255 research outputs found
Exactly solvable models of adaptive networks
A satisfiability (SAT-UNSAT) transition takes place for many optimization
problems when the number of constraints, graphically represented by links
between variables nodes, is brought above some threshold. If the network of
constraints is allowed to adapt by redistributing its links, the SAT-UNSAT
transition may be delayed and preceded by an intermediate phase where the
structure self-organizes to satisfy the constraints. We present an analytic
approach, based on the recently introduced cavity method for large deviations,
which exactly describes the two phase transitions delimiting this adaptive
intermediate phase. We give explicit results for random bond models subject to
the connectivity or rigidity percolation transitions, and compare them with
numerical simulations.Comment: 4 pages, 4 figure
Landscape of solutions in constraint satisfaction problems
We present a theoretical framework for characterizing the geometrical
properties of the space of solutions in constraint satisfaction problems,
together with practical algorithms for studying this structure on particular
instances. We apply our method to the coloring problem, for which we obtain the
total number of solutions and analyze in detail the distribution of distances
between solutions.Comment: 4 pages, 4 figures. Replaced with published versio
Statistical Mechanics of the Hyper Vertex Cover Problem
We introduce and study a new optimization problem called Hyper Vertex Cover.
This problem is a generalization of the standard vertex cover to hypergraphs:
one seeks a configuration of particles with minimal density such that every
hyperedge of the hypergraph contains at least one particle. It can also be used
in important practical tasks, such as the Group Testing procedures where one
wants to detect defective items in a large group by pool testing. Using a
Statistical Mechanics approach based on the cavity method, we study the phase
diagram of the HVC problem, in the case of random regualr hypergraphs.
Depending on the values of the variables and tests degrees different situations
can occur: The HVC problem can be either in a replica symmetric phase, or in a
one-step replica symmetry breaking one. In these two cases, we give explicit
results on the minimal density of particles, and the structure of the phase
space. These problems are thus in some sense simpler than the original vertex
cover problem, where the need for a full replica symmetry breaking has
prevented the derivation of exact results so far. Finally, we show that
decimation procedures based on the belief propagation and the survey
propagation algorithms provide very efficient strategies to solve large
individual instances of the hyper vertex cover problem.Comment: Submitted to PR
The cavity method for large deviations
A method is introduced for studying large deviations in the context of
statistical physics of disordered systems. The approach, based on an extension
of the cavity method to atypical realizations of the quenched disorder, allows
us to compute exponentially small probabilities (rate functions) over different
classes of random graphs. It is illustrated with two combinatorial optimization
problems, the vertex-cover and coloring problems, for which the presence of
replica symmetry breaking phases is taken into account. Applications include
the analysis of models on adaptive graph structures.Comment: 18 pages, 7 figure
Statistical mechanics of error exponents for error-correcting codes
Error exponents characterize the exponential decay, when increasing message
length, of the probability of error of many error-correcting codes. To tackle
the long standing problem of computing them exactly, we introduce a general,
thermodynamic, formalism that we illustrate with maximum-likelihood decoding of
low-density parity-check (LDPC) codes on the binary erasure channel (BEC) and
the binary symmetric channel (BSC). In this formalism, we apply the cavity
method for large deviations to derive expressions for both the average and
typical error exponents, which differ by the procedure used to select the codes
from specified ensembles. When decreasing the noise intensity, we find that two
phase transitions take place, at two different levels: a glass to ferromagnetic
transition in the space of codewords, and a paramagnetic to glass transition in
the space of codes.Comment: 32 pages, 13 figure
Message passing for vertex covers
Constructing a minimal vertex cover of a graph can be seen as a prototype for
a combinatorial optimization problem under hard constraints. In this paper, we
develop and analyze message passing techniques, namely warning and survey
propagation, which serve as efficient heuristic algorithms for solving these
computational hard problems. We show also, how previously obtained results on
the typical-case behavior of vertex covers of random graphs can be recovered
starting from the message passing equations, and how they can be extended.Comment: 25 pages, 9 figures - version accepted for publication in PR
Random multi-index matching problems
The multi-index matching problem (MIMP) generalizes the well known matching
problem by going from pairs to d-uplets. We use the cavity method from
statistical physics to analyze its properties when the costs of the d-uplets
are random. At low temperatures we find for d>2 a frozen glassy phase with
vanishing entropy. We also investigate some properties of small samples by
enumerating the lowest cost matchings to compare with our theoretical
predictions.Comment: 22 pages, 16 figure
An algorithm for counting circuits: application to real-world and random graphs
We introduce an algorithm which estimates the number of circuits in a graph
as a function of their length. This approach provides analytical results for
the typical entropy of circuits in sparse random graphs. When applied to
real-world networks, it allows to estimate exponentially large numbers of
circuits in polynomial time. We illustrate the method by studying a graph of
the Internet structure.Comment: 7 pages, 3 figures, minor corrections, accepted versio
HAMAP in 2015: updates to the protein family classification and annotation system
HAMAP (High-quality Automated and Manual Annotation of Proteins—available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorith
HAMAP in 2013, new developments in the protein family classification and annotation system
HAMAP (High-quality Automated and Manual Annotation of Proteins—available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. HAMAP was originally developed to support the manual curation of UniProtKB/Swiss-Prot records describing microbial proteins. Here we describe new developments in HAMAP, including the extension of HAMAP to eukaryotic proteins, the use of HAMAP in the automated annotation of UniProtKB/TrEMBL, providing high-quality annotation for millions of protein sequences, and the future integration of HAMAP into a unified system for UniProtKB annotation, UniRule. HAMAP is continuously updated by expert curators with new family profiles and annotation rules as new protein families are characterized. The collection of HAMAP family classification profiles and annotation rules can be browsed and viewed on the HAMAP website, which also provides an interface to scan user sequences against HAMAP profile
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