Ahlfors circle maps and total reality: from Riemann to Rohlin

This is a prejudiced survey on the Ahlfors (extremal) function and the weaker {\it circle maps} (Garabedian-Schiffer's translation of "Kreisabbildung"), i.e. those (branched) maps effecting the conformal representation upon the disc of a {\it compact bordered Riemann surface}. The theory in question has some well-known intersection with real algebraic geometry, especially Klein's ortho-symmetric curves via the paradigm of {\it total reality}. This leads to a gallery of pictures quite pleasant to visit of which we have attempted to trace the simplest representatives. This drifted us toward some electrodynamic motions along real circuits of dividing curves perhaps reminiscent of Kepler's planetary motions along ellipses. The ultimate origin of circle maps is of course to be traced back to Riemann's Thesis 1851 as well as his 1857 Nachlass. Apart from an abrupt claim by Teichm\"uller 1941 that everything is to be found in Klein (what we failed to assess on printed evidence), the pivotal contribution belongs to Ahlfors 1950 supplying an existence-proof of circle maps, as well as an analysis of an allied function-theoretic extremal problem. Works by Yamada 1978--2001, Gouma 1998 and Coppens 2011 suggest sharper degree controls than available in Ahlfors' era. Accordingly, our partisan belief is that much remains to be clarified regarding the foundation and optimal control of Ahlfors circle maps. The game of sharp estimation may look narrow-minded "Absch\"atzungsmathematik" alike, yet the philosophical outcome is as usual to contemplate how conformal and algebraic geometry are fighting together for the soul of Riemann surfaces. A second part explores the connection with Hilbert's 16th as envisioned by Rohlin 1978.Comment: 675 pages, 199 figures; extended version of the former text (v.1) by including now Rohlin's theory (v.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

The art and architecture of mathematics education: a study in metaphors

This chapter presents the summary of a talk given at the Eighth European Summer University, held in Oslo in 2018. It attempts to show how art, literature, and history, can paint images of mathematics that are not only useful but relevant to learners as they can support their personal development as well as their appreciation of mathematics as a discipline. To achieve this goal, several metaphors about and of mathematics are explored

"Die Freude an der Gestalt" : méthodes, figures et pratiques de la géométrie au début du dix-neuvième siècle

The standard history of nineteenth century geometry began with Jean Victor Poncelet's contributions which then spread to Germany alongside an opposition between Julius Plücker, an analytic geometer, and Jakob Steiner, a synthetic geometer. Our questions centre on how geometers distinguished methods, when opposition arose, in what ways geometry disseminated from Poncelet to Plücker and Steiner, and whether this geometry was "modern'' as claimed.We first examine Poncelet's argument that within pure geometry the figure was never lost from view, while it could be obscured by the calculations of algebra. Our case study reveals visual attention within constructive problem solving, regardless of method. Further, geometers manipulated and represented figures through textual descriptions and coordinate equations. We also consider the debates involved as a medium for communicating geometry in which Poncelet and Gergonne in particular developed strategies for introducing new geometry to a conservative audience. We then turn to Plücker and Steiner. Through comparing their common research, we find that Plücker practiced a "pure analytic geometry'' that avoided calculation, while Steiner admired "synthetic geometry'' because of its organic unity. These qualities contradict usual descriptions of analytic geometry as computational or synthetic geometry as ad-hoc.Finally, we study contemporary French books on geometry and show that their methodological divide was grounded in student prerequisites, where "modern'' implied the use of algebra. By contrast, research publications exhibited evolving forms of geometry that evaded dichotomous categorization.The standard history of nineteenth century geometry began with Jean Victor Poncelet's contributions which then spread to Germany alongside an opposition between Julius Plücker, an analytic geometer, and Jakob Steiner, a synthetic geometer. Our questions centre on how geometers distinguished methods, when opposition arose, in what ways geometry disseminated from Poncelet to Plücker and Steiner, and whether this geometry was "modern'' as claimed.We first examine Poncelet's argument that within pure geometry the figure was never lost from view, while it could be obscured by the calculations of algebra. Our case study reveals visual attention within constructive problem solving, regardless of method. Further, geometers manipulated and represented figures through textual descriptions and coordinate equations. We also consider the debates involved as a medium for communicating geometry in which Poncelet and Gergonne in particular developed strategies for introducing new geometry to a conservative audience. We then turn to Plücker and Steiner. Through comparing their common research, we find that Plücker practiced a "pure analytic geometry'' that avoided calculation, while Steiner admired "synthetic geometry'' because of its organic unity. These qualities contradict usual descriptions of analytic geometry as computational or synthetic geometry as ad-hoc.Finally, we study contemporary French books on geometry and show that their methodological divide was grounded in student prerequisites, where "modern'' implied the use of algebra. By contrast, research publications exhibited evolving forms of geometry that evaded dichotomous categorization.L'histoire standard de la géométrie projective souligne l'opposition au 19e siècle entre méthodes analytiques et synthétiques. Nous nous interrogeons sur la manière dont les géomètres du 19e siècle ont vraiment opéré ou non des distinctions entre leurs méthodes et dans quelle mesure cette géométrie était "moderne'' comme le clamaient ses praticiens, et plus tard leurs historiens. Poncelet insistait sur le rôle central de la figure, qui selon lui pourrait être obscurci par les calculs de l'algèbre. Nous étudions son argument en action dans des problèmes de construction résolus par plusieurs auteurs différents -comme la construction d'une courbe du second ordre ayant un contact d'ordre trois avec une courbe plane donnée, dont cinq solutions paraissent entre 1817 et 1826. Nous montrons que l'attention visuelle est au coeur de la résolution, indépendamment de la méthode suivie, qu'elle n'est pas réservée aux figures, et que les débats sont aussi un moyen de signaler de nouvelles zones de recherche à un public en formation. Nous approfondissons ensuite la réception des techniques nouvelles et l'usage des figures dans les travaux de deux mathématiciens décrits d'ordinaire comme opposés, l'un algébriste, Plücker, et l'autre défendant l'approche synthétique, Steiner. Nous examinons enfin les affirmations de modernité dans les manuels français de géométrie publiés pendant le premier tiers du dix-neuvième siècle. Tant Gergonne et Plücker que Steiner ont développé des formes de géométrie qui ne se pliaient pas en fait à une caractérisation dichotomique, mais répondaient de manière spécifique aux pratiques mathématiques et aux modes d'interaction de leur temps

Putting Chinese natural knowledge to work in an eighteenth-century Swiss canton: the case of Dr Laurent Garcin

Symposium: S048 - Putting Chinese natural knowledge to work in the long eighteenth centuryThis paper takes as a case study the experience of the eighteenth-century Swiss physician, Laurent Garcin (1683-1752), with Chinese medical and pharmacological knowledge. A Neuchâtel bourgeois of Huguenot origin, who studied in Leiden with Hermann Boerhaave, Garcin spent nine years (1720-1729) in South and Southeast Asia as a surgeon in the service of the Dutch East India Company. Upon his return to Neuchâtel in 1739 he became primus inter pares in the small local community of physician-botanists, introducing them to the artificial sexual system of classification. He practiced medicine, incorporating treatments acquired during his travels. taught botany, collected rare plants for major botanical gardens, and contributed to the Journal Helvetique on a range of topics; he was elected a Fellow of the Royal Society of London, where two of his papers were read in translation and published in the Philosophical Transactions; one of these concerned the mangosteen (Garcinia mangostana), leading Linnaeus to name the genus Garcinia after Garcin. He was likewise consulted as an expert on the East Indies, exotic flora, and medicines, and contributed to important publications on these topics. During his time with the Dutch East India Company Garcin encountered Chinese medical practitioners whose work he evaluated favourably as being on a par with that of the Brahmin physicians, whom he particularly esteemed. Yet Garcin never went to China, basing his entire experience of Chinese medical practice on what he witnessed in the Chinese diaspora in Southeast Asia (the ‘East Indies’). This case demonstrates that there were myriad routes to Europeans developing an understanding of Chinese natural knowledge; the Chinese diaspora also afforded a valuable opportunity for comparisons of its knowledge and practice with other non-European bodies of medical and natural (e.g. pharmacological) knowledge.postprin