## J. Computer Applications

### Refine

#### Year of publication

#### Document Type

- ZIB-Report (33)
- Master's Thesis (2)
- Bachelor's Thesis (1)

#### Keywords

#### Institute

- Mathematical Optimization (17)
- Visual Data Analysis (10)
- Numerical Mathematics (5)
- Distributed Algorithms and Supercomputing (3)
- Mathematical Optimization Methods (2)
- Computational Nano Optics (1)
- Mathematical Algorithmic Intelligence (1)
- Network Optimization (1)
- Scientific Information (1)
- Therapy Planning (1)

We investigate polyhedral aspects of the Periodic Event Scheduling Problem (PESP), the mathematical basis for periodic timetabling problems in public transport. Flipping the orientation of arcs, we obtain a new class of valid inequalities, the flip inequalities, comprising both the known cycle and change-cycle inequalities. For a point of the LP relaxation, a violated flip inequality can be found in pseudo-polynomial time, and even in linear time for a spanning tree solution. Our main result is that the integer vertices of the polytope described by the flip inequalities are exactly the vertices of the PESP polytope, i.e., the convex hull of all feasible periodic slacks with corresponding modulo parameters. Moreover, we show that this flip polytope equals the PESP polytope in some special cases. On the computational side, we devise several heuristic approaches concerning the separation of cutting planes from flip inequalities. These produce better dual bounds for the smallest and largest instance of the benchmarking library PESPlib.

In a recent paper, Conte et al. [CGMR2017] presented an algorithm for enumerating all acyclic orientations of a graph G=(V,E) with a single source (and related orientations) with delay O(|V||E|). In this paper we revisit the problem by going back to an early paper by de Fraysseix et al. [FMR1995], who proposed an algorithm for enumerating all bipolar orientations of a graph based on a recursion formula. We first formalize de Fraysseix et al.'s algorithm for bipolar orientations and determine that its delay is also O(|V||E|). We then apply their recursion formula to the case of Conte et al.'s enumeration problem and show that this yields a more efficient enumeration algorithm with delay O(\sqrt(|V|)|E|). Finally, a way to further streamline the algorithm that leads to a particularly simple implementation is suggested.

Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms
(2019)

Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies.

Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.

The Periodic Event Scheduling Problem is a well-studied NP-hard problem with applications in public transportation to find good periodic timetables. Among the most powerful heuristics to solve the periodic timetabling problem is the modulo network simplex method. In this paper, we consider the more difficult version with integrated passenger routing and propose a refined integrated variant to solve this problem on real-world-based instances.

In the planning process of public transportation companies, designing the timetable is among the core planning steps. In particular in the case of periodic (or cyclic) services, the Periodic Event Scheduling Problem (PESP) is well-established to compute high-quality periodic timetables.
We are considering algorithms for computing good solutions for the very basic PESP with no additional extra features as add-ons. The first of these algorithms generalizes several primal heuristics that had been proposed in the past, such as single-node cuts and the modulo network simplex algorithm. We consider partitions of the graph, and identify so-called delay cuts as a structure that allows to generalize several previous heuristics. In particular, when no more improving delay cut can be found, we already know that the other heuristics could not improve either.
The second of these algorithms turns a strategy, that had been discussed in the past, upside-down: Instead of gluing together the network line-by-line in a bottom-up way, we develop a divide-and-conquer-like top-down approach to separate the initial problem into two easier subproblems such that the information loss along their cutset edges is as small as possible.
We are aware that there may be PESP instances that do not fit well the separator setting. Yet, on the RxLy-instances of PESPlib in our experimental computations, we come up with good primal solutions and dual bounds. In particular, on the largest instance (R4L4), this new separator approach, which applies a state-of-the-art solver as subroutine, is able to come up with better dual bounds than purely applying this state-of-the-art solver in the very same time.

Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Grüneisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori.

A great amount of material properties is strongly influenced by dislocations, the carriers of plastic deformation. It is therefore paramount to have appropriate tools to quantify dislocation substructures with regard to their features, e.g., dislocation density, Burgers vectors or line direction. While the transmission electron microscope (TEM) has been the most widely-used equipment implemented to investigate dislocations, it usually is limited to the two-dimensional (2D) observation of three-dimensional (3D) structures. We reconstruct, visualize and quantify 3D dislocation substructure models from only two TEM images (stereo-pairs) and assess the results. The reconstruction is based on the manual interactive tracing of filiform objects on both images of the stereo-pair. The reconstruction and quantification method are demonstrated on dark field (DF) scanning (S)TEM micrographs of dislocation substructures imaged under diffraction contrast conditions. For this purpose, thick regions (> 300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo-pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3 % and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed.

Cycle inequalities play an important role in the polyhedral study of the periodic
timetabling problem. We give the first pseudo-polynomial time separation algo-
rithm for cycle inequalities, and we give a rigorous proof for the pseudo-polynomial
time separability of the change-cycle inequalities. Moreover, we provide several
NP-completeness results, indicating that pseudo-polynomial time is best possible.
The efficiency of these cutting planes is demonstrated on real-world instances of the
periodic timetabling problem.

A Simple Way to Compute the Number of Vehicles That Are Required to Operate a Periodic Timetable
(2018)

We consider the following planning problem in public transportation: Given a
periodic timetable, how many vehicles are required to operate it?
In [9], for this sequential approach, it is proposed to first expand the periodic
timetable over time, and then answer the above question by solving a flow-based
aperiodic optimization problem.
In this contribution we propose to keep the compact periodic representation of
the timetable and simply solve a particular perfect matching problem. For practical
networks, it is very much likely that the matching problem decomposes into several
connected components. Our key observation is that there is no need to change any
turnaround decision for the vehicles of a line during the day, as long as the timetable
stays exactly the same.