arXiv subjects

A. Braunstein

Publications and source records attributed to A. Braunstein.

At least 19 recordsLinked to original sources

arXiv2023

Effectiveness of probabilistic contact tracing in epidemic containment: the role of super-spreaders and transmission path reconstruction

The recent COVID-19 pandemic underscores the significance of early-stage non-pharmacological intervention strategies. The widespread use of masks and the systematic implementation of contact tracing strategies provide a potentially equally effective and socially less impactful alternative to more conventional approaches, such as large-scale mobility restrictions. However, manual contact tracing faces strong limitations in accessing the network of contacts, and the scalability of currently implemented protocols for smartphone-based digital contact tracing becomes impractical during the rapid expansion phases of the outbreaks, due to the surge in exposure notifications and associated tests. A substantial improvement in digital contact tracing can be obtained through the integration of probabilistic techniques for risk assessment that can more effectively guide the allocation of new diagnostic tests. In this study, we first quantitatively analyze the diagnostic and social costs associated with these containment measures based on contact tracing, employing three state-of-the-art models of SARS-CoV-2 spreading. Our results suggest that probabilistic techniques allow for more effective mitigation at a lower cost. Secondly, our findings reveal a remarkable efficacy of probabilistic contact-tracing techniques in performing backward and multi-step tracing and capturing super-spreading events.

q-bio.PE↗

arXiv2015

Statics and dynamics of selfish interactions in distributed service systems

We study a class of games which model the competition among agents to access some service provided by distributed service units and which exhibit congestion and frustration phenomena when service units have limited capacity. We propose a technique, based on the cavity method of statistical physics, to characterize the full spectrum of Nash equilibria of the game. The analysis reveals a large variety of equilibria, with very different statistical properties. Natural selfish dynamics, such as best-response, usually tend to large-utility equilibria, even though those of smaller utility are exponentially more numerous. Interestingly, the latter actually can be reached by selecting the initial conditions of the best-response dynamics close to the saturation limit of the service unit capacities. We also study a more realistic stochastic variant of the game by means of a simple and effective approximation of the average over the random parameters, showing that the properties of the average-case Nash equilibria are qualitatively similar to the deterministic ones.

cs.GT↗

arXiv2013

Stochastic Optimization of Service Provision with Selfish Users

We develop a computationally efficient technique to solve a fairly general distributed service provision problem with selfish users and imperfect information. In particular, in a context in which the service capacity of the existing infrastructure can be partially adapted to the user load by activating just some of the service units, we aim at finding the configuration of active service units that achieves the best trade-off between maintenance (e.g.\ energetic) costs for the provider and user satisfaction. The core of our technique resides in the implementation of a belief-propagation (BP) algorithm to evaluate the cost configurations. Numerical results confirm the effectiveness of our approach.

cs.GT↗

arXiv2013

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.

physics.soc-ph↗

arXiv2013

Large deviations of cascade processes on graphs

Simple models of irreversible dynamical processes such as Bootstrap Percolation have been successfully applied to describe cascade processes in a large variety of different contexts. However, the problem of analyzing non-typical trajectories, which can be crucial for the understanding of the out-of-equilibrium phenomena, is still considered to be intractable in most cases. Here we introduce an efficient method to find and analyze optimized trajectories of cascade processes. We show that for a wide class of irreversible dynamical rules, this problem can be solved efficiently on large-scale systems.

cond-mat.stat-mech↗

arXiv2011

Inference and learning in sparse systems with multiple states

We discuss how inference can be performed when data are sampled from the non-ergodic phase of systems with multiple attractors. We take as model system the finite connectivity Hopfield model in the memory phase and suggest a cavity method approach to reconstruct the couplings when the data are separately sampled from few attractor states. We also show how the inference results can be converted into a learning protocol for neural networks in which patterns are presented through weak external fields. The protocol is simple and fully local, and is able to store patterns with a finite overlap with the input patterns without ever reaching a spin glass phase where all memories are lost.

cond-mat.dis-nn↗

arXiv2011

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.

q-bio.MN↗

arXiv2010

Aligning graphs and finding substructures by a cavity approach

We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The algorithm allows to analyze large graphs and may find applications in fields such as computational biology. As a proof of concept we use our algorithm to align the similarity graphs of two interacting protein families involved in bacterial signal transduction, and to predict actually interacting protein partners between these families.

q-bio.QM↗

arXiv2009

Clustering with shallow trees

We propose a new method for hierarchical clustering based on the optimisation of a cost function over trees of limited depth, and we derive a message--passing method that allows to solve it efficiently. The method and algorithm can be interpreted as a natural interpolation between two well-known approaches, namely single linkage and the recently presented Affinity Propagation. We analyze with this general scheme three biological/medical structured datasets (human population based on genetic information, proteins based on sequences and verbal autopsies) and show that the interpolation technique provides new insight.

cond-mat.dis-nn↗

arXiv2009

Statistical mechanics of budget-constrained auctions

Finding the optimal assignment in budget-constrained auctions is a combinatorial optimization problem with many important applications, a notable example being the sale of advertisement space by search engines (in this context the problem is often referred to as the off-line AdWords problem). Based on the cavity method of statistical mechanics, we introduce a message passing algorithm that is capable of solving efficiently random instances of the problem extracted from a natural distribution, and we derive from its properties the phase diagram of the problem. As the control parameter (average value of the budgets) is varied, we find two phase transitions delimiting a region in which long-range correlations arise.

cs.GT↗

arXiv2009

A rigorous analysis of the cavity equations for the minimum spanning tree

We analyze a new general representation for the Minimum Weight Steiner Tree (MST) problem which translates the topological connectivity constraint into a set of local conditions which can be analyzed by the so called cavity equations techniques. For the limit case of the Spanning tree we prove that the fixed point of the algorithm arising from the cavity equations leads to the global optimum.

cond-mat.stat-mech↗

arXiv2008

Inference algorithms for gene networks: a statistical mechanics analysis

The inference of gene regulatory networks from high throughput gene expression data is one of the major challenges in systems biology. This paper aims at analysing and comparing two different algorithmic approaches. The first approach uses pairwise correlations between regulated and regulating genes; the second one uses message-passing techniques for inferring activating and inhibiting regulatory interactions. The performance of these two algorithms can be analysed theoretically on well-defined test sets, using tools from the statistical physics of disordered systems like the replica method. We find that the second algorithm outperforms the first one since it takes into account collective effects of multiple regulators.

q-bio.QM↗

arXiv2008

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.

q-bio.QM↗

arXiv2008

Statistical Mechanics of Steiner trees

The Minimum Weight Steiner Tree (MST) is an important combinatorial optimization problem over networks that has applications in a wide range of fields. Here we discuss a general technique to translate the imposed global connectivity constrain into many local ones that can be analyzed with cavity equation techniques. This approach leads to a new optimization algorithm for MST and allows to analyze the statistical mechanics properties of MST on random graphs of various types.

cond-mat.stat-mech↗

arXiv2007

Encoding for the Blackwell Channel with Reinforced Belief Propagation

A key idea in coding for the broadcast channel (BC) is binning, in which the transmitter encode information by selecting a codeword from an appropriate bin (the messages are thus the bin indexes). This selection is normally done by solving an appropriate (possibly difficult) combinatorial problem. Recently it has been shown that binning for the Blackwell channel --a particular BC-- can be done by iterative schemes based on Survey Propagation (SP). This method uses decimation for SP and suffers a complexity of O(n^2). In this paper we propose a new variation of the Belief Propagation (BP) algorithm, named Reinforced BP algorithm, that turns BP into a solver. Our simulations show that this new algorithm has complexity O(n log n). Using this new algorithm together with a non-linear coding scheme, we can efficiently achieve rates close to the border of the capacity region of the Blackwell channel.

cs.IT↗

arXiv2006

Survey propagation: an algorithm for satisfiability

We study the satisfiability of randomly generated formulas formed by $M$ clauses of exactly $K$ literals over $N$ Boolean variables. For a given value of $N$ the problem is known to be most difficult with $α=M/N$ close to the experimental threshold $α_c$ separating the region where almost all formulas are SAT from the region where all formulas are UNSAT. Recent results from a statistical physics analysis suggest that the difficulty is related to the existence of a clustering phenomenon of the solutions when $α$ is close to (but smaller than) $α_c$. We introduce a new type of message passing algorithm which allows to find efficiently a satisfiable assignment of the variables in the difficult region. This algorithm is iterative and composed of two main parts. The first is a message-passing procedure which generalizes the usual methods like Sum-Product or Belief Propagation: it passes messages that are surveys over clusters of the ordinary messages. The second part uses the detailed probabilistic information obtained from the surveys in order to fix variables and simplify the problem. Eventually, the simplified problem that remains is solved by a conventional heuristic.

cs.CC↗

arXiv2004

Survey Propagation as local equilibrium equations

It has been shown experimentally that a decimation algorithm based on Survey Propagation (SP) equations allows to solve efficiently some combinatorial problems over random graphs. We show that these equations can be derived as sum-product equations for the computation of marginals in an extended space where the variables are allowed to take an additional value -- $*$ -- when they are not forced by the combinatorial constraints. An appropriate ``local equilibrium condition'' cost/energy function is introduced and its entropy is shown to coincide with the expected logarithm of the number of clusters of solutions as computed by SP. These results may help to clarify the geometrical notion of clusters assumed by SP for the random K-SAT or random graph coloring (where it is conjectured to be exact) and helps to explain which kind of clustering operation or approximation is enforced in general/small sized models in which it is known to be inexact.

cond-mat.dis-nn↗

arXiv2003

Constraint Satisfaction by Survey Propagation

Survey Propagation is an algorithm designed for solving typical instances of random constraint satisfiability problems. It has been successfully tested on random 3-SAT and random $G(n,\frac{c}{n})$ graph 3-coloring, in the hard region of the parameter space. Here we provide a generic formalism which applies to a wide class of discrete Constraint Satisfaction Problems.

cond-mat.dis-nn↗