222 research outputs found
On the performance of a cavity method based algorithm for the Prize-Collecting Steiner Tree Problem on graphs
We study the behavior of an algorithm derived from the cavity method for the
Prize-Collecting Steiner Tree (PCST) problem on graphs. The algorithm is based
on the zero temperature limit of the cavity equations and as such is formally
simple (a fixed point equation resolved by iteration) and distributed
(parallelizable). We provide a detailed comparison with state-of-the-art
algorithms on a wide range of existing benchmarks networks and random graphs.
Specifically, we consider an enhanced derivative of the Goemans-Williamson
heuristics and the DHEA solver, a Branch and Cut Linear/Integer Programming
based approach. The comparison shows that the cavity algorithm outperforms the
two algorithms in most large instances both in running time and quality of the
solution. Finally we prove a few optimality properties of the solutions
provided by our algorithm, including optimality under the two post-processing
procedures defined in the Goemans-Williamson derivative and global optimality
in some limit cases
The cavity approach for Steiner trees packing problems
The Belief Propagation approximation, or cavity method, has been recently
applied to several combinatorial optimization problems in its zero-temperature
implementation, the max-sum algorithm. In particular, recent developments to
solve the edge-disjoint paths problem and the prize-collecting Steiner tree
problem on graphs have shown remarkable results for several classes of graphs
and for benchmark instances. Here we propose a generalization of these
techniques for two variants of the Steiner trees packing problem where multiple
"interacting" trees have to be sought within a given graph. Depending on the
interaction among trees we distinguish the vertex-disjoint Steiner trees
problem, where trees cannot share nodes, from the edge-disjoint Steiner trees
problem, where edges cannot be shared by trees but nodes can be members of
multiple trees. Several practical problems of huge interest in network design
can be mapped into these two variants, for instance, the physical design of
Very Large Scale Integration (VLSI) chips. The formalism described here relies
on two components edge-variables that allows us to formulate a massage-passing
algorithm for the V-DStP and two algorithms for the E-DStP differing in the
scaling of the computational time with respect to some relevant parameters. We
will show that one of the two formalisms used for the edge-disjoint variant
allow us to map the max-sum update equations into a weighted maximum matching
problem over proper bipartite graphs. We developed a heuristic procedure based
on the max-sum equations that shows excellent performance in synthetic networks
(in particular outperforming standard multi-step greedy procedures by large
margins) and on large benchmark instances of VLSI for which the optimal
solution is known, on which the algorithm found the optimum in two cases and
the gap to optimality was never larger than 4 %
Finding undetected protein associations in cell signaling by belief propagation
External information propagates in the cell mainly through signaling cascades
and transcriptional activation, allowing it to react to a wide spectrum of
environmental changes. High throughput experiments identify numerous molecular
components of such cascades that may, however, interact through unknown
partners. Some of them may be detected using data coming from the integration
of a protein-protein interaction network and mRNA expression profiles. This
inference problem can be mapped onto the problem of finding appropriate optimal
connected subgraphs of a network defined by these datasets. The optimization
procedure turns out to be computationally intractable in general. Here we
present a new distributed algorithm for this task, inspired from statistical
physics, and apply this scheme to alpha factor and drug perturbations data in
yeast. We identify the role of the COS8 protein, a member of a gene family of
previously unknown function, and validate the results by genetic experiments.
The algorithm we present is specially suited for very large datasets, can run
in parallel, and can be adapted to other problems in systems biology. On
renowned benchmarks it outperforms other algorithms in the field.Comment: 6 pages, 3 figures, 1 table, Supporting Informatio
Solving the undirected feedback vertex set problem by local search
An undirected graph consists of a set of vertices and a set of undirected
edges between vertices. Such a graph may contain an abundant number of cycles,
then a feedback vertex set (FVS) is a set of vertices intersecting with each of
these cycles. Constructing a FVS of cardinality approaching the global minimum
value is a optimization problem in the nondeterministic polynomial-complete
complexity class, therefore it might be extremely difficult for some large
graph instances. In this paper we develop a simulated annealing local search
algorithm for the undirected FVS problem. By defining an order for the vertices
outside the FVS, we replace the global cycle constraints by a set of local
vertex constraints on this order. Under these local constraints the cardinality
of the focal FVS is then gradually reduced by the simulated annealing dynamical
process. We test this heuristic algorithm on large instances of Er\"odos-Renyi
random graph and regular random graph, and find that this algorithm is
comparable in performance to the belief propagation-guided decimation
algorithm.Comment: 6 page
Optimizing spread dynamics on graphs by message passing
Cascade processes are responsible for many important phenomena in natural and
social sciences. Simple models of irreversible dynamics on graphs, in which
nodes activate depending on the state of their neighbors, have been
successfully applied to describe cascades in a large variety of contexts. Over
the last decades, many efforts have been devoted to understand the typical
behaviour of the cascades arising from initial conditions extracted at random
from some given ensemble. However, the problem of optimizing the trajectory of
the system, i.e. of identifying appropriate initial conditions to maximize (or
minimize) the final number of active nodes, is still considered to be
practically intractable, with the only exception of models that satisfy a sort
of diminishing returns property called submodularity. Submodular models can be
approximately solved by means of greedy strategies, but by definition they lack
cooperative characteristics which are fundamental in many real systems. Here we
introduce an efficient algorithm based on statistical physics for the
optimization of trajectories in cascade processes on graphs. We show that for a
wide class of irreversible dynamics, even in the absence of submodularity, the
spread optimization problem can be solved efficiently on large networks.
Analytic and algorithmic results on random graphs are complemented by the
solution of the spread maximization problem on a real-world network (the
Epinions consumer reviews network).Comment: Replacement for "The Spread Optimization Problem
Statistical mechanics approaches to optimization and inference
Nowadays, typical methodologies employed in statistical physics are successfully applied to a huge set of problems arising from different research fields. In this thesis I will propose several statistical mechanics based models able to deal with two types of problems: optimization and inference problems. The intrinsic difficulty that characterizes both problems is that, due to the hard combinatorial nature of optimization and inference, finding exact solutions would require hard and impractical computations. In fact, the time needed to perform these calculations, in almost all cases, scales exponentially with respect to relevant parameters of the system and thus cannot be accomplished in practice. As combinatorial optimization addresses the problem of finding a fair configuration of variables able to minimize/maximize an objective function, inference seeks a posteriori the most fair assignment of a set of variables given a partial knowledge of the system. These two problems can be re-phrased in a statistical mechanics framework where elementary components of a physical system interact according to the constraints of the original problem. The information at our disposal can be encoded in the Boltzmann distribution of the new variables which, if properly investigated, can provide the solutions to the original problems. As a consequence, the methodologies originally adopted in statistical mechanics to study and, eventually, approximate the Boltzmann distribution can be fruitfully applied for solving inference and optimization problems.
The structure of the thesis follows the path covered during the three years of my Ph.D. At first, I will propose a set of combinatorial optimization problems on graphs, the Prize collecting and the Packing of Steiner trees problems. The tools used to face these hard problems rely on the zero-temperature implementation of the Belief Propagation algorithm, called Max Sum algorithm. The second set of problems proposed in this thesis falls under the name of linear estimation problems. One of them, the compressed sensing problem, will guide us in the modelling of these problems within a Bayesian framework along with the introduction of a powerful algorithm known as Expectation Propagation or Expectation Consistent in statistical physics. I will propose a similar approach to other challenging problems: the inference of metabolic fluxes, the inverse problem of the electro-encephalography and the reconstruction of tomographic images
Cavity algorithms under global constraints: classical and quantum problems
The starting point of my thesis work was the study of optimization algorithms based on cavity method. These algorithms have been developed to a high degree of complexity in the last decade and they are also known as message passing algorithms (MPAs). My work has started by a question posed by my supervisor: what links can be found between those different approaches to the same problems? The starting aim of the PhD project was to explore the new ideas and algorithms that could result from a cross-fertilization between different approaches. During the first years we made a long and accurate comparison between different algorithms on a specific COP: the prize collecting Steiner tree problem. Looking to MPAs as an evolution of probability distributions of discrete variables led me to find some possible links with many body quantum physics, where typically we deal with probability amplitudes over discrete variables. In the recent years several results have appeared concerning the extension of the cavity method and message passing technics to quantum context. In 2012 Ramezanpour proposed a method, the variational quantum cavity method (VQCM), for finding approximate ground state wave functions based on a new messages passing algorithm used in stochastic optimization. Ramezanpour and I have extended this approach to find low excited states. In the last year of my Ph.D. I simplify the VQCM using imaginary time evolution operator. Moreover I extend this approach to find finite temperature density matri
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