility of the systems and the reversibility of its components. We show that a system can be reversible with non-reversible components, and the other way around, the reversibility of the components does not necessarily imply the reversibility of the system as a whole. We also investigate the computational power of deterministic centralized reversible PCFA. We show that these very simple types of PCFA (returning or non-returning) can recognize regular languages which cannot be accepted by reversible (deterministic) finite automata, and that they can even accept languages that are not context-free. We also separate the deterministic and non-deterministic variants in the case of systems with non-returning communication. We show that there are languages accepted by non-deterministic centralized PCFA, which cannot be recognized by any deterministic variant of the same type.},
  language  = {en}
}
@article{BordihnHolzer2021,
  author    = {Bordihn, Henning and Holzer, Markus},
  title     = {On the number of active states in finite automata},
  series = {Acta informatica},
  volume    = {58},
  journal   = {Acta informatica},
  number    = {4},
  publisher = {Springer},
  address   = {Berlin ; Heidelberg [u.a.]},
  issn      = {0001-5903},
  doi       = {10.1007/s00236-021-00397-8},
  pages     = {301 -- 318},
  year      = {2021},
  abstract  = {We introduce a new measure of descriptional complexity on finite automata, called the number of active states. Roughly speaking, the number of active states of an automaton A on input w counts the number of different states visited during the most economic computation of the automaton A for the word w. This concept generalizes to finite automata and regular languages in a straightforward way. We show that the number of active states of both finite automata and regular languages is computable, even with respect to nondeterministic finite automata. We further compare the number of active states to related measures for regular languages. In particular, we show incomparability to the radius of regular languages and that the difference between the number of active states and the total number of states needed in finite automata for a regular language can be of exponential order.},
  language  = {en}
}
@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     = {Correction to: 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/bbab246},
  pages     = {1},
  year      = {2021},
  language  = {en}
}
@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}
}
@article{BonnetDongNaumannetal.2021,
  author    = {Bonnet, Philippe and Dong, Xin Luna and Naumann, Felix and T{\"o}z{\"u}n, P{\i}nar},
  title     = {VLDB 2021},
  series = {SIGMOD record},
  volume    = {50},
  journal   = {SIGMOD record},
  number    = {4},
  publisher = {Association for Computing Machinery},
  address   = {New York},
  issn      = {0163-5808},
  doi       = {10.1145/3516431.3516447},
  pages     = {50 -- 53},
  year      = {2021},
  abstract  = {The 47th International Conference on Very Large Databases (VLDB'21) was held on August 16-20, 2021 as a hybrid conference. It attracted 180 in-person attendees in Copenhagen and 840 remote attendees. In this paper, we describe our key decisions as general chairs and program committee chairs and share the lessons we learned.},
  language  = {en}
}
@article{Boissier2021,
  author    = {Boissier, Martin},
  title     = {Robust and budget-constrained encoding configurations for in-memory database systems},
  series = {Proceedings of the VLDB Endowment},
  volume    = {15},
  journal   = {Proceedings of the VLDB Endowment},
  number    = {4},
  publisher = {Association for Computing Machinery (ACM)},
  address   = {[New York]},
  issn      = {2150-8097},
  doi       = {10.14778/3503585.3503588},
  pages     = {780 -- 793},
  year      = {2021},
  abstract  = {Data encoding has been applied to database systems for decades as it mitigates bandwidth bottlenecks and reduces storage requirements. But even in the presence of these advantages, most in-memory database systems use data encoding only conservatively as the negative impact on runtime performance can be severe. Real-world systems with large parts being infrequently accessed and cost efficiency constraints in cloud environments require solutions that automatically and efficiently select encoding techniques, including heavy-weight compression. In this paper, we introduce workload-driven approaches to automaticaly determine memory budget-constrained encoding configurations using greedy heuristics and linear programming. We show for TPC-H, TPC-DS, and the Join Order Benchmark that optimized encoding configurations can reduce the main memory footprint significantly without a loss in runtime performance over state-of-the-art dictionary encoding. To yield robust selections, we extend the linear programming-based approach to incorporate query runtime constraints and mitigate unexpected performance regressions.},
  language  = {en}
}
@misc{BensonMakaitRabl2021,
  author    = {Benson, Lawrence and Makait, Hendrik and Rabl, Tilmann},
  title     = {Viper},
  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    = {9},
  issn      = {2150-8097},
  doi       = {10.25932/publishup-55966},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-559664},
  pages     = {15},
  year      = {2021},
  abstract  = {Key-value stores (KVSs) have found wide application in modern software systems. For persistence, their data resides in slow secondary storage, which requires KVSs to employ various techniques to increase their read and write performance from and to the underlying medium. Emerging persistent memory (PMem) technologies offer data persistence at close-to-DRAM speed, making them a promising alternative to classical disk-based storage. However, simply drop-in replacing existing storage with PMem does not yield good results, as block-based access behaves differently in PMem than on disk and ignores PMem's byte addressability, layout, and unique performance characteristics. In this paper, we propose three PMem-specific access patterns and implement them in a hybrid PMem-DRAM KVS called Viper. We employ a DRAM-based hash index and a PMem-aware storage layout to utilize the random-write speed of DRAM and efficient sequential-write performance PMem. Our evaluation shows that Viper significantly outperforms existing KVSs for core KVS operations while providing full data persistence. Moreover, Viper outperforms existing PMem-only, hybrid, and disk-based KVSs by 4-18x for write workloads, while matching or surpassing their get performance.},
  language  = {en}
}
@article{BensonMakaitRabl2021,
  author    = {Benson, Lawrence and Makait, Hendrik and Rabl, Tilmann},
  title     = {Viper},
  series = {Proceedings of the VLDB Endowment},
  volume    = {14},
  journal   = {Proceedings of the VLDB Endowment},
  number    = {9},
  publisher = {Association for Computing Machinery},
  address   = {New York},
  issn      = {2150-8097},
  doi       = {10.14778/3461535.3461543},
  pages     = {1544 -- 1556},
  year      = {2021},
  abstract  = {Key-value stores (KVSs) have found wide application in modern software systems. For persistence, their data resides in slow secondary storage, which requires KVSs to employ various techniques to increase their read and write performance from and to the underlying medium. Emerging persistent memory (PMem) technologies offer data persistence at close-to-DRAM speed, making them a promising alternative to classical disk-based storage. However, simply drop-in replacing existing storage with PMem does not yield good results, as block-based access behaves differently in PMem than on disk and ignores PMem's byte addressability, layout, and unique performance characteristics. In this paper, we propose three PMem-specific access patterns and implement them in a hybrid PMem-DRAM KVS called Viper. We employ a DRAM-based hash index and a PMem-aware storage layout to utilize the random-write speed of DRAM and efficient sequential-write performance PMem. Our evaluation shows that Viper significantly outperforms existing KVSs for core KVS operations while providing full data persistence. Moreover, Viper outperforms existing PMem-only, hybrid, and disk-based KVSs by 4-18x for write workloads, while matching or surpassing their get performance.},
  language  = {en}
}
@book{BartzKrestel2021,
  author    = {Bartz, Christian and Krestel, Ralf},
  title     = {Deep learning for computer vision in the art domain},
  number    = {139},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-514-9},
  issn      = {1613-5652},
  doi       = {10.25932/publishup-51290},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-512906},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {vii, 79},
  year      = {2021},
  abstract  = {In recent years, computer vision algorithms based on machine learning have seen rapid development. In the past, research mostly focused on solving computer vision problems such as image classification or object detection on images displaying natural scenes. Nowadays other fields such as the field of cultural heritage, where an abundance of data is available, also get into the focus of research. In the line of current research endeavours, we collaborated with the Getty Research Institute which provided us with a challenging dataset, containing images of paintings and drawings. In this technical report, we present the results of the seminar "Deep Learning for Computer Vision". In this seminar, students of the Hasso Plattner Institute evaluated state-of-the-art approaches for image classification, object detection and image recognition on the dataset of the Getty Research Institute. The main challenge when applying modern computer vision methods to the available data is the availability of annotated training data, as the dataset provided by the Getty Research Institute does not contain a sufficient amount of annotated samples for the training of deep neural networks. However, throughout the report we show that it is possible to achieve satisfying to very good results, when using further publicly available datasets, such as the WikiArt dataset, for the training of machine learning models.},
  language  = {en}
}
@book{BaltzerHradilakPfennigschmidtetal.2021,
  author    = {Baltzer, Wanda and Hradilak, Theresa and Pfennigschmidt, Lara and Prestin, Luc Maurice and Spranger, Moritz and Stadlinger, Simon and Wendt, Leo and Lincke, Jens and Rein, Patrick and Church, Luke and Hirschfeld, Robert},
  title     = {An individual-centered approach to visualize people's opinions and demographic information},
  number    = {136},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-504-0},
  issn      = {1613-5652},
  doi       = {10.25932/publishup-49145},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-491457},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {326},
  year      = {2021},
  abstract  = {The noble way to substantiate decisions that affect many people is to ask these people for their opinions. For governments that run whole countries, this means asking all citizens for their views to consider their situations and needs. Organizations such as Africa's Voices Foundation, who want to facilitate communication between decision-makers and citizens of a country, have difficulty mediating between these groups. To enable understanding, statements need to be summarized and visualized. Accomplishing these goals in a way that does justice to the citizens' voices and situations proves challenging. Standard charts do not help this cause as they fail to create empathy for the people behind their graphical abstractions. Furthermore, these charts do not create trust in the data they are representing as there is no way to see or navigate back to the underlying code and the original data. To fulfill these functions, visualizations would highly benefit from interactions to explore the displayed data, which standard charts often only limitedly provide. To help improve the understanding of people's voices, we developed and categorized 80 ideas for new visualizations, new interactions, and better connections between different charts, which we present in this report. From those ideas, we implemented 10 prototypes and two systems that integrate different visualizations. We show that this integration allows consistent appearance and behavior of visualizations. The visualizations all share the same main concept: representing each individual with a single dot. To realize this idea, we discuss technologies that efficiently allow the rendering of a large number of these dots. With these visualizations, direct interactions with representations of individuals are achievable by clicking on them or by dragging a selection around them. This direct interaction is only possible with a bidirectional connection from the visualization to the data it displays. We discuss different strategies for bidirectional mappings and the trade-offs involved. Having unified behavior across visualizations enhances exploration. For our prototypes, that includes grouping, filtering, highlighting, and coloring of dots. Our prototyping work was enabled by the development environment Lively4. We explain which parts of Lively4 facilitated our prototyping process. Finally, we evaluate our approach to domain problems and our developed visualization concepts. Our work provides inspiration and a starting point for visualization development in this domain. Our visualizations can improve communication between citizens and their government and motivate empathetic decisions. Our approach, combining low-level entities to create visualizations, provides value to an explorative and empathetic workflow. We show that the design space for visualizing this kind of data has a lot of potential and that it is possible to combine qualitative and quantitative approaches to data analysis.},
  language  = {en}
}
@article{AyzelHeistermann2021,
  author    = {Ayzel, Georgy and Heistermann, Maik},
  title     = {The effect of calibration data length on the performance of a conceptual hydrological model versus LSTM and GRU},
  series = {Computers \& geosciences : an international journal devoted to the publication of papers on all aspects of geocomputation and to the distribution of computer programs and test data sets ; an official journal of the International Association for Mathematical Geology},
  volume    = {149},
  journal   = {Computers \& geosciences : an international journal devoted to the publication of papers on all aspects of geocomputation and to the distribution of computer programs and test data sets ; an official journal of the International Association for Mathematical Geology},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0098-3004},
  doi       = {10.1016/j.cageo.2021.104708},
  pages     = {12},
  year      = {2021},
  abstract  = {We systematically explore the effect of calibration data length on the performance of a conceptual hydrological model, GR4H, in comparison to two Artificial Neural Network (ANN) architectures: Long Short-Term Memory Networks (LSTM) and Gated Recurrent Units (GRU), which have just recently been introduced to the field of hydrology. We implemented a case study for six river basins across the contiguous United States, with 25 years of meteorological and discharge data. Nine years were reserved for independent validation; two years were used as a warm-up period, one year for each of the calibration and validation periods, respectively; from the remaining 14 years, we sampled increasing amounts of data for model calibration, and found pronounced differences in model performance. While GR4H required less data to converge, LSTM and GRU caught up at a remarkable rate, considering their number of parameters. Also, LSTM and GRU exhibited the higher calibration instability in comparison to GR4H. These findings confirm the potential of modern deep-learning architectures in rainfall runoff modelling, but also highlight the noticeable differences between them in regard to the effect of calibration data length.},
  language  = {en}
}
@article{AngeleskaOmranianNikoloski2021,
  author    = {Angeleska, Angela and Omranian, Sara and Nikoloski, Zoran},
  title     = {Coherent network partitions},
  series = {Theoretical computer science : the journal of the EATCS},
  volume    = {894},
  journal   = {Theoretical computer science : the journal of the EATCS},
  publisher = {Elsevier},
  address   = {Amsterdam [u.a.]},
  issn      = {0304-3975},
  doi       = {10.1016/j.tcs.2021.10.002},
  pages     = {3 -- 11},
  year      = {2021},
  abstract  = {We continue to study coherent partitions of graphs whereby the vertex set is partitioned into subsets that induce biclique spanned subgraphs. The problem of identifying the minimum number of edges to obtain biclique spanned connected components (CNP), called the coherence number, is NP-hard even on bipartite graphs. Here, we propose a graph transformation geared towards obtaining an O (log n)-approximation algorithm for the CNP on a bipartite graph with n vertices. The transformation is inspired by a new characterization of biclique spanned subgraphs. In addition, we study coherent partitions on prime graphs, and show that finding coherent partitions reduces to the problem of finding coherent partitions in a prime graph. Therefore, these results provide future directions for approximation algorithms for the coherence number of a given graph.},
  language  = {en}
}
@inproceedings{AbramovaGundlachBilda2021,
  author    = {Abramova, Olga and Gundlach, Jana and Bilda, Juliane},
  title     = {Understanding the role of newsfeed clutter in stereotype activation},
  series = {PACIS 2021 proceedings},
  booktitle = {PACIS 2021 proceedings},
  number    = {473},
  publisher = {AIS Electronic Library (AISeL)},
  address   = {[Erscheinungsort nicht ermittelbar]},
  isbn      = {978-1-7336325-7-7},
  year      = {2021},
  abstract  = {Despite the phenomenal growth of Big Data Analytics in the last few years, little research is done to explicate the relationship between Big Data Analytics Capability (BDAC) and indirect strategic value derived from such digital capabilities. We attempt to address this gap by proposing a conceptual model of the BDAC - Innovation relationship using dynamic capability theory. The work expands on BDAC business value research and extends the nominal research done on BDAC - innovation. We focus on BDAC's relationship with different innovation objects, namely product, business process, and business model innovation, impacting all value chain activities. The insights gained will stimulate academic and practitioner interest in explicating strategic value generated from BDAC and serve as a framework for future research on the subject},
  language  = {en}
}
@inproceedings{AbramovaGladkayaKrasnova2021,
  author    = {Abramova, Olga and Gladkaya, Margarita and Krasnova, Hanna},
  title     = {An unusual encounter with oneself},
  series = {ICIS 2021: IS and the future of work},
  booktitle = {ICIS 2021: IS and the future of work},
  publisher = {AIS Electronic Library (AISeL)},
  address   = {[Erscheinungsort nicht ermittelbar]},
  year      = {2021},
  abstract  = {Helping overcome distance, the use of videoconferencing tools has surged during the pandemic. To shed light on the consequences of videoconferencing at work, this study takes a granular look at the implications of the self-view feature for meeting outcomes. Building on self-awareness research and self-regulation theory, we argue that by heightening the state of self-awareness, self-view engagement depletes participants' mental resources and thereby can undermine online meeting outcomes. Evaluation of our theoretical model on a sample of 179 employees reveals a nuanced picture. Self-view engagement while speaking and while listening is positively associated with self-awareness, which, in turn, is negatively associated with satisfaction with meeting process, perceived productivity, and meeting enjoyment. The criticality of the communication role is put forward: looking at self while listening to other attendees has a negative direct and indirect effect on meeting outcomes; however, looking at self while speaking produces equivocal effects.},
  language  = {en}
}