22,869 research outputs found
Analysis of Reaction Network Systems Using Tropical Geometry
We discuss a novel analysis method for reaction network systems with
polynomial or rational rate functions. This method is based on computing
tropical equilibrations defined by the equality of at least two dominant
monomials of opposite signs in the differential equations of each dynamic
variable. In algebraic geometry, the tropical equilibration problem is
tantamount to finding tropical prevarieties, that are finite intersections of
tropical hypersurfaces. Tropical equilibrations with the same set of dominant
monomials define a branch or equivalence class. Minimal branches are
particularly interesting as they describe the simplest states of the reaction
network. We provide a method to compute the number of minimal branches and to
find representative tropical equilibrations for each branch.Comment: Proceedings Computer Algebra in Scientific Computing CASC 201
A hard-sphere model on generalized Bethe lattices: Statics
We analyze the phase diagram of a model of hard spheres of chemical radius
one, which is defined over a generalized Bethe lattice containing short loops.
We find a liquid, two different crystalline, a glassy and an unusual
crystalline glassy phase. Special attention is also paid to the close-packing
limit in the glassy phase. All analytical results are cross-checked by
numerical Monte-Carlo simulations.Comment: 24 pages, revised versio
Approximating the Permanent with Fractional Belief Propagation
We discuss schemes for exact and approximate computations of permanents, and
compare them with each other. Specifically, we analyze the Belief Propagation
(BP) approach and its Fractional Belief Propagation (FBP) generalization for
computing the permanent of a non-negative matrix. Known bounds and conjectures
are verified in experiments, and some new theoretical relations, bounds and
conjectures are proposed. The Fractional Free Energy (FFE) functional is
parameterized by a scalar parameter , where
corresponds to the BP limit and corresponds to the exclusion
principle (but ignoring perfect matching constraints) Mean-Field (MF) limit.
FFE shows monotonicity and continuity with respect to . For every
non-negative matrix, we define its special value to be the
for which the minimum of the -parameterized FFE functional is
equal to the permanent of the matrix, where the lower and upper bounds of the
-interval corresponds to respective bounds for the permanent. Our
experimental analysis suggests that the distribution of varies for
different ensembles but always lies within the interval.
Moreover, for all ensembles considered the behavior of is highly
distinctive, offering an emprirical practical guidance for estimating
permanents of non-negative matrices via the FFE approach.Comment: 42 pages, 14 figure
Nonlinear Integer Programming
Research efforts of the past fifty years have led to a development of linear
integer programming as a mature discipline of mathematical optimization. Such a
level of maturity has not been reached when one considers nonlinear systems
subject to integrality requirements for the variables. This chapter is
dedicated to this topic.
The primary goal is a study of a simple version of general nonlinear integer
problems, where all constraints are still linear. Our focus is on the
computational complexity of the problem, which varies significantly with the
type of nonlinear objective function in combination with the underlying
combinatorial structure. Numerous boundary cases of complexity emerge, which
sometimes surprisingly lead even to polynomial time algorithms.
We also cover recent successful approaches for more general classes of
problems. Though no positive theoretical efficiency results are available, nor
are they likely to ever be available, these seem to be the currently most
successful and interesting approaches for solving practical problems.
It is our belief that the study of algorithms motivated by theoretical
considerations and those motivated by our desire to solve practical instances
should and do inform one another. So it is with this viewpoint that we present
the subject, and it is in this direction that we hope to spark further
research.Comment: 57 pages. To appear in: M. J\"unger, T. Liebling, D. Naddef, G.
Nemhauser, W. Pulleyblank, G. Reinelt, G. Rinaldi, and L. Wolsey (eds.), 50
Years of Integer Programming 1958--2008: The Early Years and State-of-the-Art
Surveys, Springer-Verlag, 2009, ISBN 354068274
A Novel SAT-Based Approach to the Task Graph Cost-Optimal Scheduling Problem
The Task Graph Cost-Optimal Scheduling Problem consists in scheduling a certain number of interdependent tasks onto a set of heterogeneous processors (characterized by idle and running rates per time unit), minimizing the cost of the entire process. This paper provides a novel formulation for this scheduling puzzle, in which an optimal solution is computed through a sequence of Binate Covering Problems, hinged within a Bounded Model Checking paradigm. In this approach, each covering instance, providing a min-cost trace for a given schedule depth, can be solved with several strategies, resorting to Minimum-Cost Satisfiability solvers or Pseudo-Boolean Optimization tools. Unfortunately, all direct resolution methods show very low efficiency and scalability. As a consequence, we introduce a specialized method to solve the same sequence of problems, based on a traditional all-solution SAT solver. This approach follows the "circuit cofactoring" strategy, as it exploits a powerful technique to capture a large set of solutions for any new SAT counter-example. The overall method is completed with a branch-and-bound heuristic which evaluates lower and upper bounds of the schedule length, to reduce the state space that has to be visited. Our results show that the proposed strategy significantly improves the blind binate covering schema, and it outperforms general purpose state-of-the-art tool
Euclidean distance geometry and applications
Euclidean distance geometry is the study of Euclidean geometry based on the
concept of distance. This is useful in several applications where the input
data consists of an incomplete set of distances, and the output is a set of
points in Euclidean space that realizes the given distances. We survey some of
the theory of Euclidean distance geometry and some of the most important
applications: molecular conformation, localization of sensor networks and
statics.Comment: 64 pages, 21 figure
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