50 research outputs found
Zero temperature solutions of the Edwards-Anderson model in random Husimi Lattices
We solve the Edwards-Anderson model (EA) in different Husimi lattices. We
show that, at T=0, the structure of the solution space depends on the parity of
the loop sizes. Husimi lattices with odd loop sizes have always a trivial
paramagnetic solution stable under 1RSB perturbations while, in Husimi lattices
with even loop sizes, this solution is absent. The range of stability under
1RSB perturbations of this and other RS solutions is computed analytically
(when possible) or numerically. We compute the free-energy, the complexity and
the ground state energy of different Husimi lattices at the level of the 1RSB
approximation. We also show, when the fraction of ferromagnetic couplings
increases, the existence, first, of a discontinuous transition from a
paramagnetic to a spin glass phase and latter of a continuous transition from a
spin glass to a ferromagnetic phase.Comment: 20 pages, 10 figures (v3: Corrected analysis of transitions. Appendix
proof fixed
Annotation of the modular polyketide synthase and nonribosomal peptide synthetase gene clusters in the genome of Streptomyces tsukubaensis NRRL18488
et al.The high G+C content and large genome size make the sequencing and assembly of Streptomyces genomes more difficult than for other bacteria. Many pharmaceutically important natural products are synthesized by modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The analysis of such gene clusters is difficult if the genome sequence is not of the highest quality, because clusters can be distributed over several contigs, and sequencing errors can introduce apparent frameshifts into the large PKS and NRPS proteins. An additional problem is that the modular nature of the clusters results in the presence of imperfect repeats, which may cause assembly errors. The genome sequence of Streptomyces tsukubaensis NRRL18488 was scanned for potential PKS and NRPS modular clusters. A phylogenetic approach was used to identify multiple contigs belonging to the same cluster. Four PKS clusters and six NRPS clusters were identified. Contigs containing cluster sequences were analyzed in detail by using the ClustScan program, which suggested the order and orientation of the contigs. The sequencing of the appropriate PCR products confirmed the ordering and allowed the correction of apparent frameshifts resulting from sequencing errors. The product chemistry of such correctly assembled clusters could also be predicted. The analysis of one PKS cluster showed that it should produce a bafilomycin-like compound, and reverse transcription (RT)-PCR was used to show that the cluster was transcribed. © 2012, American Society for Microbiology.We thank the Government of Slovenia, Ministry of Higher Education, Science and Technology (Slovenian Research Agency [ARRS]), for the award of grant no. J4-9331 and L4-2188 to H.P. We also thank the Ministry of the Economy, the JAPTI Agency, and the European Social Fund (contract no. 102/2008) for the funds awarded for the employment of G.K. This work was also funded by a cooperation grant of the German Academic Exchange Service (DAAD) and the Ministry of Science, Education, and Sports, Republic of Croatia (to J.C. and D.H.), and by grant 09/5 (to D.H.) from the Croatian Science Foundation.Peer Reviewe
Polynomial iterative algorithms for coloring and analyzing random graphs
We study the graph coloring problem over random graphs of finite average
connectivity . Given a number 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 , we find the precise value
of the critical average connectivity . Moreover, we show that below
there exist a clustering phase 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 .Comment: 23 pages, 10 eps figure
Score-Based Bayesian Skill Learning
We extend the Bayesian skill rating system of TrueSkill to accommodate score-based match outcomes. TrueSkill has proven to be a very effective algorithm for matchmaking - the process of pairing competitors based on similar skill-level - in competitive online gaming. However, for the case of two teams/players, TrueSkill only learns from win, lose, or draw outcomes and cannot use additional match outcome information such as scores. To address this deficiency, we propose novel Bayesian graphical models as extensions of TrueSkill that (1) model player's offence and defence skills separately and (2) model how these offence and defence skills interact to generate score-based match outcomes. We derive efficient (approximate) Bayesian inference methods for inferring latent skills in these new models and evaluate them on three real data sets including Halo 2 XBox Live matches. Empirical evaluations demonstrate that the new score-based models (a) provide more accurate win/loss probability estimates than TrueSkill when training data is limited, (b) provide competitive and often better win/loss classification performance than TrueSkill, and (c) provide reasonable score outcome predictions with an appropriate choice of likelihood - prediction for which TrueSkill was not designed, but which can be useful in many applications. © 2012 Springer-Verlag
Random subcubes as a toy model for constraint satisfaction problems
We present an exactly solvable random-subcube model inspired by the structure
of hard constraint satisfaction and optimization problems. Our model reproduces
the structure of the solution space of the random k-satisfiability and
k-coloring problems, and undergoes the same phase transitions as these
problems. The comparison becomes quantitative in the large-k limit. Distance
properties, as well the x-satisfiability threshold, are studied. The model is
also generalized to define a continuous energy landscape useful for studying
several aspects of glassy dynamics.Comment: 21 pages, 4 figure
On the freezing of variables in random constraint satisfaction problems
The set of solutions of random constraint satisfaction problems (zero energy
groundstates of mean-field diluted spin glasses) undergoes several structural
phase transitions as the amount of constraints is increased. This set first
breaks down into a large number of well separated clusters. At the freezing
transition, which is in general distinct from the clustering one, some
variables (spins) take the same value in all solutions of a given cluster. In
this paper we study the critical behavior around the freezing transition, which
appears in the unfrozen phase as the divergence of the sizes of the
rearrangements induced in response to the modification of a variable. The
formalism is developed on generic constraint satisfaction problems and applied
in particular to the random satisfiability of boolean formulas and to the
coloring of random graphs. The computation is first performed in random tree
ensembles, for which we underline a connection with percolation models and with
the reconstruction problem of information theory. The validity of these results
for the original random ensembles is then discussed in the framework of the
cavity method.Comment: 32 pages, 7 figure
Region graph partition function expansion and approximate free energy landscapes: Theory and some numerical results
Graphical models for finite-dimensional spin glasses and real-world
combinatorial optimization and satisfaction problems usually have an abundant
number of short loops. The cluster variation method and its extension, the
region graph method, are theoretical approaches for treating the complicated
short-loop-induced local correlations. For graphical models represented by
non-redundant or redundant region graphs, approximate free energy landscapes
are constructed in this paper through the mathematical framework of region
graph partition function expansion. Several free energy functionals are
obtained, each of which use a set of probability distribution functions or
functionals as order parameters. These probability distribution
function/functionals are required to satisfy the region graph
belief-propagation equation or the region graph survey-propagation equation to
ensure vanishing correction contributions of region subgraphs with dangling
edges. As a simple application of the general theory, we perform region graph
belief-propagation simulations on the square-lattice ferromagnetic Ising model
and the Edwards-Anderson model. Considerable improvements over the conventional
Bethe-Peierls approximation are achieved. Collective domains of different sizes
in the disordered and frustrated square lattice are identified by the
message-passing procedure. Such collective domains and the frustrations among
them are responsible for the low-temperature glass-like dynamical behaviors of
the system.Comment: 30 pages, 11 figures. More discussion on redundant region graphs. To
be published by Journal of Statistical Physic