Near Optimal Subdivision Algorithms for Real Root Isolation

We describe a subroutine that improves the running time of any subdivision algorithm for real root isolation. The subroutine first detects clusters of roots using a result of Ostrowski, and then uses Newton iteration to converge to them. Near a cluster, we switch to subdivision, and proceed recursively. The subroutine has the advantage that it is independent of the predicates used to terminate the subdivision. This gives us an alternative and simpler approach to recent developments of Sagraloff (2012) and Sagraloff-Mehlhorn (2013), assuming exact arithmetic. The subdivision tree size of our algorithm using predicates based on Descartes's rule of signs is bounded by $O(n\log n)$, which is better by $O(n\log L)$ compared to known results. Our analysis differs in two key aspects. First, we use the general technique of continuous amortization from Burr-Krahmer-Yap (2009), and second, we use the geometry of clusters of roots instead of the Davenport-Mahler bound. The analysis naturally extends to other predicates.Comment: 19 pages, 3 figure

The Nature of Computation : Logic, Algorithms, Applications:9th Conference on Computability in Europe, CiE 2013, Milan, Italy, July 1-5, 2013 : proceedings

This book constitutes the refereed proceedings of the 9th Conference on Computability in Europe, CiE 2013, held in Milan, Italy, in July 2013. The 48 revised papers presented together with 1 invited lecture and 2 tutorials were carefully reviewed and selected with an acceptance rate of under 31,7%. Both the conference series and the association promote the development of computability-related science, ranging over mathematics, computer science and applications in various natural and engineering sciences such as physics and biology, and also including the promotion of related non-scientific fields such as philosophy and history of computing

A full complexity dichotomy for immanant families

Given an integer $n\geq 1$ and an irreducible character $\chi_{\lambda}$ of $S_{n}$ for some partition $\lambda$ of $n$, the immanant $\mathrm{imm}_{\lambda}:\mathbb{C}^{n\times n}\to\mathbb{C}$ maps matrices $A\in\mathbb{C}^{n\times n}$ to $\mathrm{imm}_{\lambda}(A)=\sum_{\pi\in S_{n}}\chi_{\lambda}(\pi)\prod_{i=1}^{n}A_{i,\pi(i)}$. Important special cases include the determinant and permanent, which are the immanants associated with the sign and trivial character, respectively. It is known that immanants can be evaluated in polynomial time for characters that are close to the sign character: Given a partition $\lambda$ of $n$ with $s$ parts, let $b(\lambda):=n-s$ count the boxes to the right of the first column in the Young diagram of $\lambda$. For a family of partitions $\Lambda$, let $b(\Lambda):=\max_{\lambda\in\Lambda}b(\lambda)$ and write Imm$(\Lambda)$ for the problem of evaluating $\mathrm{imm}_{\lambda}(A)$ on input $A$ and $\lambda\in\Lambda$. If $b(\Lambda)<\infty$, then Imm$(\Lambda)$ is known to be polynomial-time computable. This subsumes the case of the determinant. On the other hand, if $b(\Lambda)=\infty$, then previously known hardness results suggest that Imm$(\Lambda)$ cannot be solved in polynomial time. However, these results only address certain restricted classes of families $\Lambda$. In this paper, we show that the parameterized complexity assumption FPT $\neq$ #W[1] rules out polynomial-time algorithms for Imm$(\Lambda)$ for any computationally reasonable family of partitions $\Lambda$ with $b(\Lambda)=\infty$. We give an analogous result in algebraic complexity under the assumption VFPT $\neq$ VW[1]. Furthermore, if $b(\lambda)$ even grows polynomially in $\Lambda$, we show that Imm$(\Lambda)$ is hard for #P and VNP. This concludes a series of partial results on the complexity of immanants obtained over the last 35 years.Comment: 28 pages, to appear at STOC'2

Novel computational techniques for mapping and classifying Next-Generation Sequencing data

Since their emergence around 2006, Next-Generation Sequencing technologies have been revolutionizing biological and medical research. Quickly obtaining an extensive amount of short or long reads of DNA sequence from almost any biological sample enables detecting genomic variants, revealing the composition of species in a metagenome, deciphering cancer biology, decoding the evolution of living or extinct species, or understanding human migration patterns and human history in general. The pace at which the throughput of sequencing technologies is increasing surpasses the growth of storage and computer capacities, which creates new computational challenges in NGS data processing. In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved. However, the vast majority of mappers follow the same paradigm and only little attention has been paid to non-standard mapping approaches. Here, we propound the so-called dynamic mapping that we show to significantly improve the resulting alignments compared to traditional mapping approaches. Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads. We provide the first comprehensive overview of this method and demonstrate its qualities using Dynamic Mapping Simulator, a pipeline that compares various dynamic mapping scenarios to static mapping and iterative referencing. An important component of a dynamic mapper is an online consensus caller, i.e., a program collecting alignment statistics and guiding updates of the reference in the online fashion. We provide Ococo, the first online consensus caller that implements a smart statistics for individual genomic positions using compact bit counters. Beyond its application to dynamic mapping, Ococo can be employed as an online SNP caller in various analysis pipelines, enabling SNP calling from a stream without saving the alignments on disk. Metagenomic classification of NGS reads is another major topic studied in the thesis. Having a database with thousands of reference genomes placed on a taxonomic tree, the task is to rapidly assign a huge amount of NGS reads to tree nodes, and possibly estimate the relative abundance of involved species. In this thesis, we propose improved computational techniques for this task. In a series of experiments, we show that spaced seeds consistently improve the classification accuracy. We provide Seed-Kraken, a spaced seed extension of Kraken, the most popular classifier at present. Furthermore, we suggest ProPhyle, a new indexing strategy based on a BWT-index, obtaining a much smaller and more informative index compared to Kraken. We provide a modified version of BWA that improves the BWT-index for a quick k-mer look-up

On Flows, Paths, Roots, and Zeros

This thesis has two parts; in the first of which we give new results for various network flow problems. (1) We present a novel dual ascent algorithm for min-cost flow and show that an implementation of it is very efficient on certain instance classes. (2) We approach the problem of numerical stability of interior point network flow algorithms by giving a path following method that works with integer arithmetic solely and is thus guaranteed to be free of any nu-merical instabilities. (3) We present a gradient descent approach for the undirected transship-ment problem and its special case, the single source shortest path problem (SSSP). For distrib-uted computation models this yields the first SSSP-algorithm with near-optimal number of communication rounds. The second part deals with fundamental topics from algebraic computation. (1) We give an algorithm for computing the complex roots of a complex polynomial. While achieving a com-parable bit complexity as previous best results, our algorithm is simple and promising to be of practical impact. It uses a test for counting the roots of a polynomial in a region that is based on Pellet's theorem. (2) We extend this test to polynomial systems, i.e., we develop an algorithm that can certify the existence of a k-fold zero of a zero-dimensional polynomial system within a given region. For bivariate systems, we show experimentally that this approach yields signifi-cant improvements when used as inclusion predicate in an elimination method.Im ersten Teil dieser Dissertation präsentieren wir neue Resultate für verschiedene Netzwerkflussprobleme. (1)Wir geben eine neue Duale-Aufstiegsmethode für das Min-Cost-Flow- Problem an und zeigen, dass eine Implementierung dieser Methode sehr effizient auf gewissen Instanzklassen ist. (2)Wir behandeln numerische Stabilität von Innere-Punkte-Methoden fürNetwerkflüsse, indem wir eine solche Methode angeben die mit ganzzahliger Arithmetik arbeitet und daher garantiert frei von numerischen Instabilitäten ist. (3) Wir präsentieren ein Gradienten-Abstiegsverfahren für das ungerichtete Transshipment-Problem, und seinen Spezialfall, das Single-Source-Shortest-Problem (SSSP), die für SSSP in verteilten Rechenmodellen die erste mit nahe-optimaler Anzahl von Kommunikationsrunden ist. Der zweite Teil handelt von fundamentalen Problemen der Computeralgebra. (1) Wir geben einen Algorithmus zum Berechnen der komplexen Nullstellen eines komplexen Polynoms an, der eine vergleichbare Bitkomplexität zu vorherigen besten Resultaten hat, aber vergleichsweise einfach und daher vielversprechend für die Praxis ist. (2)Wir erweitern den darin verwendeten Pellet-Test zum Zählen der Nullstellen eines Polynoms auf Polynomsysteme, sodass wir die Existenz einer k-fachen Nullstelle eines Systems in einer gegebenen Region zertifizieren können. Für bivariate Systeme zeigen wir experimentell, dass eine Integration dieses Ansatzes in eine Eliminationsmethode zu einer signifikanten Verbesserung führt