415 research outputs found
A Fixed Parameter Tractable Integer Program for Finding the Maximum Order Preserving Submatrix
International audienceOrder-preserving submatrices are an important tool for the analysis of gene expression data. As finding large order-preserving submatrices is a computationally hard problem, previous work has investigated both exact but exponential-time as well as polynomial-time but inexact algorithms for finding large order-preserving submatrices. In this paper, we propose a novel exact algorithm to find maximum order preserving submatrices which is fixed parameter tractable with respect to the number of columns of the provided gene expression data. In particular, our algorithm is based on solving a sequence of mixed integer linear programs and it exhibits better guarantees as well as better runtime performance as compared to the state-of-the-art exact algorithms. Our empirical study in benchmark datasets shows large improvement in terms of computational speed
Conic Optimization Theory: Convexification Techniques and Numerical Algorithms
Optimization is at the core of control theory and appears in several areas of
this field, such as optimal control, distributed control, system
identification, robust control, state estimation, model predictive control and
dynamic programming. The recent advances in various topics of modern
optimization have also been revamping the area of machine learning. Motivated
by the crucial role of optimization theory in the design, analysis, control and
operation of real-world systems, this tutorial paper offers a detailed overview
of some major advances in this area, namely conic optimization and its emerging
applications. First, we discuss the importance of conic optimization in
different areas. Then, we explain seminal results on the design of hierarchies
of convex relaxations for a wide range of nonconvex problems. Finally, we study
different numerical algorithms for large-scale conic optimization problems.Comment: 18 page
A structural approach to kernels for ILPs: Treewidth and Total Unimodularity
Kernelization is a theoretical formalization of efficient preprocessing for
NP-hard problems. Empirically, preprocessing is highly successful in practice,
for example in state-of-the-art ILP-solvers like CPLEX. Motivated by this,
previous work studied the existence of kernelizations for ILP related problems,
e.g., for testing feasibility of Ax <= b. In contrast to the observed success
of CPLEX, however, the results were largely negative. Intuitively, practical
instances have far more useful structure than the worst-case instances used to
prove these lower bounds.
In the present paper, we study the effect that subsystems with (Gaifman graph
of) bounded treewidth or totally unimodularity have on the kernelizability of
the ILP feasibility problem. We show that, on the positive side, if these
subsystems have a small number of variables on which they interact with the
remaining instance, then we can efficiently replace them by smaller subsystems
of size polynomial in the domain without changing feasibility. Thus, if large
parts of an instance consist of such subsystems, then this yields a substantial
size reduction. We complement this by proving that relaxations to the
considered structures, e.g., larger boundaries of the subsystems, allow
worst-case lower bounds against kernelization. Thus, these relaxed structures
can be used to build instance families that cannot be efficiently reduced, by
any approach.Comment: Extended abstract in the Proceedings of the 23rd European Symposium
on Algorithms (ESA 2015
Festparameter-Algorithmen fuer die Konsens-Analyse Genomischer Daten
Fixed-parameter algorithms offer a constructive and powerful approach
to efficiently obtain solutions for NP-hard problems combining two
important goals: Fixed-parameter algorithms compute optimal solutions
within provable time bounds despite the (almost inevitable)
computational intractability of NP-hard problems. The essential idea
is to identify one or more aspects of the input to a problem as the
parameters, and to confine the combinatorial explosion of
computational difficulty to a function of the parameters such that the
costs are polynomial in the non-parameterized part of the input. This
makes especially sense for parameters which have small values in
applications. Fixed-parameter algorithms have become an established
algorithmic tool in a variety of application areas, among them
computational biology where small values for problem parameters are
often observed. A number of design techniques for fixed-parameter
algorithms have been proposed and bounded search trees are one of
them. In computational biology, however, examples of bounded search
tree algorithms have been, so far, rare.
This thesis investigates the use of bounded search tree algorithms for
consensus problems in the analysis of DNA and RNA data. More
precisely, we investigate consensus problems in the contexts of
sequence analysis, of quartet methods for phylogenetic reconstruction,
of gene order analysis, and of RNA secondary structure comparison. In
all cases, we present new efficient algorithms that incorporate the
bounded search tree paradigm in novel ways. On our way, we also obtain
results of parameterized hardness, showing that the respective
problems are unlikely to allow for a fixed-parameter algorithm, and we
introduce integer linear programs (ILP's) as a tool for classifying
problems as fixed-parameter tractable, i.e., as having fixed-parameter
algorithms. Most of our algorithms were implemented and tested on
practical data.Festparameter-Algorithmen bieten einen konstruktiven Ansatz zur
Loesung von kombinatorisch schwierigen, in der Regel NP-harten
Problemen, der zwei Ziele beruecksichtigt: innerhalb von beweisbaren
Laufzeitschranken werden optimale Ergebnisse berechnet. Die
entscheidende Idee ist dabei, einen oder mehrere Aspekte der
Problemeingabe als Parameter der Problems aufzufassen und die
kombinatorische Explosion der algorithmischen Schwierigkeit auf diese
Parameter zu beschraenken, so dass die Laufzeitkosten polynomiell in
Bezug auf den nicht-parametrisierten Teil der Eingabe sind. Gibt es
einen Festparameter-Algorithmus fuer ein kombinatorisches Problem,
nennt man das Problem festparameter-handhabbar. Die Entwicklung von
Festparameter-Algorithmen macht vor allem dann Sinn, wenn die
betrachteten Parameter im Anwendungsfall nur kleine Werte
annehmen. Festparameter-Algorithmen sind zu einem algorithmischen
Standardwerkzeug in vielen Anwendungsbereichen geworden, unter anderem
in der algorithmischen Biologie, wo in vielen Anwendungen kleine
Parameterwerte beobachtet werden koennen. Zu den bekannten Techniken
fuer den Entwurf von Festparameter-Algorithmen gehoeren unter anderem
groessenbeschraenkte Suchbaeume. In der algorithmischen Biologie gibt
es bislang nur wenige Beispiele fuer die Anwendung von
groessenbeschraenkten Suchbaeumen.
Diese Arbeit untersucht den Einsatz groessenbeschraenkter Suchbaeume
fuer NP-harte Konsens-Probleme in der Analyse von DNS- und
RNS-Daten. Wir betrachten Konsens-Probleme in der Analyse von
DNS-Sequenzdaten, in der Analyse von sogenannten Quartettdaten zur
Erstellung von phylogenetischen Hypothesen, in der Analyse von Daten
ueber die Anordnung von Genen und beim Vergleich von
RNS-Strukturdaten. In allen Faellen stellen wir neue effiziente
Algorithmen vor, in denen das Paradigma der groessenbeschraenkten
Suchbaeume auf neuartige Weise realisiert wird. Auf diesem Weg zeigen
wir auch Ergebnisse parametrisierter Haerte, die zeigen, dass fuer
die dabei betrachteten Probleme ein Festparameter-Algorithmus
unwahrscheinlich ist. Ausserdem fuehren wir ganzzahliges lineares
Programmieren als eine neue Technik ein, um die
Festparameter-Handhabbarkeit eines Problems zu zeigen. Die Mehrzahl
der hier vorgestellten Algorithmen wurde implementiert und auf
Anwendungsdaten getestet
Twin-width IV: ordered graphs and matrices
We establish a list of characterizations of bounded twin-width for
hereditary, totally ordered binary structures. This has several consequences.
First, it allows us to show that a (hereditary) class of matrices over a finite
alphabet either contains at least matrices of size , or at
most for some constant . This generalizes the celebrated Stanley-Wilf
conjecture/Marcus-Tardos theorem from permutation classes to any matrix class
over a finite alphabet, answers our small conjecture [SODA '21] in the case of
ordered graphs, and with more work, settles a question first asked by Balogh,
Bollob\'as, and Morris [Eur. J. Comb. '06] on the growth of hereditary classes
of ordered graphs. Second, it gives a fixed-parameter approximation algorithm
for twin-width on ordered graphs. Third, it yields a full classification of
fixed-parameter tractable first-order model checking on hereditary classes of
ordered binary structures. Fourth, it provides a model-theoretic
characterization of classes with bounded twin-width.Comment: 53 pages, 18 figure
Speeding-up Dynamic Programming with Representative Sets - An Experimental Evaluation of Algorithms for Steiner Tree on Tree Decompositions
Dynamic programming on tree decompositions is a frequently used approach to
solve otherwise intractable problems on instances of small treewidth. In recent
work by Bodlaender et al., it was shown that for many connectivity problems,
there exist algorithms that use time, linear in the number of vertices, and
single exponential in the width of the tree decomposition that is used. The
central idea is that it suffices to compute representative sets, and these can
be computed efficiently with help of Gaussian elimination.
In this paper, we give an experimental evaluation of this technique for the
Steiner Tree problem. A comparison of the classic dynamic programming algorithm
and the improved dynamic programming algorithm that employs the table reduction
shows that the new approach gives significant improvements on the running time
of the algorithm and the size of the tables computed by the dynamic programming
algorithm, and thus that the rank based approach from Bodlaender et al. does
not only give significant theoretical improvements but also is a viable
approach in a practical setting, and showcases the potential of exploiting the
idea of representative sets for speeding up dynamic programming algorithms
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