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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., Comment: 5 pages, 4 figures

Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes enables various statistical approaches to this problem. In this context covariance-based methods have been used to identify correlation between amino acid positions in interacting proteins. However, these methods have an important shortcoming, in that they cannot distinguish between directly and indirectly correlated residues. We developed a method that combines covariance analysis with global inference analysis, adopted from use in statistical physics. Applied to a set of >2,500 representatives of the bacterial two-component signal transduction system, the combination of covariance with global inference successfully and robustly identified residue pairs that are proximal in space without resorting to ad hoc tuning parameters, both for heterointeractions between sensor kinase (SK) and response regulator (RR) proteins and for homointeractions between RR proteins. The spectacular success of this approach illustrates the effectiveness of the global inference approach in identifying direct interaction based on sequence information alone. We expect this method to be applicable soon to interaction surfaces between proteins present in only 1 copy per genome as the number of sequenced genomes continues to expand. Use of this method could significantly increase the potential targets for therapeutic intervention, shed light on the mechanism of protein-protein interaction, and establish the foundation for the accurate prediction of interacting protein partners., Comment: Supplementary information available on http://www.pnas.org/content/106/1/67.abstract

In this paper, we analyse large random Boolean networks in terms of a constraint satisfaction problem. We first develop an algorithmic scheme which allows to prune simple logical cascades and under-determined variables, returning thereby the computational core of the network. Second we apply the cavity method to analyse number and organisation of fixed points. We find in particular a phase transition between an easy and a complex regulatory phase, the latter one being characterised by the existence of an exponential number of macroscopically separated fixed-point clusters. The different techniques developed are reinterpreted as algorithms for the analysis of single Boolean networks, and they are applied to analysis and in silico experiments on the gene-regulatory networks of baker's yeast (saccaromices cerevisiae) and the segment-polarity genes of the fruit-fly drosophila melanogaster., Comment: 29 pages, 18 figures, version accepted for publication in JSTAT

We study the graph coloring problem over random graphs of finite average connectivity $c$. Given a number $q$ of available colors, we find that graphs with low connectivity admit almost always a proper coloring whereas graphs with high connectivity are uncolorable. Depending on $q$, we find the precise value of the critical average connectivity $c_q$. Moreover, we show that below $c_q$ there exist a clustering phase $c\in [c_d,c_q]$ in which ground states spontaneously divide into an exponential number of clusters. Furthermore, we extended our considerations to the case of single instances showing consistent results. This lead us to propose a new algorithm able to color in polynomial time random graphs in the hard but colorable region, i.e when $c\in [c_d,c_q]$., Comment: 23 pages, 10 eps figures

We introduce a hard-core lattice-gas model on generalized Bethe lattices and investigate analytically and numerically its compaction behavior. If compactified slowly, the system undergoes a first-order crystallization transition. If compactified much faster, the system stays in a meta-stable liquid state and undergoes a glass transition under further compaction. We show that this behavior is induced by geometrical frustration which appears due to the existence of short loops in the generalized Bethe lattices. We also compare our results to numerical simulations of a three-dimensional analog of the model., Comment: 7 pages, 4 figures, revised version

We study the graph coloring problem over random graphs of finite average connectivity $c$. Given a number $q$ of available colors, we find that graphs with low connectivity admit almost always a proper coloring whereas graphs with high connectivity are uncolorable. Depending on $q$, we find the precise value of the critical average connectivity $c_q$. Moreover, we show that below $c_q$ there exist a clustering phase $c\in [c_d,c_q]$ in which ground states spontaneously divide into an exponential number of clusters and where the proliferation of metastable states is responsible for the onset of complexity in local search algorithms., Comment: 4 pages, 1 figure, version to app. in PRL

A major problem in evaluating stochastic local search algorithms for NP-complete problems is the need for a systematic generation of hard test instances having previously known properties of the optimal solutions. On the basis of statistical mechanics results, we propose random generators of hard and satisfiable instances for the 3-satisfiability problem (3SAT). The design of the hardest problem instances is based on the existence of a first order ferromagnetic phase transition and the glassy nature of excited states. The analytical predictions are corroborated by numerical results obtained from complete as well as stochastic local algorithms., Comment: 5 pages, 4 figures, revised version to app. in PRL

We introduce a finite-connectivity ferromagnetic model with a three-spin interaction which has a crystalline (ferromagnetic) phase as well as a glass phase. The model is not frustrated, it has a ferromagnetic equilibrium phase at low temperature which is not reached dynamically in a quench from the high-temperature phase. Instead it shows a glass transition which can be studied in detail by a one step replica-symmetry broken calculation. This spin model exhibits the main properties of the structural glass transition at a solvable mean-field level., Comment: 7 pages, 2 figures, uses epl.cls (included)

We study a simple and exactly solvable model for the generation of random satisfiability problems. These consist of $\gamma N$ random boolean constraints which are to be satisfied simultaneously by $N$ logical variables. In statistical-mechanics language, the considered model can be seen as a diluted p-spin model at zero temperature. While such problems become extraordinarily hard to solve by local search methods in a large region of the parameter space, still at least one solution may be superimposed by construction. The statistical properties of the model can be studied exactly by the replica method and each single instance can be analyzed in polynomial time by a simple global solution method. The geometrical/topological structures responsible for dynamic and static phase transitions as well as for the onset of computational complexity in local search method are thoroughly analyzed. Numerical analysis on very large samples allows for a precise characterization of the critical scaling behaviour., Comment: 14 pages, 5 figures, to appear in Phys. Rev. E (Feb 2001). v2: minor errors and references corrected