101 research outputs found

    Dynamic discrete tomography

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    We consider the problem of reconstructing the paths of a set of points over time, where, at each of a finite set of moments in time the current positions of points in space are only accessible through some small number of their X-rays. This particular particle tracking problem, with applications, e.g., in plasma physics, is the basic problem in dynamic discrete tomography. We introduce and analyze various different algorithmic models. In particular, we determine the computational complexity of the problem (and various of its relatives) and derive algorithms that can be used in practice. As a byproduct we provide new results on constrained variants of min-cost flow and matching problems.Comment: In Pres

    SAR by MS for Functional Genomics (Structure-Activity Relation by Mass Spectrometry)

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    Large-scale functional genomics will require fast, high-throughput experimental techniques, coupled with sophisticated computer algorithms for data analysis and experiment planning. In this paper, we introduce a combined experimental-computational protocol called Structure-Activity Relation by Mass Spectrometry (SAR by MS), which can be used to elucidate the function of protein-DNA or protein-protein complexes. We present algorithms for SAR by MS and analyze their complexity. Carefully-designed Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI TOF) and Electrospray Ionization (ESI) assays require only femtomolar samples, take only microseconds per spectrum to record, enjoy a resolution of up to one dalton in 10610^6, and (in the case of MALDI) can operate on protein complexes up to a megadalton in mass. Hence, the technique is attractive for high-throughput functional genomics. In SAR by MS, selected residues or nucleosides are 2H-, 13C-, and/or 15N-labeled. Second, the complex is crosslinked. Third, the complex is cleaved with proteases and/or endonucleases. Depending on the binding mode, some cleavage sites will be shielded by the crosslinking. Finally, a mass spectrum of the resulting fragments is obtained and analyzed. The last step is the Data Analysis phase, in which the mass signatures are interpreted to obtain constraints on the functional binding mode. Experiment Planning entails deciding what labeling strategy and cleaving agents to employ, so as to minimize mass degeneracy and spectral overlap, in order that the constraints derived in data analysis yield a small number of binding hypotheses. A number of combinatorial and algorithmic questions arise in deriving algorithms for both Experiment Planning and Data Analysis. We explore the complexity of these problems, obtaining upper and lower bounds. Experimental results are reported from an implementation of our algorithms

    Dagstuhl Reports : Volume 1, Issue 2, February 2011

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    Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn

    Dagstuhl News January - December 2002

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    "Dagstuhl News" is a publication edited especially for the members of the Foundation "Informatikzentrum Schloss Dagstuhl" to thank them for their support. The News give a summary of the scientific work being done in Dagstuhl. Each Dagstuhl Seminar is presented by a small abstract describing the contents and scientific highlights of the seminar as well as the perspectives or challenges of the research topic

    Decision making under uncertainty

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    Almost all important decision problems are inevitably subject to some level of uncertainty either about data measurements, the parameters, or predictions describing future evolution. The significance of handling uncertainty is further amplified by the large volume of uncertain data automatically generated by modern data gathering or integration systems. Various types of problems of decision making under uncertainty have been subject to extensive research in computer science, economics and social science. In this dissertation, I study three major problems in this context, ranking, utility maximization, and matching, all involving uncertain datasets. First, we consider the problem of ranking and top-k query processing over probabilistic datasets. By illustrating the diverse and conflicting behaviors of the prior proposals, we contend that a single, specific ranking function may not suffice for probabilistic datasets. Instead we propose the notion of parameterized ranking functions, that generalize or can approximate many of the previously proposed ranking functions. We present novel exact or approximate algorithms for efficiently ranking large datasets according to these ranking functions, even if the datasets exhibit complex correlations or the probability distributions are continuous. The second problem concerns with the stochastic versions of a broad class of combinatorial optimization problems. We observe that the expected value is inadequate in capturing different types of risk-averse or risk-prone behaviors, and instead we consider a more general objective which is to maximize the expected utility of the solution for some given utility function. We present a polynomial time approximation algorithm with additive error ε for any ε > 0, under certain conditions. Our result generalizes and improves several prior results on stochastic shortest path, stochastic spanning tree, and stochastic knapsack. The third is the stochastic matching problem which finds interesting applications in online dating, kidney exchange and online ad assignment. In this problem, the existence of each edge is uncertain and can be only found out by probing the edge. The goal is to design a probing strategy to maximize the expected weight of the matching. We give linear programming based constant-factor approximation algorithms for weighted stochastic matching, which answer an open question raised in prior work

    Prophet inequalities made easy: stochastic optimization by pricing nonstochastic inputs

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    We present a general framework for stochastic online maximization problems with combinatorial feasibility constraints. The framework establishes prophet inequalities by constructing price-based online approximation algorithms, a natural extension of threshold algorithms for settings beyond binary selection. Our analysis takes the form of an extension theorem: we derive sufficient conditions on prices when all weights are known in advance, then prove that the resulting approxima- tion guarantees extend directly to stochastic settings. Our framework unifies and simplifies much of the existing literature on prophet inequalities and posted price mechanisms and is used to derive new and improved results for combinatorial markets (with and without complements), multidimensional matroids, and sparse packing problems. Finally, we highlight a surprising connection between the smoothness framework for bounding the price of anarchy of mechanisms and our framework, and show that many smooth mechanisms can be recast as posted price mechanisms with comparable performance guarantees

    35th Symposium on Theoretical Aspects of Computer Science: STACS 2018, February 28-March 3, 2018, Caen, France

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    Routing and scheduling optimisation under uncertainty for engineering applications

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    The thesis aims to develop a viable computational approach suitable for solving large vehicle routing and scheduling optimisation problems affected by uncertainty. The modelling framework is built upon recent advances in Stochastic Optimisation, Robust Optimisation and Distributionally Robust Optimization. The utility of the methodology is presented on two classes of discrete optimisation problems: scheduling satellite communication, which is a variant of Machine Scheduling, and the Vehicle Routing Problem with Time Windows and Synchronised Visits. For each problem class, a practical engineering application is formulated using data coming from the real world. The significant size of the problem instances reinforced the need to apply a different computational approach for each problem class. Satellite communication is scheduled using a Mixed-Integer Programming solver. In contrast, the vehicle routing problem with synchronised visits is solved using a hybrid method that combines Iterated Local Search, Constraint Programming and the Guided Local Search metaheuristic. The featured application of scheduling satellite communication is the Satellite Quantum Key Distribution for a system that consists of one spacecraft placed in the Lower Earth Orbit and a network of optical ground stations located in the United Kingdom. The satellite generates cryptographic keys and transmits them to individual ground stations. Each ground station should receive the number of keys in proportion to the importance of the ground station in the network. As clouds containing water attenuate the signal, reliable scheduling needs to account for cloud cover predictions, which are naturally affected by uncertainty. A new uncertainty sets tailored for modelling uncertainty in predictions of atmospheric phenomena is the main contribution to the methodology. The uncertainty set models the evolution of uncertain parameters using a Multivariate Vector Auto-Regressive Time Series, which preserves correlations over time and space. The problem formulation employing the new uncertainty set compares favourably to a suite of alternative models adapted from the literature considering both the computational time and the cost-effectiveness of the schedule evaluated in the cloud cover conditions observed in the real world. The other contribution of the thesis in the satellite scheduling domain is the formulation of the Satellite Quantum Key Distribution problem. The proof of computational complexity and thorough performance analysis of an example Satellite Quantum Key Distribution system accompany the formulation. The Home Care Scheduling and Routing Problem, which instances are solved for the largest provider of such services in Scotland, is the application of the Vehicle Routing Problem with Time Windows and Synchronised Visits. The problem instances contain over 500 visits. Around 20% of them require two carers simultaneously. Such problem instances are well beyond the scalability limitations of the exact method and considerably larger than instances of similar problems considered in the literature. The optimisation approach proposed in the thesis found effective solutions in attractive computational time (i.e., less than 30 minutes) and the solutions reduced the total travel time threefold compared to alternative schedules computed by human planners. The Essential Riskiness Index Optimisation was incorporated into the Constraint Programming model to address uncertainty in visits' duration. Besides solving large problem instances from the real world, the solution method reproduced the majority of the best results reported in the literature and strictly improved the solutions for several instances of a well-known benchmark for the Vehicle Routing Problem with Time Windows and Synchronised Visits.The thesis aims to develop a viable computational approach suitable for solving large vehicle routing and scheduling optimisation problems affected by uncertainty. The modelling framework is built upon recent advances in Stochastic Optimisation, Robust Optimisation and Distributionally Robust Optimization. The utility of the methodology is presented on two classes of discrete optimisation problems: scheduling satellite communication, which is a variant of Machine Scheduling, and the Vehicle Routing Problem with Time Windows and Synchronised Visits. For each problem class, a practical engineering application is formulated using data coming from the real world. The significant size of the problem instances reinforced the need to apply a different computational approach for each problem class. Satellite communication is scheduled using a Mixed-Integer Programming solver. In contrast, the vehicle routing problem with synchronised visits is solved using a hybrid method that combines Iterated Local Search, Constraint Programming and the Guided Local Search metaheuristic. The featured application of scheduling satellite communication is the Satellite Quantum Key Distribution for a system that consists of one spacecraft placed in the Lower Earth Orbit and a network of optical ground stations located in the United Kingdom. The satellite generates cryptographic keys and transmits them to individual ground stations. Each ground station should receive the number of keys in proportion to the importance of the ground station in the network. As clouds containing water attenuate the signal, reliable scheduling needs to account for cloud cover predictions, which are naturally affected by uncertainty. A new uncertainty sets tailored for modelling uncertainty in predictions of atmospheric phenomena is the main contribution to the methodology. The uncertainty set models the evolution of uncertain parameters using a Multivariate Vector Auto-Regressive Time Series, which preserves correlations over time and space. The problem formulation employing the new uncertainty set compares favourably to a suite of alternative models adapted from the literature considering both the computational time and the cost-effectiveness of the schedule evaluated in the cloud cover conditions observed in the real world. The other contribution of the thesis in the satellite scheduling domain is the formulation of the Satellite Quantum Key Distribution problem. The proof of computational complexity and thorough performance analysis of an example Satellite Quantum Key Distribution system accompany the formulation. The Home Care Scheduling and Routing Problem, which instances are solved for the largest provider of such services in Scotland, is the application of the Vehicle Routing Problem with Time Windows and Synchronised Visits. The problem instances contain over 500 visits. Around 20% of them require two carers simultaneously. Such problem instances are well beyond the scalability limitations of the exact method and considerably larger than instances of similar problems considered in the literature. The optimisation approach proposed in the thesis found effective solutions in attractive computational time (i.e., less than 30 minutes) and the solutions reduced the total travel time threefold compared to alternative schedules computed by human planners. The Essential Riskiness Index Optimisation was incorporated into the Constraint Programming model to address uncertainty in visits' duration. Besides solving large problem instances from the real world, the solution method reproduced the majority of the best results reported in the literature and strictly improved the solutions for several instances of a well-known benchmark for the Vehicle Routing Problem with Time Windows and Synchronised Visits

    LIPIcs, Volume 248, ISAAC 2022, Complete Volume

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    LIPIcs, Volume 248, ISAAC 2022, Complete Volum
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