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- Faruck Morcos, Andrea Pagnani, +7 authors Martin Weigt
- Proceedings of the National Academy of Sciences…
- 2011

The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long been suggested that the resulting correlations among amino acid compositions at different sequence positions can be exploited to infer spatial contacts within the tertiary protein structure. Crucial to this… (More)

- M Mézard, G Parisi, R Zecchina
- Science
- 2002

We study the satisfiability of random Boolean expressions built from many clauses with K variables per clause (K-satisfiability). Expressions with a ratio alpha of clauses to variables less than a threshold alphac are almost always satisfiable, whereas those with a ratio above this threshold are almost always unsatisfiable. We show the existence of an… (More)

- Alfredo Braunstein, Marc Mézard, Riccardo Zecchina
- Random Struct. Algorithms
- 2005

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 when α = M/N is close to the experimental threshold αc separating the region where almost all formulas are SAT from the region where all formulas are UNSAT. Recent… (More)

- Marc Mézard, Riccardo Zecchina
- Physical review. E, Statistical, nonlinear, and…
- 2002

We study the problem of satisfiability of randomly chosen clauses, each with K Boolean variables. Using the cavity method at zero temperature, we find the phase diagram for the K=3 case. We show the existence of an intermediate phase in the satisfiable region, where the proliferation of metastable states is at the origin of the slowdown of search… (More)

- Debora S. Marks, Lucy J. Colwell, +4 authors Chris Sander
- PloS one
- 2011

The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering… (More)

- Riccardo Zecchina, Scott Kirkpatrick, Bart Selman, Lidror Troyanskyk
- 1999

* CNRS-Laboratoire de Physique The Âorique, 24, Rue Lhomond, 75231 Paris Cedex, France 2 The Abdus Salam International Centre for Theoretical Physics, Strada Costieri 11, 34100 Trieste, Italy 3 IBM, Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA § Computer Science Department, Cornell University, Ithaca, New York 14853, USA k… (More)

- Marc Mézard, Federico Ricci-Tersenghi, Riccardo Zecchina
- ArXiv
- 2002

We derive analytical solutions for p-spin models with finite connectivity at zero temperature. These models are the statistical mechanics equivalent of p-XORSAT problems in theoretical computer science. We give a full characterization of the phase diagram: location of the phase transitions (static and dynamic), together with a description of the clustering… (More)

- Mohsen Bayati, Christian Borgs, Jennifer T. Chayes, Riccardo Zecchina
- SIAM J. Discrete Math.
- 2011

We consider the general problem of finding the minimum weight b-matching on arbitrary graphs. We prove that, whenever the linear programming (LP) relaxation of the problem has no fractional solutions, then the belief propagation (BP) algorithm converges to the correct solution. We also show that when the LP relaxation has fractional solution then BP… (More)

- Rémi Monasson, Riccardo Zecchina, Scott Kirkpatrick, Bart Selman, Lidror Troyansky
- Random Struct. Algorithms
- 1999

Heuristic methods for solution of problems in the NP-complete class of decision problems often reach exact solutions, but fail badly at ‘‘phase boundaries,’’ across which the decision to be reached changes from almost always having one value to almost always having a different value. We report an analytic solution and experimental investigations of the… (More)

- Stephan Mertens, Marc Mézard, Riccardo Zecchina
- Random Struct. Algorithms
- 2006

Using the cavity equations of Mézard, Parisi, and Zecchina [Science 297 (2002), 812; Mézard and Zecchina, Phys Rev E 66 (2002), 056126] we derive the various threshold values for the number of clauses per variable of the random K-satisfiability problem, generalizing the previous results to K ≥ 4. We also give an analytic solution of the equations, and some… (More)