111 research outputs found

### 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 %

### 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

### Loop corrections in spin models through density consistency

Computing marginal distributions of discrete or semidiscrete Markov random
fields (MRFs) is a fundamental, generally intractable problem with a vast
number of applications in virtually all fields of science. We present a new
family of computational schemes to approximately calculate the marginals of
discrete MRFs. This method shares some desirable properties with belief
propagation, in particular, providing exact marginals on acyclic graphs, but it
differs with the latter in that it includes some loop corrections; i.e., it
takes into account correlations coming from all cycles in the factor graph. It
is also similar to the adaptive Thouless-Anderson-Palmer method, but it differs
with the latter in that the consistency is not on the first two moments of the
distribution but rather on the value of its density on a subset of values. The
results on finite-dimensional Isinglike models show a significant improvement
with respect to the Bethe-Peierls (tree) approximation in all cases and with
respect to the plaquette cluster variational method approximation in many
cases. In particular, for the critical inverse temperature $\beta_{c}$ of the
homogeneous hypercubic lattice, the expansion of $\left(d\beta_{c}\right)^{-1}$
around $d=\infty$ of the proposed scheme is exact up to the $d^{-4}$ order,
whereas the two latter are exact only up to the $d^{-2}$ order.Comment: 12 pages, 3 figures, 1 tabl

### Estimating the size of the solution space of metabolic networks

In this work we propose a novel algorithmic strategy that allows for an
efficient characterization of the whole set of stable fluxes compatible with
the metabolic constraints. The algorithm, based on the well-known Bethe
approximation, allows the computation in polynomial time of the volume of a non
full-dimensional convex polytope in high dimensions. The result of our
algorithm match closely the prediction of Monte Carlo based estimations of the
flux distributions of the Red Blood Cell metabolic network but in incomparably
shorter time. We also analyze the statistical properties of the average fluxes
of the reactions in the E-Coli metabolic network and finally to test the effect
of gene knock-outs on the size of the solution space of the E-Coli central
metabolism.Comment: 8 pages, 7 pdf figure

### Efficient LDPC Codes over GF(q) for Lossy Data Compression

In this paper we consider the lossy compression of a binary symmetric source.
We present a scheme that provides a low complexity lossy compressor with near
optimal empirical performance. The proposed scheme is based on b-reduced
ultra-sparse LDPC codes over GF(q). Encoding is performed by the Reinforced
Belief Propagation algorithm, a variant of Belief Propagation. The
computational complexity at the encoder is O(.n.q.log q), where is the
average degree of the check nodes. For our code ensemble, decoding can be
performed iteratively following the inverse steps of the leaf removal
algorithm. For a sparse parity-check matrix the number of needed operations is
O(n).Comment: 5 pages, 3 figure

### Predicting epidemic evolution on contact networks from partial observations

The massive employment of computational models in network epidemiology calls
for the development of improved inference methods for epidemic forecast. For
simple compartment models, such as the Susceptible-Infected-Recovered model,
Belief Propagation was proved to be a reliable and efficient method to identify
the origin of an observed epidemics. Here we show that the same method can be
applied to predict the future evolution of an epidemic outbreak from partial
observations at the early stage of the dynamics. The results obtained using
Belief Propagation are compared with Monte Carlo direct sampling in the case of
SIR model on random (regular and power-law) graphs for different observation
methods and on an example of real-world contact network. Belief Propagation
gives in general a better prediction that direct sampling, although the quality
of the prediction depends on the quantity under study (e.g. marginals of
individual states, epidemic size, extinction-time distribution) and on the
actual number of observed nodes that are infected before the observation time

### Contamination source inference in water distribution networks

We study the inference of the origin and the pattern of contamination in
water distribution networks. We assume a simplified model for the dyanmics of
the contamination spread inside a water distribution network, and assume that
at some random location a sensor detects the presence of contaminants. We
transform the source location problem into an optimization problem by
considering discrete times and a binary contaminated/not contaminated state for
the nodes of the network. The resulting problem is solved by Mixed Integer
Linear Programming. We test our results on random networks as well as in the
Modena city network

### An analytic approximation of the feasible space of metabolic networks

Assuming a steady-state condition within a cell, metabolic fluxes satisfy an
under-determined linear system of stoichiometric equations. Characterizing the
space of fluxes that satisfy such equations along with given bounds (and
possibly additional relevant constraints) is considered of utmost importance
for the understanding of cellular metabolism. Extreme values for each
individual flux can be computed with Linear Programming (as Flux Balance
Analysis), and their marginal distributions can be approximately computed with
Monte-Carlo sampling. Here we present an approximate analytic method for the
latter task based on Expectation Propagation equations that does not involve
sampling and can achieve much better predictions than other existing analytic
methods. The method is iterative, and its computation time is dominated by one
matrix inversion per iteration. With respect to sampling, we show through
extensive simulation that it has some advantages including computation time,
and the ability to efficiently fix empirically estimated distributions of
fluxes

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