Containing epidemic outbreaks by message-passing techniques

The problem of targeted network immunization can be defined as the one of finding a subset of nodes in a network to immunize or vaccinate in order to minimize a tradeoff between the cost of vaccination and the final (stationary) expected infection under a given epidemic model. Although computing the expected infection is a hard computational problem, simple and efficient mean-field approximations have been put forward in the literature in recent years. The optimization problem can be recast into a constrained one in which the constraints enforce local mean-field equations describing the average stationary state of the epidemic process. For a wide class of epidemic models, including the susceptible-infected-removed and the susceptible-infected-susceptible models, we define a message-passing approach to network immunization that allows us to study the statistical properties of epidemic outbreaks in the presence of immunized nodes as well as to find (nearly) optimal immunization sets for a given choice of parameters and costs. The algorithm scales linearly with the size of the graph and it can be made efficient even on large networks. We compare its performance with topologically based heuristics, greedy methods, and simulated annealing

Entropy inequalities and Bell inequalities for two-qubit systems

Sufficient conditions for (the non-violation of) the Bell-CHSH inequalities in a mixed state of a two-qubit system are: 1) The linear entropy of the state is not smaller than 0.5, 2) The sum of the conditional linear entropies is non-negative, 3) The von Neumann entropy is not smaller than 0.833, 4) The sum of the conditional von Neumann entropies is not smaller than 0.280.Comment: Errors corrected. See L. Jakobcyk, quant-ph/040908

Non-Gaussian two-mode squeezing and continuous variable entanglement of linearly and circularly polarized light beams interacting with cold atoms

We investigate how entangled coherent states and superpositions of low intensity coherent states of non-Gaussian nature can be generated via non-resonant interaction between either two linearly or circularly polarized field modes and an ensemble of X-like four-level atoms placed in an optical cavity. We compare our results to recent experimental observations and argue that the non-Gaussian structure of the field states may be present in those systems.Comment: 10 pages, 7 figures, replaced with final published versio

Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

Directed percolation depinning models: Evolution equations

We present the microscopic equation for the growing interface with quenched noise for the model first presented by Buldyrev et al. [Phys. Rev. A 45, R8313 (1992)]. The evolution equation for the height, the mean height, and the roughness are reached in a simple way. The microscopic equation allows us to express these equations in two contributions: the contact and the local one. We compare this two contributions with the ones obtained for the Tang and Leschhorn model [Phys. Rev A 45, R8309 (1992)] by Braunstein et al. [Physica A 266, 308 (1999)]. Even when the microscopic mechanisms are quiet different in both model, the two contribution are qualitatively similar. An interesting result is that the diffusion contribution, in the Tang and Leschhorn model, and the contact one, in the Buldyrev model, leads to an increase of the roughness near the criticality.Comment: 10 pages and 4 figures. To be published in Phys. Rev.

Bicoloring Random Hypergraphs

We study the problem of bicoloring random hypergraphs, both numerically and analytically. We apply the zero-temperature cavity method to find analytical results for the phase transitions (dynamic and static) in the 1RSB approximation. These points appear to be in agreement with the results of the numerical algorithm. In the second part, we implement and test the Survey Propagation algorithm for specific bicoloring instances in the so called HARD-SAT phase.Comment: 14 pages, 10 figure

Phase-Covariant Quantum Benchmarks

We give a quantum benchmark for teleportation and quantum storage experiments suited for pure and mixed test states. The benchmark is based on the average fidelity over a family of phase-covariant states and certifies that an experiment can not be emulated by a classical setup, i.e., by a measure-and-prepare scheme. We give an analytical solution for qubits, which shows important differences with standard state estimation approach, and compute the value of the benchmark for coherent and squeezed states, both pure and mixed.Comment: 4 pages, 2 figure

Optical implementation and entanglement distribution in Gaussian valence bond states

We study Gaussian valence bond states of continuous variable systems, obtained as the outputs of projection operations from an ancillary space of M infinitely entangled bonds connecting neighboring sites, applied at each of $N$ sites of an harmonic chain. The entanglement distribution in Gaussian valence bond states can be controlled by varying the input amount of entanglement engineered in a (2M+1)-mode Gaussian state known as the building block, which is isomorphic to the projector applied at a given site. We show how this mechanism can be interpreted in terms of multiple entanglement swapping from the chain of ancillary bonds, through the building blocks. We provide optical schemes to produce bisymmetric three-mode Gaussian building blocks (which correspond to a single bond, M=1), and study the entanglement structure in the output Gaussian valence bond states. The usefulness of such states for quantum communication protocols with continuous variables, like telecloning and teleportation networks, is finally discussed.Comment: 15 pages, 6 figures. To appear in Optics and Spectroscopy, special issue for ICQO'2006 (Minsk). This preprint contains extra material with respect to the journal versio