3,935 research outputs found
Geometric Reasoning with polymake
The mathematical software system polymake provides a wide range of functions
for convex polytopes, simplicial complexes, and other objects. A large part of
this paper is dedicated to a tutorial which exemplifies the usage. Later
sections include a survey of research results obtained with the help of
polymake so far and a short description of the technical background
Dagstuhl Reports : Volume 1, Issue 2, February 2011
Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn
Approximate Computation and Implicit Regularization for Very Large-scale Data Analysis
Database theory and database practice are typically the domain of computer
scientists who adopt what may be termed an algorithmic perspective on their
data. This perspective is very different than the more statistical perspective
adopted by statisticians, scientific computers, machine learners, and other who
work on what may be broadly termed statistical data analysis. In this article,
I will address fundamental aspects of this algorithmic-statistical disconnect,
with an eye to bridging the gap between these two very different approaches. A
concept that lies at the heart of this disconnect is that of statistical
regularization, a notion that has to do with how robust is the output of an
algorithm to the noise properties of the input data. Although it is nearly
completely absent from computer science, which historically has taken the input
data as given and modeled algorithms discretely, regularization in one form or
another is central to nearly every application domain that applies algorithms
to noisy data. By using several case studies, I will illustrate, both
theoretically and empirically, the nonobvious fact that approximate
computation, in and of itself, can implicitly lead to statistical
regularization. This and other recent work suggests that, by exploiting in a
more principled way the statistical properties implicit in worst-case
algorithms, one can in many cases satisfy the bicriteria of having algorithms
that are scalable to very large-scale databases and that also have good
inferential or predictive properties.Comment: To appear in the Proceedings of the 2012 ACM Symposium on Principles
of Database Systems (PODS 2012
Propagators and Violation Functions for Geometric and Workload Constraints Arising in Airspace Sectorisation
Airspace sectorisation provides a partition of a given airspace into sectors,
subject to geometric constraints and workload constraints, so that some cost
metric is minimised. We make a study of the constraints that arise in airspace
sectorisation. For each constraint, we give an analysis of what algorithms and
properties are required under systematic search and stochastic local search
Specific "scientific" data structures, and their processing
Programming physicists use, as all programmers, arrays, lists, tuples,
records, etc., and this requires some change in their thought patterns while
converting their formulae into some code, since the "data structures" operated
upon, while elaborating some theory and its consequences, are rather: power
series and Pad\'e approximants, differential forms and other instances of
differential algebras, functionals (for the variational calculus), trajectories
(solutions of differential equations), Young diagrams and Feynman graphs, etc.
Such data is often used in a [semi-]numerical setting, not necessarily
"symbolic", appropriate for the computer algebra packages. Modules adapted to
such data may be "just libraries", but often they become specific, embedded
sub-languages, typically mapped into object-oriented frameworks, with
overloaded mathematical operations. Here we present a functional approach to
this philosophy. We show how the usage of Haskell datatypes and - fundamental
for our tutorial - the application of lazy evaluation makes it possible to
operate upon such data (in particular: the "infinite" sequences) in a natural
and comfortable manner.Comment: In Proceedings DSL 2011, arXiv:1109.032
An Introduction to Programming for Bioscientists: A Python-based Primer
Computing has revolutionized the biological sciences over the past several
decades, such that virtually all contemporary research in the biosciences
utilizes computer programs. The computational advances have come on many
fronts, spurred by fundamental developments in hardware, software, and
algorithms. These advances have influenced, and even engendered, a phenomenal
array of bioscience fields, including molecular evolution and bioinformatics;
genome-, proteome-, transcriptome- and metabolome-wide experimental studies;
structural genomics; and atomistic simulations of cellular-scale molecular
assemblies as large as ribosomes and intact viruses. In short, much of
post-genomic biology is increasingly becoming a form of computational biology.
The ability to design and write computer programs is among the most
indispensable skills that a modern researcher can cultivate. Python has become
a popular programming language in the biosciences, largely because (i) its
straightforward semantics and clean syntax make it a readily accessible first
language; (ii) it is expressive and well-suited to object-oriented programming,
as well as other modern paradigms; and (iii) the many available libraries and
third-party toolkits extend the functionality of the core language into
virtually every biological domain (sequence and structure analyses,
phylogenomics, workflow management systems, etc.). This primer offers a basic
introduction to coding, via Python, and it includes concrete examples and
exercises to illustrate the language's usage and capabilities; the main text
culminates with a final project in structural bioinformatics. A suite of
Supplemental Chapters is also provided. Starting with basic concepts, such as
that of a 'variable', the Chapters methodically advance the reader to the point
of writing a graphical user interface to compute the Hamming distance between
two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables,
numerous exercises, and 19 pages of Supporting Information; currently in
press at PLOS Computational Biolog
Lower Bounds on Complexity of Lyapunov Functions for Switched Linear Systems
We show that for any positive integer , there are families of switched
linear systems---in fixed dimension and defined by two matrices only---that are
stable under arbitrary switching but do not admit (i) a polynomial Lyapunov
function of degree , or (ii) a polytopic Lyapunov function with facets, or (iii) a piecewise quadratic Lyapunov function with
pieces. This implies that there cannot be an upper bound on the size of the
linear and semidefinite programs that search for such stability certificates.
Several constructive and non-constructive arguments are presented which connect
our problem to known (and rather classical) results in the literature regarding
the finiteness conjecture, undecidability, and non-algebraicity of the joint
spectral radius. In particular, we show that existence of an extremal piecewise
algebraic Lyapunov function implies the finiteness property of the optimal
product, generalizing a result of Lagarias and Wang. As a corollary, we prove
that the finiteness property holds for sets of matrices with an extremal
Lyapunov function belonging to some of the most popular function classes in
controls
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