Parallel Mapper

The construction of Mapper has emerged in the last decade as a powerful and effective topological data analysis tool that approximates and generalizes other topological summaries, such as the Reeb graph, the contour tree, split, and joint trees. In this paper, we study the parallel analysis of the construction of Mapper. We give a provably correct parallel algorithm to execute Mapper on multiple processors and discuss the performance results that compare our approach to a reference sequential Mapper implementation. We report the performance experiments that demonstrate the efficiency of our method

Modeling of Covalent Bonding in Solids by Inversion of Cohesive Energy Curves

We provide a systematic test of empirical theories of covalent bonding in solids using an exact procedure to invert ab initio cohesive energy curves. By considering multiple structures of the same material, it is possible for the first time to test competing angular functions, expose inconsistencies in the basic assumption of a cluster expansion, and extract general features of covalent bonding. We test our methods on silicon, and provide the direct evidence that the Tersoff-type bond order formalism correctly describes coordination dependence. For bond-bending forces, we obtain skewed angular functions that favor small angles, unlike existing models. As a proof-of-principle demonstration, we derive a Si interatomic potential which exhibits comparable accuracy to existing models.Comment: 4 pages revtex (twocolumn, psfig), 3 figures. Title and some wording (but no content) changed since original submission on 24 April 199

Sparse Nerves in Practice

Topological data analysis combines machine learning with methods from algebraic topology. Persistent homology, a method to characterize topological features occurring in data at multiple scales is of particular interest. A major obstacle to the wide-spread use of persistent homology is its computational complexity. In order to be able to calculate persistent homology of large datasets, a number of approximations can be applied in order to reduce its complexity. We propose algorithms for calculation of approximate sparse nerves for classes of Dowker dissimilarities including all finite Dowker dissimilarities and Dowker dissimilarities whose homology is Cech persistent homology. All other sparsification methods and software packages that we are aware of calculate persistent homology with either an additive or a multiplicative interleaving. In dowker_homology, we allow for any non-decreasing interleaving function $\alpha$. We analyze the computational complexity of the algorithms and present some benchmarks. For Euclidean data in dimensions larger than three, the sizes of simplicial complexes we create are in general smaller than the ones created by SimBa. Especially when calculating persistent homology in higher homology dimensions, the differences can become substantial

A geometric constraint over k-dimensional objects and shapes subject to business rules

This report presents a global constraint that enforces rules written in a language based on arithmetic and first-order logic to hold among a set of objects. In a first step, the rules are rewritten to Quantifier-Free Presburger Arithmetic (QFPA) formulas. Secondly, such formulas are compiled to generators of k-dimensional forbidden sets. Such generators are a generalization of the indexicals of cc(FD). Finally, the forbidden sets generated by such indexicals are aggregated by a sweep-based algorithm and used for filtering. The business rules allow to express a great variety of packing and placement constraints, while admitting efficient and effective filtering of the domain variables of the k-dimensional object, without the need to use spatial data structures. The constraint was used to directly encode the packing knowledge of a major car manufacturer and tested on a set of real packing problems under these rules, as well as on a packing-unpacking problem

Giant Monopole Resonances and nuclear incompressibilities studied for the zero-range and separable pairing interactions

Background: Following the 2007 precise measurements of monopole strengths in tin isotopes, there has been a continuous theoretical effort to obtain a precise description of the experimental results. Up to now, there is no satisfactory explanation of why the tin nuclei appear to be significantly softer than 208Pb. Purpose: We determine the influence of finite-range and separable pairing interactions on monopole strength functions in semi-magic nuclei. Methods: We employ self-consistently the Quasiparticle Random Phase Approximation on top of spherical Hartree-Fock-Bogolyubov solutions. We use the Arnoldi method to solve the linear-response problem with pairing. Results: We found that the difference between centroids of Giant Monopole Resonances measured in lead and tin (about 1 MeV) always turns out to be overestimated by about 100%. We also found that the volume incompressibility, obtained by adjusting the liquid-drop expression to microscopic results, is significantly larger than the infinite-matter incompressibility. Conclusions: The zero-range and separable pairing forces cannot induce modifications of monopole strength functions in tin to match experimental data.Comment: 11 RevTeX pages, 16 figures, 1 table, extended versio

Individual Patient Data Meta-analysis of Survival and Psychosomatic Self-regulation from Published Prospective Controlled Cohort Studies for Long-term Therapy of Breast Cancer Patients with a Mistletoe Preparation (Iscador)

Mistletoe preparations such as Iscador are in common use as complementary/anthroposophic medications for many cancer indications, particularly for solid cancers. The efficacy is still discussed controversially. This paper presents an individual patient data meta-analysis of all published prospective matched-pair studies with breast cancer patients concerned with long-term application of a complementary/anthroposophic therapy with the mistletoe preparation Iscador. Six sets of data were available for individual patient meta-analysis of breast cancer patients, matched according to prognostic factors into pairs with and without mistletoe (Iscador) therapy. The main outcome measures were overall survival and psychosomatic self-regulation. Overall survival was almost significant in favor of the Iscador group in the combined data set of the randomized studies: estimate of the hazard ratio with 95% confidence interval 0.59 (0.34, 1.02). Overall survival was highly significant in the combined data set of the non-randomized studies: 0.43 (0.34, 0.56). In the combined analysis of the randomized studies, improvement of psychosomatic self-regulation, as a measure of autonomous coping with the disease, was highly significant in favor of the Iscador group: estimate of the median difference 0.45 (0.15, 0.80), P = 0.0051. The analyzed studies show that therapy with Iscador might prolong overall survival and improve psychosomatic self-regulation of breast cancer patients