Library

Description: The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.

Description: Die Bestimmung optimaler Treiberfunktionen von Lautsprechern mit frequenzabhängiger Richtcharakteristik ist ein schlecht gestelltes Optimierungsproblem. Zu dessen Lösung haben die Autoren in vorangegangenen Beiträgen eine adjungierten-basierte Methode zur Optimierung von Lautsprecher-Arrays im Zeitbereich vorgestellt [5, 6, 8]. Diese ermöglicht unter anderem die Berücksichtigung von Berandungen und Umgebungseffekten wie Wind, war jedoch bisher auf monopol-artige Quellen beschränkt. Um diese Einschränkung zu beheben, haben die Autoren einen adjungierten-basierten Zeitbereichsansatz mit Finiten-Differenzen (FDTD) zur Synthese komplexer synthetischer Schallquellen durch diskrete, gitter-basierte Monopole vorgestellt [4, 9]. In diesem Beitrag demonstrieren die Autoren die entsprechende Modellierung eines realen Zweiwege-Monitors (A). Zudem wird gezeigt, wie sich die Vielzahl der zur Synthese verwendeten Monopole in eine Lautsprecher-Treiberfunktion überführen lassen (B).

Description: We report on the selection process leading to the sixth version of the Mixed Integer Programming Library. Selected from an initial pool of over 5,000 instances, the new MIPLIB 2017 collection consists of 1,065 instances. A subset of 240 instances was specially selected for benchmarking solver performance. For the first time, the compilation of these sets was done using a data-driven selection process supported by the solution of a sequence of mixed integer optimization problems, which encoded requirements on diversity and balancedness with respect to instance features and performance data.

Description: We used transition path theory (TPT) to infer "reactive" pathways of floating marine debris trajectories. The TPT analysis was applied on a pollution-aware time-homogeneous Markov chain model constructed from trajectories produced by satellite-tracked undrogued buoys from the NOAA Global Drifter Program. The latter involved coping with the openness of the system in physical space, which further required an adaptation of the standard TPT setting. Directly connecting pollution sources along coastlines with garbage patches of varied strengths, the unveiled reactive pollution routes represent alternative targets for ocean cleanup efforts. Among our specific findings we highlight: constraining a highly probable pollution source for the Great Pacific Garbage Patch; characterizing the weakness of the Indian Ocean gyre as a trap for plastic waste; and unveiling a tendency of the subtropical gyres to export garbage toward the coastlines rather than to other gyres in the event of anomalously intense winds.

Description: We report our progress on the project for solving larger scale quadratic assignment problems (QAPs). Our main approach to solve large scale NP-hard combinatorial optimization problems such as QAPs is a parallel branch-and-bound method efficiently implemented on a powerful computer system using the Ubiquity Generator(UG) framework that can utilize more than 100,000 cores. Lower bounding procedures incorporated in the branch-and-bound method play a crucial role in solving the problems. For a strong lower bounding procedure, we employ the Lagrangian doubly nonnegative (DNN) relaxation and the Newton-bracketing method developed by the authors’ group. In this report, we describe some basic tools used in the project including the lower bounding procedure and branching rules, and present some preliminary numerical results. Our next target problem is QAPs with dimension at least 50, as we have succeeded to solve tai30a and sko42 from QAPLIB for the first time.

Description: The Portable Computing Language (PoCL) is a vendor independent open-source OpenCL implementation that aims to support a variety of compute devices in a single platform. Evaluating PoCL versus the Intel OpenCL implementation reveals significant performance drawbacks of PoCL on Intel CPUs – which run 92 % of the TOP500 list. Using a selection of benchmarks, we identify and analyse performance issues in PoCL with a focus on scheduling and vectorisation. We propose a new CPU device-driver based on Intel Threading Building Blocks (TBB), and evaluate LLVM with respect to automatic compiler vectorisation across work-items in PoCL. Using the TBB driver, it is possible to narrow the gap to Intel OpenCL and even outperform it by a factor of up to 1.3× in our proxy application benchmark with a manual vectorisation strategy.

Description: In practice, transient gas transport problems frequently have to be solved for large-scale gas networks. Gas network optimization problems typically belong to the class of Mixed-Integer Nonlinear Programming Problems (MINLP). However current state-of-the-art MINLP solvers are not yet mature enough to solve large-scale real-world instances. Therefore, an established approach in practice is to solve the problems with respect to a coarser representation of the network and thereby reducing the size of the underlying model. Two well-known aggregation methods that effectively reduce the network size are parallel and serial pipe merges. However, these methods have only been studied in stationary gas transport problems so far. This paper closes this gap and presents parallel and serial pipe merging methods in the context of transient gas transport. To this end, we introduce the concept of equivalent and heuristic subnetwork replacements. For the heuristic methods, we conduct a huge empirical evaluation based on real-world data taken from one of the largest gas networks in Europe. It turns out that both, parallel and serial pipe merging can be considered as appropriate aggregation methods for real-world transient gas flow problems.

Description: The aim of this paper is to provide a comprehensive overview of the MICCAI 2020 AutoImplant Challenge. The approaches and publications submitted and accepted within the challenge will be summarized and reported, highlighting common algorithmic trends and algorithmic diversity. Furthermore, the evaluation results will be presented, compared and discussed in regard to the challenge aim: seeking for low cost, fast and fully automated solutions for cranial implant design. Based on feedback from collaborating neurosurgeons, this paper concludes by stating open issues and post-challenge requirements for intra-operative use.

Description: We present a heuristic based on linear programming (LP) for the integrated tour and crew roster planning of toll enforcement inspectors. Their task is to enforce the proper paying of a distance-based toll on German motorways. This leads to an integrated tour planning and duty rostering problem; it is called Toll Enforcement Problem (TEP). We tackle the TEP by a standard multi-commodity flow model with some extensions in order to incorporate the control tours. The heuristic consists of two variants. The first, called Price & Branch, is a column generation approach to solve the model’s LP relaxation by pricing tour and roster arc variables. Then, we compute an integer feasible solution by restricting to all variables that were priced. The second is a coarse-to-fine approach. Its basic idea is projecting variables to an aggregated variable space, which is much smaller. The aim is to spend as much algorithmic effort in this coarse model as possible. For both heuristic procedures we will show that feasible solutions of high quality can be computed even for large scale industrial instances.

Description: This report presents a method to integrate highly flexible technology models for distributed energy resources such as electric vehicles, power-to-heat systems, or home battery systems into a Lagrangian relaxation of the pan-European day-ahead electricity market (EULR). These flexible technology models are highly sensitive to the changes of Lagrangian multipliers within the iterative Lagrangian relaxation process, leading to volatile behavior. Furthermore, they show a high concurrency in their market behavior due to their technical homogeneity. Therefore, the method proposed in this report is an extension of the existing EULR modeling approach to improve the model's convergence. The methodological extension comprises a convex combination of iteration solutions for the Lagrangian relaxation subproblems similar to Dantzig-Wolfe decomposition. An exemplary case study shows the effectiveness of this extended approach.

Description: Consider a flow network, i.e., a directed graph where each arc has a nonnegative capacity value and an associated length, together with nonempty supply intervals for the sources and nonempty demand intervals for the sinks. The Maximum Min-Cost-Flow Problem (MaxMCF) is to find fixed supply and demand values within these intervals such that the optimal objective value of the induced Min-Cost-Flow Problem (MCF) is maximized. In this paper, we show that MaxMCF as well as its uncapacitated variant, the Maximum Transportation Problem (MaxTP), are NP-hard. Further, we prove that MaxMCF is APX-hard if a connectedness-condition regarding the sources and the sinks of the flow network is dropped. Finally, we show how the Minimum Min-Cost-Flow Problem (MinMCF) can be solved in polynomial time.

Description: Secure energy transport is considered as highly relevant for the basic infrastructure of nowadays society and economy. To satisfy increasing demands and to handle more diverse transport situations, operators of energy networks regularly expand the capacity of their network by building new network elements, known as the expansion planning problem. A key constraint function in expansion planning problems is a nonlinear and nonconvex potential loss function. In order to improve the algorithmic performance of state-of-the-art MINLP solvers, this paper presents an algebraic description for the convex envelope of this function. Through a thorough computational study, we show that this tighter relaxation tremendously improve the performance of the MINLP solver SCIP on a large test set of practically relevant instances for the expansion planning problem. In particular, the results show that our achievements lead to an improvement of the solver performance for a development version by up to 58%.

Description: The benefits of cutting planes based on the perspective function are well known for many specific classes of mixed-integer nonlinear programs with on/off structures. However, we are not aware of any empirical studies that evaluate their applicability and computational impact over large, heterogeneous test sets in general-purpose solvers. This paper provides a detailed computational study of perspective cuts within a linear programming based branch-and-cut solver for general mixed-integer nonlinear programs. Within this study, we extend the applicability of perspective cuts from convex to nonconvex nonlinearities. This generalization is achieved by applying a perspective strengthening to valid linear inequalities which separate solutions of linear relaxations. The resulting method can be applied to any constraint where all variables appearing in nonlinear terms are semi-continuous and depend on at least one common indicator variable. Our computational experiments show that adding perspective cuts for convex constraints yields a consistent improvement of performance, and adding perspective cuts for nonconvex constraints reduces branch-and-bound tree sizes and strengthens the root node relaxation, but has no significant impact on the overall mean time.

Description: The stable assembly of fluctuating nanoparticle clusters on a surface represents a technological challenge of widespread interest for both fundamental and applied research. Here we demonstrate a technique to stably confine in two dimensions clusters of interacting nanoparticles via size-tunable, virtual magnetic traps. We use cylindrical Bloch walls arranged to form a triangular lattice of ferromagnetic domains within an epitaxially grown ferrite garnet film. At each domain, the magnetic stray field generates an effective harmonic potential with a field tunable stifness. The experiments are combined with theory to show that the magnetic confinement is effectively harmonic and pairwise interactions are of dipolar nature, leading to central, strictly repulsive forces. For clusters of magnetic nanoparticles, the stationary collective states arise from the competition between repulsion, confinement and the tendency to fill the central potential well. Using a numerical simulation model as a quantitative map between the experiment and theory we explore the field-induced crystallization process for larger clusters and unveil the existence of three different dynamical regimes. The present method provides a model platform for investigations of the collective phenomena emerging when strongly confined nanoparticle clusters are forced to move in an idealized, harmonic-like potential.

Description: A common approach to reduce the Euler equations' complexity for the simulation and optimization of gas networks is to neglect small terms that contribute little to the overall equations. An example is the inertia term of the momentum equation since it is said to be of negligible size under real-world operating conditions. However, this justification has always only been based on experience or single sets of artificial data points. This study closes this gap by presenting a large-scale empirical evaluation of the absolute and relative size of the inertia term when operating a real-world gas network. Our data consists of three years of fine-granular state data of one of the largest gas networks in Europe, featuring over 6,000 pipes with a total length of over 10,000 km. We found that there are only 120 events in which a subnetwork consisting of multiple pipes has an inertia term of high significance for more than three minutes. On average, such an event occurs less often than once every ten days. Therefore, we conclude that the inertia term is indeed negligible for real-world transient gas network control problems.

Description: We investigate preprocessing for single-source shortest path queries in digraphs, where arc costs are only known to lie in an interval. More precisely, we want to decide for each arc whether it is part of some shortest path tree for some realization of costs. We show that this problem is solvable in polynomial time by giving a combinatorial algorithm, using optimal structures that we call forks. Our algorithm turns out to be very efficient in practice, and is sometimes even superior in quality to a heuristic developed for the one-to-one shortest path problem in the context of passenger routing in public transport.

Description: Scheduling ist ein wichtiger Forschungsgegenstand im Bereich der diskreten Optimierung. Es geht darum, einen Schedule, d.h. einen Ablaufplan, für gegebene Ereignisse zu finden. Dieser soll optimal hinsichtlich einer Zielfunktion wie zum Beispiel minimaler Dauer oder Kosten sein. Dabei gibt es in der Regel Nebenbedingungen wie Vorrangbeziehungen zwischen den Ereignissen oder zeitliche Einschränkungen, die zu erfüllen sind. Falls die Ereignisse periodisch wiederkehren, spricht man von periodischem Scheduling. Beispiele sind das Erstellen von Zugfahrplänen, die Schaltungvon Ampelsignalen oder die Planung von Produktionsabläufen. Mathematisch können diese Probleme mit dem Periodic Event Scheduling Problem (PESP) modelliert werden, das als gemischt-ganzzahliges Programm formuliert werden kann. In dieser Bachelorarbeit wird ein Ansatz zur Lösung des PESP mittels Zerlegung und Dualisierung entwickelt. In den Kapiteln 2 und 3 werden zunächst die notwendigen graphentheoretischen Grundlagen und das PESP eingeführt. In Kapitel 4 wird das PESP durch Fixierung der ganzzahligen Variablen in lineare Programme zerlegt. Dieses Unterproblem wird dualisiert und wieder in das PESP eingesetzt. Dafür ist eine weitere Nebenbedingung nötig. Im fünften Kapitel behandeln wir die Lösung des teildualisierten PESP. Eine Möglichkeit ist es, sich auf eine Teilmenge der Nebenbedingungen zu beschränken. Eine weitere Möglichkeit ist ein Algorithmus, derähnlich wie BendersZerlegung die Nebenbedingungen dynamisch erzeugt. Dieser Algorithmus wird in Kapitel 6 implementiert und an vier Beispielen getestet.

Description: Algorithms that solve the shortest path problem can largely be split into the two categories of label setting and label correcting. The Multiobjective Shortest Path (MOSP) problem is a generalization of the classical shortest path problem in terms of the dimension of the cost function. We explore the differences of two similar MOSP label setting algorithms. Furthermore, we present and prove a general method of how to derive Fully Polynomial Time Approximation Schemes (FPTAS) for MOSP label setting algorithms. Finally, we explore two pruning techniques for the one to one variants of exact label setting MOSP algorithms and adapt them to their FPTAS variants.

Description: Im Juni 2021 fand die jüngste Urheberrechtsreform statt. Sie bietet neue Chancen für das kulturelle Erbe, sei es in den Archiven und Bibliotheken sozialer Bewegungen, kleinen und großen Museen oder staatlichen Archiven und Bibliotheken. Denn die Novelle beinhaltet neue gesetzliche Erlaubnisse, die insbesondere die Online-Stellung von Archivmaterialien (“nicht verfügbare Werke”) und den Schutz der Gemeinfreiheit betreffen. Das vorliegende Bulletin geht komprimiert auf diese Neuerungen ein und erklärt, was sich in Zukunft ändern wird. Darauf aufbauend wird Mitte 2022 eine ausführliche und aktualisierte Publikation zur Rechteklärung erscheinen. Diese Vorveröffentlichung soll erste drängende Fragen klären. Herausgeber:innen sind das Digitale Deutsche Frauenarchiv (DDF) und das Forschungs- und Kompetenzzentrum Digitalisierung Berlin (digiS), die bereits unabhängig voneinander Handreichungen zu rechtlichen Aspekten der Digitalisierung veröffentlichten.

Description: We study the formation of trails in populations of self-propelled agents that make oriented deposits of pheromones and also sense such deposits to which they then respond with gradual changes of their direction of motion. Based on extensive off-lattice computer simulations aiming at the scale of insects, e.g., ants, we identify a number of emerging stationary patterns and obtain qualitatively the non-equilibrium \add{state} diagram of the model, spanned by the strength of the agent--pheromone interaction and the number density of the population. In particular, we demonstrate the spontaneous formation of persistent, macroscopic trails, and highlight some behaviour that is consistent with a dynamic phase transition. This includes a characterisation of the mass of system-spanning trails as a potential order parameter. We also propose a dynamic model for a few macroscopic observables, including the sub-population size of trail-following agents, which captures the early phase of trail formation.

Description: We present a new label-setting algorithm for the Multiobjective Shortest Path (MOSP) problem that computes a minimum complete set of efficient paths for a given instance. The size of the priority queue used in the algorithm is bounded by the number of nodes in the input graph and extracted labels are guaranteed to be efficient. These properties allow us to give a tight output-sensitive running time bound for the new algorithm that can almost be expressed in terms of the running time of Dijkstra’s algorithm for the Shortest Path problem. Hence, we suggest to call the algorithm Multiobjective Dijkstra Algorithm (MDA). The simplified label management in the MDA allows us to parallelize some subroutines. In our computational experiments, we compare the MDA and the classical label-setting MOSP algorithm by Martins, which we improved using new data structures and pruning techniques. On average, the MDA is 2 to 9 times faster on all used graph types. On some instances the speedup reaches an order of magnitude.

Description: Boolean delay equations (BDEs), with their relatively simple and intuitive mode of modelling, have been used in many research areas including, for example, climate dynamics and earthquake propagation. Their application to biological systems has been scarce and limited to the molecular level. Here, we derive and present two BDE models. One is directly derived from a previously published ordinary differential equation (ODE) model for the bovine estrous cycle, whereas the second model includes a modification of a particular biological mechanism. We not only compare the simulation results from the BDE models with the trajectories of the ODE model, but also validate the BDE models with two additional numerical experiments. One experiment induces a switch in the oscillatory pattern upon changes in the model parameters, and the other simulates the administration of a hormone that is known to shift the estrous cycle in time. The models presented here are the first BDE models for hormonal oscillators, and the first BDE models for drug administration. Even though automatic parameter estimation still remains challenging, our results support the role of BDEs as a framework for the systematic modelling of complex biological oscillators.

Description: Deutsche Bahn (DB) operates a large fleet of rolling stock (locomotives, wagons, and train sets) that must be combined into trains to perform rolling stock rotations. This train composition is a special characteristic of railway operations that distinguishes rolling stock rotation planning from the vehicle scheduling problems prevalent in other industries. DB models train compositions using hyperarcs. The resulting hypergraph models are ad-dressed using a novel coarse-to-fine method that implements a hierarchical column genera-tion over three levels of detail. This algorithm is the mathematical core of DB’s fleet em-ployment optimization (FEO) system for rolling stock rotation planning. FEO’s impact within DB’s planning departments has been revolutionary. DB has used it to support the company’s procurements of its newest high-speed passenger train fleet and its intermodal cargo locomotive fleet for cross-border operations. FEO is the key to successful tendering in regional transport and to construction site management in daily operations. DB’s plan-ning departments appreciate FEO’s high-quality results, ability to reoptimize (quickly), and ease of use. Both employees and customers benefit from the increased regularity of operations. DB attributes annual savings of 74 million euro, an annual reduction of 34,000 tons of CO2 emissions, and the elimination of 600 coupling operations in cross-border operations to the implementation of FEO.

Description: New approaches to ovarian stimulation protocols, such as luteal start, random start or double stimulation, allow for flexibility in ovarian stimulation at different phases of the menstrual cycle which is especially useful when time for assisted reproductive technology is limited, e.g. for emergency fertility preservation in cancer patients. It has been proposed that the success of these methods is based on the continuous growth of multiple cohorts ("waves") of follicles throughout the menstrual cycle which leads to the availability of ovarian follicles for ovarian controlled stimulation at several time points. Though several preliminary studies have been published, their scientific evidence has not been considered as being strong enough to integrate these results into routine clinical practice. This work aims at adding further scientific evidence about the efficiency of variable-start protocols and underpinning the theory of follicular waves by using mathematical modelling and numerical simulations. For this purpose, we have modified and coupled two previously published models, one describing the time course of hormones and one describing competitive follicular growth in a normal menstrual cycle. The coupled model is used to test stimulation protocols in silico. Simulation results show the occurrence of follicles in a wave-like manner during a normal menstrual cycle and qualitatively predict the outcome of ovarian stimulation initiated at different time points of the menstrual cycle.

Description: We present an optimization model which is capable of routing and ordering trains on a microscopic level under a moving block regime. Based on a general timetabling definition (GTTP) that allows the plug in of arbitrarily detailed methods to compute running and headway times, we describe a layered graph approach using velocity expansion, and develop a mixed integer linear programming formulation. Finally, we present promising results for a German corridor scenario with mixed traffic, indicating that applying branch-and-cut to our model is able to solve reasonably sized instances with up to hundred trains to optimality.

Description: The covering of a graph with (possibly disjoint) connected subgraphs is a fundamental problem in graph theory. In this paper, we study a version to cover a graph's vertices by connected subgraphs subject to lower and upper weight bounds, and propose a column generation approach to dynamically generate feasible and promising subgraphs. Our focus is on the solution of the pricing problem which turns out to be a variant of the NP-hard Maximum Weight Connected Subgraph Problem. We compare different formulations to handle connectivity, and find that a single-commodity flow formulation performs best. This is notable since the respective literature seems to have dismissed this formulation. We improve it to a new coarse-to-fine flow formulation that is theoretically and computationally superior, especially for large instances with many vertices of degree 2 like highway networks, where it provides a speed-up factor of 10 over the non-flow-based formulations. We also propose a preprocessing method that exploits a median property of weight constrained subgraphs, a primal heuristic, and a local search heuristic. In an extensive computational study we evaluate the presented connectivity formulations on different classes of instances, and demonstrate the effectiveness of the proposed enhancements. Their speed-ups essentially multiply to an overall factor of 20. Overall, our approach allows the reliabe solution of instances with several hundreds of nodes in a few minutes. These findings are further corroborated in a comparison to existing districting models on a set of test instances from the literature.

Description: Most female meiotic spindles undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of meiotic spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown. To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic \textit{Caenorhabditis elegans} spindles. Combining these approaches, we find that meiotic spindles are dynamic arrays of short microtubules that turn over within seconds. The results show that the metaphase to anaphase transition correlates with an increase in microtubule numbers and a decrease in their average length. Detailed analysis of the tomographic data revealed that the microtubule length changes significantly during the metaphase-to-anaphase transition. This effect is most pronounced for microtubules located within 150 nm of the chromosome surface. To understand the mechanisms that drive this transition, we developed a mathematical model for the microtubule length distribution that considers microtubule growth, catastrophe, and severing. Using Bayesian inference to compare model predictions and data, we find that microtubule turn-over is the major driver of the spindle reorganizations. Our data suggest that in metaphase only a minor fraction of microtubules, those closest to the chromosomes, are severed. The large majority of microtubules, which are not in close contact with chromosomes, do not undergo severing. Instead, their length distribution is fully explained by growth and catastrophe. This suggests that the most prominent drivers of spindle rearrangements are changes in nucleation and catastrophe rate. In addition, we provide evidence that microtubule severing is dependent on katanin.

Description: We investigate preprocessing for single-source shortest path queries in digraphs, where arc costs are only known to lie in an interval. More precisely, we want to decide for each arc whether it is part of some shortest path tree for some realization of costs. We show that this problem is solvable in polynomial time by giving a combinatorial algorithm, using optimal structures that we call forks. Our algorithm turns out to be very efficient in practice, and is sometimes even superior in quality to a heuristic developed for the one-to-one shortest path problem in the context of passenger routing in public transport.

Description: A common approach to reduce the Euler equations' complexity for the simulation and optimization of gas networks is to neglect small terms that contribute little to the overall equations. An example is the inertia term of the momentum equation, which is said to be of negligible size under real-world operating conditions. However, this justification has always only been based on experience or single sets of artificial data points. This study closes this gap by presenting a large-scale empirical evaluation of the absolute and relative size of the inertia term when operating a real-world gas network. Our data consists of three years of fine-granular state data of one of the largest gas networks in Europe, featuring over 6,000 pipes with a total length of over 10,000 km. We found that there are only 120 events in which a subnetwork consisting of multiple pipes has an inertia term of high significance for more than three minutes. On average, such an event occurs less often than once every ten days. Therefore, we conclude that the inertia term is indeed negligible for real-world transient gas network control problems.

Description: For mating, leafhoppers (Cicadellidae) use substrate-borne vibrational signals to communicate. We provide the first complete description of the abdominal chordotonal organs that enable the perception of these signals. This supplementary data provides the aligned stack of 450 semithin serial sections of the first and second abdominal segment of an adult male Rhododendron leafhopper (Graphocephala fennahi). Further, this supplementary data comprises the segmentation files of five chordotonal organs, the exoskeleton, the segmental nerves and the spiracles of the first and the second abdominal segment. Due to time limitations, the structures of only one half of the body were segmented. The specimen was caught by hand net in September 2018 in Berlin-Tiergarten, Germany. Samples were embedded in Araldite® 502 resin and cut transversally in 1 μm thick sections using a Leica ultramicrotome and a DIATOME Histo Jumbo 6.0 mm diamond knife. Sections were placed on microscopic slides and stained with methylene blue/azur II. The images were taken by means of a 3DHISTECH PANNORAMIC SCAN II slide scanner in the Institute of Pathology Charité in Berlin-Mitte, Germany. Images with a voxel size of 0.273809 μm x 0.273809 μm x 1 μm where obtained. The images were converted from MRXS-files to TIFF-files with the 3DHistech software Slide Converter 2.3. Using Photoshop, the images were cropped to the same canvas size and artefacts were removed. All further steps, such as alignment and segmentation, were done with the software Amira. In order to facilitate the further processing of the dataset, the voxels where resampled to a size of 0.547619 μm x 0.547619 μm x 1 μm.

Description: A connected partition is a partition of the vertices of a graph into sets that induce connected subgraphs. Such partitions naturally occur in many application areas such as road networks, and image processing. In these settings, it is often desirable to partition into a fixed number of parts of roughly of the same size or weight. The resulting computational problem is called Balanced Connected Partition (BCP). The two classical objectives for BCP are to maximize the weight of the smallest, or minimize the weight of the largest component. We study BCP on c-claw-free graphs, the class of graphs that do not have K_{1,c} as an induced subgraph, and present efficient (c −1)-approximation algorithms for both objectives. In particular, for 3-claw-free graphs, also simply known as claw-free graphs, we obtain a 2-approximation. Due to the claw-freeness of line graphs, this also implies a 2-approximation for the edge-partition version of BCP in general graphs. A harder connected partition problem arises from demanding a connected partition into k parts that have (possibly) heterogeneous target weights w_1, ..., w_k. In the 1970s Győri and Lovász showed that if G is k-connected and the target weights sum to the total size of G, such a partition exists. However, to this day no polynomial algorithm to compute such partitions exists for k 〉 4. Towards finding such a partition T_1, ..., T_k in k-connected graphs for general k, we show how to efficiently compute connected partitions that at least approximately meet the target weights, subject to the mild assumption that each w_i is greater than the weight of the heaviest vertex. In particular, we give a 3-approximation for both the lower and the upper bounded version i.e. we guarantee that each T_i has weight at least w_i/3 or that each T_i has weight most 3w_i, respectively. Also, we present a both-side bounded version that produces a connected partition where each T_i has size at least w_i/3 and at most max({r, 3})w_i, where r ≥1 is the ratio between the largest and smallest value in w_1, ..., w_k. In particular for the balanced version, i.e. w_1 = w_2 = ... = w_k, this gives a partition with 1/3 w_i ≤ w(T_i) ≤ 3w_i.

Description: Periodic timetable optimization problems in public transport can be modeled as mixed-integer linear programs by means of the Periodic Event Scheduling Problem (PESP). In order to keep the branch-and-bound tree small, minimum integral cycle bases have been proven successful. We examine forward cycle bases, where no cycle is allowed to contain a backward arc. After reviewing the theory of these bases, we describe the construction of an integral forward cycle basis on a line-based event-activity network. Adding turnarounds to the instance R1L1 of the benchmark library PESPlib, we computationally evaluate three types of forward cycle bases in the Pareto sense, and come up with significant improvements concerning dual bounds.

Description: Päschke et al. (J Fluid Mech, 2012) studied the nonlinear dynamics of strongly tilted vortices subject to asymmetric diabatic heating by asymptotic methods. They found, inter alia, that an azimuthal Fourier mode 1 heating pattern can intensify or attenuate such a vortex depending on the relative orientation of the tilt and the heating asymmetries. The theory originally addressed the gradient wind regime which, asymptotically speaking, corresponds to vortex Rossby numbers of order unity in the limit. Formally, this restricts the applicability of the theory to rather weak vortices. It is shown below that said theory is, in contrast, uniformly valid for vanishing Coriolis parameter and thus applicable to vortices up to low hurricane strengths. An extended discussion of the asymptotics as regards their physical interpretation and their implications for the overall vortex dynamics is also provided in this context. The paper’s second contribution is a series of three-dimensional numerical simulations examining the effect of different orientations of dipolar diabatic heating on idealized tropical cyclones. Comparisons with numerical solutions of the asymptotic equations yield evidence that supports the original theoretical predictions of Päschke et al. In addition, the influence of asymmetric diabatic heating on the time evolution of the vortex centerline is further analyzed, and a steering mechanism that depends on the orientation of the heating dipole is revealed. Finally, the steering mechanism is traced back to the correlation of dipolar perturbations of potential temperature, induced by the vortex tilt, and vertical velocity, for which diabatic heating not necessarily needs to be responsible, but which may have other origins.

Description: We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD, and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling, notably optimized target/decoy generation by the algorithm DecoyPyrat. Finally, we perform a reanalysis of four public datasets in PRIDE by generating cell-type specific databases for 65 cell lines using the pypgatk and pgdb workflow, revealing a wealth of non-canonical or cryptic peptides amounting to more than 10% of the total number of peptides identified (43,501 out of 402,512).

Description: UG is a generic framework to parallelize branch-and-bound based solvers (e.g., MIP, MINLP, ExactIP) in a distributed or shared memory computing environment. It exploits the powerful performance of state-of-the-art "base solvers", such as SCIP, CPLEX, etc. without the need for base solver parallelization. UG framework, ParaSCIP(ug[SCIP,MPI]) and FiberSCIP (ug[SCIP,Pthreads]) are available as a beta version. v1.0.0: new documentation and cmake, generalization of ug framework, implementation of selfsplitrampup for fiber- and parascip, better memory and time limit handling.

Description: For this thesis we study the Constrained Horizontal Flightplanning Problem (CHFPP) for which one has to find the path of minimum cost between airports s and t in a directed graph that respects a set of boolean constraints. To this end we give a survey of three different multilabel algorithms that all use a domination subroutine. We summarize an approach by Knudsen, Chiarandini and Larsen to define this domination and afterwards present our own method which builds on that approach. We suggest different implementation techniques to speed up the computation time, most notably a Reoptimization for an iterative method to solve the problem. Furthermore we implemented the different versions of the algorithm and present statistics on their computation as well as an overview of statistics on the set of real-world constraints that we were given. Finally we present two alternative approaches that tackle the problem, a heuristic with similarities to a Lagrangian relaxation and an approach that makes use of an algorithm which finds the k shortest path of a graph such as the ones of Epstein or Yen.

Description: Die Planung vom Zugumläufen ist eine der wichtigsten Aufgaben für Eisenbahnun- ternehmen. Dabei spielt auch die Einhaltung von vorgegebenen Wartungsintervallen eine zentrale Rolle für die Sicherheit und Zuverlässigkeit der Schienenfahrzeuge. Wir zeigen, wie man dieses Umlaufplanungsproblem unter Beachtung von Wartungsbe- dingungen mathematisch formuliert, modelliert und löst — sowohl in der Theorie als auch im Anwendungsfall mit Szenarien der DB Fernverkehr AG, einer Konzern- tochter der Deutschen Bahn für den Schienenpersonenfernverkehr. Markus Reuther hat sich in seiner Dissertation [11] mit diesem Problem beschäftigt und es mit Hilfe eines passenden Hypergraphen als gemischt-ganzzahliges Programm modelliert. Neben der Modellierung präsentiert Reuther in seiner Arbeit neuartige algorithmische Ideen, darunter den sogenannten Coarse-to-Fine -Ansatz, bei dem zunächst Teile des Problems auf einer weniger detaillierten ( coarse ) Ebene gelöst werden und diese Lösung dann verwendet wird, um auf effiziente Art und Weise eine Lösung für das ursprüngliche Problem zu finden. Zur Wartungsplanung nutzt Reuther einen Fluss im Hypergraphen, der den Ressourcenverbrauch der Fahrzeuge modelliert. In der linearen Relaxierung des Modells führt dies dazu, dass die Zahl der notwendigen Wartungen systematisch unterschätzt wird. Dadurch bleibt in vielen Fällen eine große Lücke zwischen dem Zielfunktionswert einer optimalen Lösung des ganzzahligen Problems und der untere Schranke, die uns die lineare Relaxierung liefert. Wir nehmen uns in dieser Arbeit dieses Problems an. Wir entwickeln ein auf Pfaden basierendes ganzzahliges Modell für das Umlaufplanungsproblem und zeigen, dass die untere Schranke mindestens so scharf oder schärfer ist als die untere Schranke, die das Modell von Reuther liefert. Um das Modell zu lösen, entwickeln wir einen Algorithmus, der Spaltengenerierung mit dem Coarse-to-Fine-Ansatz von Reuther verbindet. Weiterhin entwickeln wir eine Spaltenauswahlregel zur Beschleunigung des Algorithmus. Das Modell und alle in der Arbeit vorgestellten Algorithmen wur- den im Rahmen der Arbeit implementiert und mit Anwendungsszenarien der DB Fernverkehr AG getestet. Unsere Tests zeigen, dass unser Modell für fast alle Szena- rien deutlich schärfere untere Schranken liefert als das Modell von Reuther. In den getesteten Instanzen konnten wir durch die Verbesserung der unteren Schranke bis zu 99% der Optimalitätslücke schließen. In einem Drittel der Fälle konnten wir durch unseren Ansatz auch für das ganzzahlige Programm verbesserte Zielfunktionswerte erreichen

Description: In order to plan and schedule a demand-responsive public transportation system, both temporal and spatial changes in demand should be taken into account even at the line planning stage. We study the multi-period line planning problem with integrated decisions regarding dynamic allocation of vehicles among the lines. Given the NP-hard nature of the line planning problem, the multi-period version is clearly difficult to solve for large public transit networks even with advanced solvers. It becomes necessary to develop algorithms that are capable of solving even the very-large instances in reasonable time. For instances which belong to real public transit networks, we present results of a heuristic local branching algorithm and an exact approach based on constraint propagation.

Description: We consider the stochastic scheduling problem of minimizing the expected makespan on m parallel identical machines. While the (adaptive) list scheduling policy achieves an approximation ratio of 2, any (non-adaptive) fixed assignment policy has performance guarantee Ω(logm/loglogm). Although the performance of the latter class of policies are worse, there are applications in which non-adaptive policies are desired. In this work, we introduce the two classes of δ-delay and τ-shift policies whose degree of adaptivity can be controlled by a parameter. We present a policy - belonging to both classes - which is an O(loglogm)-approximation for reasonably bounded parameters. In other words, an exponential improvement on the performance of any fixed assignment policy can be achieved when allowing a small degree of adaptivity. Moreover, we provide a matching lower bound for any δ-delay and τ-shift policy when both parameters, respectively, are in the order of the expected makespan of an optimal non-anticipatory policy.

Description: Multigrid methods for two-body contact problems are mostly based on special mortar discretizations, nonlinear Gauss-Seidel solvers, and solution-adapted coarse grid spaces. Their high computational efficiency comes at the cost of a complex implementation and a nonsymmetric master-slave discretization of the nonpenetration condition. Here we investigate an alternative symmetric and overconstrained segment-to-segment contact formulation that allows for a simple implementation based on standard multigrid and a symmetric treatment of contact boundaries, but leads to nonunique multipliers. For the solution of the arising quadratic programs, we propose augmented Lagrangian multigrid with overlapping block Gauss-Seidel smoothers. Approximation and convergence properties are studied numerically at standard test problems.

Description: Many real-world processes can naturally be modeled as systems of interacting agents. However, the long-term simulation of such agent-based models is often intractable when the system becomes too large. In this paper, starting from a stochastic spatio-temporal agent-based model (ABM), we present a reduced model in terms of stochastic PDEs that describes the evolution of agent number densities for large populations. We discuss the algorithmic details of both approaches; regarding the SPDE model, we apply Finite Element discretization in space which not only ensures efficient simulation but also serves as a regularization of the SPDE. Illustrative examples for the spreading of an innovation among agents are given and used for comparing ABM and SPDE models.

Description: Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small to be relevant for life processes. Alternatively, particle-based reaction-diffusion models are currently the most accurate and computationally feasible approach at these scales. Their efficiency lies in modeling entire molecules as particles that can diffuse and interact with each other. In this work, we develop modeling and numerical schemes for particle-based reaction-diffusion in an open setting, where the reservoirs are mediated by reaction-diffusion PDEs. We derive two important theoretical results. The first one is the mean-field for open systems of diffusing particles; the second one is the mean-field for a particle-based reaction-diffusion system with second-order reactions. We employ these two results to develop a numerical scheme that consistently couples particle-based reaction-diffusion processes with reaction-diffusion PDEs. This allows modeling open biochemical systems in contact with reservoirs that are time-dependent and spatially inhomogeneous, as in many relevant real-world applications.

Description: Industrial parks have a high potential for recycling and reusing resources such as water across companies by creating symbiosis networks. In this study, we introduce a mathematical optimization framework for the design of water network integration in industrial parks formulated as a large-scale standard mixed-integer non-linear programming (MINLP) problem. The novelty of our approach relies on i) developing a multi-level incremental optimization framework for water network synthesis, ii) including prior knowledge of demand growth and projected water scarcity to evaluate the significance of water-saving solutions, iii) incorporating a comprehensive formulation of water network synthesis problem including multiple pollutants and different treatment units and iv) performing a multi-objective optimization of the network including freshwater savings and relative cost of the network. The significance of the proposed optimization framework is illustrated by applying it to an existing industrial park in a water-scarce region in Kenya. Firstly, we illustrated the benefits of including prior knowledge to prevent an over-design of the network at the early stages. In the case study, we achieved a more flexible and expandable water network with 36% lower unit cost at the early stage and 15% lower unit cost at later stages for the overall maximum freshwater savings of 25%. Secondly, multi-objective analysis suggests an optimum freshwater savings of 14% to reduce the unit cost of network by half. Moreover, the significance of symbiosis networks is highlighted by showing that intra-company connections can only achieve a maximum freshwater savings of 17% with significantly higher unit cost (+45%). Finally, we showed that the values of symbiosis connectivity index in the Pareto front correspond to higher freshwater savings, indicating the significant role of the symbiosis network in the industrial park under study. This is the first study, where all the above elements have been taken into account simultaneously for the design of a water reuse network.

Description: We present a new label-setting algorithm for the Multiobjective Shortest Path (MOSP) problem that computes the minimal complete set of efficient paths for a given instance. The size of the priority queue used in the algorithm is bounded by the number of nodes in the input graph and extracted labels are guaranteed to be efficient. These properties allow us to give a tight output-sensitive running time bound for the new algorithm that can almost be expressed in terms of the running time of Dijkstra's algorithm for the Shortest Path problem. Hence, we suggest to call the algorithm \emph{Multiobjective Dijkstra Algorithm} (MDA). The simplified label management in the MDA allows us to parallelize some subroutines. In our computational experiments, we compare the MDA and the classical label-setting MOSP algorithm by Martins', which we improved using new data structures and pruning techniques. On average, the MDA is $\times2$ to $\times9$ times faster on all used graph types. On some instances the speedup reaches an order of magnitude.

Description: Periodic timetable optimization problems in public transport can be modeled as mixed-integer linear programs by means of the Periodic Event Scheduling Problem (PESP). In order to keep the branch-and-bound tree small, minimum integral cycle bases have been proven successful. We examine forward cycle bases, where no cycle is allowed to contain a backward arc. After reviewing the theory of these bases, we describe the construction of an integral forward cycle basis on a line-based event-activity network. Adding turnarounds to the instance \texttt{R1L1} of the benchmark library PESPlib, we computationally evaluate three types of forward cycle bases in the Pareto sense, and come up with significant improvements concerning dual bounds.

Description: The Dynamic Multiobjective Shortest Path problem features multidimensional costs that can depend on several variables and not only on time; this setting is motivated by flight planning applications and the routing of electric vehicles. We give an exact algorithm for the FIFO case and derive from it an FPTAS for both, the static Multiobjective Shortest Path (MOSP) problems and, under mild assumptions, for the dynamic problem variant. The resulting FPTAS is computationally efficient and beats the known complexity bounds of other FPTAS for MOSP problems.

Description: We study combinatorial structures in large-scale mixed-integer (nonlinear) programming problems arising in gas network optimization. We propose a preprocessing strategy exploiting the observation that a large part of the combinatorial complexity arises in certain subnetworks. Our approach analyzes these subnetworks and the combinatorial structure of the flows within these subnetworks in order to provide alternative models with a stronger combinatorial structure that can be exploited by off-the-shelve solvers. In particular, we consider the modeling of operation modes for complex compressor stations (i.e., ones with several in- or outlets) in gas networks. We propose a refined model that allows to precompute tighter bounds for each operation mode and a number of model variants based on the refined model exploiting these tighter bounds. We provide a procedure to obtain the refined model from the input data for the original model. This procedure is based on a nontrivial reduction of the graph representing the gas flow through the compressor station in an operation mode. We evaluate our model variants on reference benchmark data, showing that they reduce the average running time between 10% for easy instances and 46% for hard instances. Moreover, for three of four considered networks, the average number of search tree nodes is at least halved, showing the effectivity of our model variants to guide the solver’s search.

Description: In this thesis, adaptive algorithms in optimization under PDE constraints have been inves- tigated. In its application, the aim of optimization is to increase the longevity of implants, namely the hip joint implant, and in doing so to minimize stress shielding and simultaneously minimize the influence of locally high stresses, that, above a threshold value, are malign to the bone structure. Under the constraint of the equilibrium of forces, describing an elastodynamic setup, coupled with a contact inequality condition, a computationally expensive problem formulation is given. The first step to make the solution of the given problem possible and efficient was to change over to the spatial equilibrium equation, thus rendering an elastostatic setup. Subsequently the intrinsically dynamic motions – trajectories in the load domain – were converted to the static setup. Thus, the trajectories are marginalized to the load domain and characterized with probability distributions. Therefore the solving of the PDE constraint, the contact problem, is simplified. Yet in the whole optimization process, the solving of the PDE, the spatial equilibrium equation together with the contact condition has the most expensive contribution still and hence needed further reduction. This was achieved by application of Kriging interpolation to the load responses of the integrated distribution of stress difference and the maximum stresses. The interpolation of the two response surfaces only needs comparatively few PDE solves to set up the models. Moreover, the Kriging models can be adaptively extended by sequentially adding sample-response pairs. For this the Kriging inherent variance is used to estimate ideal new sample locations with maximum variance values. In doing so, the overall interpolation variance and therefore the interpolation error is reduced. For the integration of the integrated stress differences and penalty values on the relative high dimensional load domain Monte Carlo integration was implemented, averting the curse of dimension. Here, the motion’s probability distribution combined with patient specific data of motion frequencies is taken advantage of, making obsolete the use of the otherwise necessary importance sampling. Throughout the optimization, the FE-discretization error and the subsequently attached errors entering the solution process via PDE discretization and approximative solving of the PDE, Kriging interpolation and Monte Carlo integration need to decrease. While the FE-discretization error and the solution of the elastostatic contact problem were assumed precise enough, numerics showed, that the interpolation and integration errors can be controlled by adaptive refinement of the respective methods. For this purpose comparable error quantities for the particular algorithms were introduced and effectively put to use. For the implant position’s optimization, the derivative of the objective function was derived using the implicit function theorem. As the FE-discretization changes with implant position modifications big enough, a special line search had to be used to deal with the discontinuities in the objective function. The interplay and performance of the subalgorithms was demonstrated numerically on a reduced 2D setup of a hip joint with and without the implant. Consequently the load domain and the control variable were also limited to the 2D case.

Description: We review various characterizations of uniform convexity and smoothness on norm balls in finite-dimensional spaces and connect results stemming from the geometry of Banach spaces with scaling inequalities used in analysing the convergence of optimization methods. In particular, we establish local versions of these conditions to provide sharper insights on a recent body of complexity results in learning theory, online learning, or offline optimization, which rely on the strong convexity of the feasible set. While they have a significant impact on complexity, these strong convexity or uniform convexity properties of feasible sets are not exploited as thoroughly as their functional counterparts, and this work is an effort to correct this imbalance. We conclude with some practical examples in optimization and machine learning where leveraging these conditions and localized assumptions lead to new complexity results.

Description: Projection-free conditional gradient (CG) methods are the algorithms of choice for constrained optimization setups in which projections are often computationally prohibitive but linear optimization over the constraint set remains computationally feasible. Unlike in projection-based methods, globally accelerated convergence rates are in general unattainable for CG. However, a very recent work on Locally accelerated CG (LaCG) has demonstrated that local acceleration for CG is possible for many settings of interest. The main downside of LaCG is that it requires knowledge of the smoothness and strong convexity parameters of the objective function. We remove this limitation by introducing a novel, Parameter-Free Locally accelerated CG (PF-LaCG) algorithm, for which we provide rigorous convergence guarantees. Our theoretical results are complemented by numerical experiments, which demonstrate local acceleration and showcase the practical improvements of PF-LaCG over non-accelerated algorithms, both in terms of iteration count and wall-clock time.

Description: 50 years of astrometric data for comet 67P/C-G (orbital period about 6.45 years) provides a unique opportunity to benchmark non-gravitational acceleration models to the in situ measurements of the volatile release performed from the Rosetta rendezvous mission (2014-2016). Taken together, the Earth-bound and in-situ data yields lower fit errors and serves as a test-case for our ability to deduce thermophysical quantities of cometary nuclei from the Earth-bound observations.

Description: We propose a tropical interpretation of the solution space of the Periodic Event Scheduling Problem as a collection of polytropes, making use of the characterization of tropical cones as weighted digraph polyhedra. General and geometric properties of the polytropal collection are inspected and understood in connection with the combinatorial properties of the underlying periodic event scheduling instance. Novel algorithmic ideas are presented and tested, making use of the aforementioned theoretical results to solve and optimize the problem.

Description: Modern methods of simulating molecular systems are based on the mathematical theory of Markov operators with a focus on autonomous equilibrated systems. However, non-autonomous physical systems or non-autonomous simulation processes are becoming more and more important. A representation of non-autonomous Markov jump processes is presented as autonomous Markov chains on space-time. Augmenting the spatial information of the embedded Markov chain by the temporal information of the associated jump times, the so-called augmented jump chain is derived. The augmented jump chain inherits the sparseness of the infinitesimal generator of the original process and therefore provides a useful tool for studying time-dependent dynamics even in high dimensions. Furthermore, possible generalizations and applications to the computation of committor functions and coherent sets in the non-autonomous setting are discussed. After deriving the theoretical foundations, the concepts with a proof-of-concept Galerkin discretization of the transfer operator of the augmented jump chain applied to simple examples are illustrated.