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Items: 1 to 50 of 56

1.

From statistical inference to a differential learning rule for stochastic neural networks.

Saglietti L, Gerace F, Ingrosso A, Baldassi C, Zecchina R.

Interface Focus. 2018 Dec 6;8(6):20180033. doi: 10.1098/rsfs.2018.0033. Epub 2018 Oct 19.

2.

Role of Synaptic Stochasticity in Training Low-Precision Neural Networks.

Baldassi C, Gerace F, Kappen HJ, Lucibello C, Saglietti L, Tartaglione E, Zecchina R.

Phys Rev Lett. 2018 Jun 29;120(26):268103. doi: 10.1103/PhysRevLett.120.268103.

PMID:
30004730
3.

Efficiency of quantum vs. classical annealing in nonconvex learning problems.

Baldassi C, Zecchina R.

Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):1457-1462. doi: 10.1073/pnas.1711456115. Epub 2018 Jan 30.

4.

RNAs competing for microRNAs mutually influence their fluctuations in a highly non-linear microRNA-dependent manner in single cells.

Bosia C, Sgrò F, Conti L, Baldassi C, Brusa D, Cavallo F, Cunto FD, Turco E, Pagnani A, Zecchina R.

Genome Biol. 2017 Feb 20;18(1):37. doi: 10.1186/s13059-017-1162-x.

5.

Unreasonable effectiveness of learning neural networks: From accessible states and robust ensembles to basic algorithmic schemes.

Baldassi C, Borgs C, Chayes JT, Ingrosso A, Lucibello C, Saglietti L, Zecchina R.

Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7655-E7662. Epub 2016 Nov 15.

6.

Learning may need only a few bits of synaptic precision.

Baldassi C, Gerace F, Lucibello C, Saglietti L, Zecchina R.

Phys Rev E. 2016 May;93(5):052313. doi: 10.1103/PhysRevE.93.052313. Epub 2016 May 27.

PMID:
27300916
7.

Subdominant Dense Clusters Allow for Simple Learning and High Computational Performance in Neural Networks with Discrete Synapses.

Baldassi C, Ingrosso A, Lucibello C, Saglietti L, Zecchina R.

Phys Rev Lett. 2015 Sep 18;115(12):128101. doi: 10.1103/PhysRevLett.115.128101. Epub 2015 Sep 18.

PMID:
26431018
8.

A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks.

Alemi A, Baldassi C, Brunel N, Zecchina R.

PLoS Comput Biol. 2015 Aug 20;11(8):e1004439. doi: 10.1371/journal.pcbi.1004439. eCollection 2015 Aug.

9.

Bridging the gaps in systems biology.

Cvijovic M, Almquist J, Hagmar J, Hohmann S, Kaltenbach HM, Klipp E, Krantz M, Mendes P, Nelander S, Nielsen J, Pagnani A, Przulj N, Raue A, Stelling J, Stoma S, Tobin F, Wodke JA, Zecchina R, Jirstrand M.

Mol Genet Genomics. 2014 Oct;289(5):727-34. doi: 10.1007/s00438-014-0843-3. Epub 2014 Apr 13. Review.

PMID:
24728588
10.

Bayesian inference of epidemics on networks via belief propagation.

Altarelli F, Braunstein A, Dall'Asta L, Lage-Castellanos A, Zecchina R.

Phys Rev Lett. 2014 Mar 21;112(11):118701. Epub 2014 Mar 17.

PMID:
24702425
11.

Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners.

Baldassi C, Zamparo M, Feinauer C, Procaccini A, Zecchina R, Weigt M, Pagnani A.

PLoS One. 2014 Mar 24;9(3):e92721. doi: 10.1371/journal.pone.0092721. eCollection 2014.

12.

Perturbation biology: inferring signaling networks in cellular systems.

Molinelli EJ, Korkut A, Wang W, Miller ML, Gauthier NP, Jing X, Kaushik P, He Q, Mills G, Solit DB, Pratilas CA, Weigt M, Braunstein A, Pagnani A, Zecchina R, Sander C.

PLoS Comput Biol. 2013;9(12):e1003290. doi: 10.1371/journal.pcbi.1003290. Epub 2013 Dec 19.

13.

Sharing information to reconstruct patient-specific pathways in heterogeneous diseases.

Gitter A, Braunstein A, Pagnani A, Baldassi C, Borgs C, Chayes J, Zecchina R, Fraenkel E.

Pac Symp Biocomput. 2014:39-50.

14.

Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells.

Neri F, Incarnato D, Krepelova A, Rapelli S, Pagnani A, Zecchina R, Parlato C, Oliviero S.

Genome Biol. 2013 Aug 29;14(8):R91. doi: 10.1186/gb-2013-14-8-r91.

15.

Shape similarity, better than semantic membership, accounts for the structure of visual object representations in a population of monkey inferotemporal neurons.

Baldassi C, Alemi-Neissi A, Pagan M, Dicarlo JJ, Zecchina R, Zoccolan D.

PLoS Comput Biol. 2013;9(8):e1003167. doi: 10.1371/journal.pcbi.1003167. Epub 2013 Aug 8.

16.

Large deviations of cascade processes on graphs.

Altarelli F, Braunstein A, Dall'Asta L, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Jun;87(6):062115. Epub 2013 Jun 11.

PMID:
23848635
17.

Modelling Competing Endogenous RNA Networks.

Bosia C, Pagnani A, Zecchina R.

PLoS One. 2013 Jun 26;8(6):e66609. doi: 10.1371/journal.pone.0066609. Print 2013.

18.

Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments.

Ala U, Karreth FA, Bosia C, Pagnani A, Taulli R, Léopold V, Tay Y, Provero P, Zecchina R, Pandolfi PP.

Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):7154-9. doi: 10.1073/pnas.1222509110. Epub 2013 Mar 27.

19.

Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem.

Tuncbag N, Braunstein A, Pagnani A, Huang SS, Chayes J, Borgs C, Zecchina R, Fraenkel E.

J Comput Biol. 2013 Feb;20(2):124-36. doi: 10.1089/cmb.2012.0092.

20.

Performance of a cavity-method-based algorithm for the prize-collecting Steiner tree problem on graphs.

Biazzo I, Braunstein A, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Aug;86(2 Pt 2):026706. Epub 2012 Aug 13.

PMID:
23005881
21.

Cavity approach to sphere packing in Hamming space.

Ramezanpour A, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Feb;85(2 Pt 1):021106. Epub 2012 Feb 6.

PMID:
22463152
22.

Efficient data compression from statistical physics of codes over finite fields.

Braunstein A, Kayhan F, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Nov;84(5 Pt 1):051111. Epub 2011 Nov 14.

PMID:
22181373
23.

Protein 3D structure computed from evolutionary sequence variation.

Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C.

PLoS One. 2011;6(12):e28766. doi: 10.1371/journal.pone.0028766. Epub 2011 Dec 7.

24.

Direct-coupling analysis of residue coevolution captures native contacts across many protein families.

Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M.

Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):E1293-301. doi: 10.1073/pnas.1111471108. Epub 2011 Nov 21.

25.

Inference and learning in sparse systems with multiple states.

Braunstein A, Ramezanpour A, Zecchina R, Zhang P.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 May;83(5 Pt 2):056114. Epub 2011 May 19.

PMID:
21728612
26.

Stochastic matching problem.

Altarelli F, Braunstein A, Ramezanpour A, Zecchina R.

Phys Rev Lett. 2011 May 13;106(19):190601. Epub 2011 May 9.

PMID:
21668134
27.

Finding undetected protein associations in cell signaling by belief propagation.

Bailly-Bechet M, Borgs C, Braunstein A, Chayes J, Dagkessamanskaia A, François JM, Zecchina R.

Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):882-7. doi: 10.1073/pnas.1004751108. Epub 2010 Dec 27.

28.

An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium.

Bailly-Bechet M, Benecke A, Hardt WD, Lanza V, Sturm A, Zecchina R.

J Math Biol. 2011 Oct;63(4):637-62. doi: 10.1007/s00285-010-0385-1. Epub 2010 Nov 24.

29.

Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach.

Bailly-Bechet M, Braunstein A, Pagnani A, Weigt M, Zecchina R.

BMC Bioinformatics. 2010 Jun 29;11:355. doi: 10.1186/1471-2105-11-355.

30.

Statistical mechanics of steiner trees.

Bayati M, Borgs C, Braunstein A, Chayes J, Ramezanpour A, Zecchina R.

Phys Rev Lett. 2008 Jul 18;101(3):037208. Epub 2008 Jul 18.

PMID:
18764290
31.

Entropy landscape and non-Gibbs solutions in constraint satisfaction problems.

Dall'Asta L, Ramezanpour A, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Mar;77(3 Pt 1):031118. Epub 2008 Mar 17.

PMID:
18517340
32.

Propagation of external regulation and asynchronous dynamics in random Boolean networks.

Mahmoudi H, Pagnani A, Weigt M, Zecchina R.

Chaos. 2007 Jun;17(2):026109.

PMID:
17614696
33.

Efficient supervised learning in networks with binary synapses.

Baldassi C, Braunstein A, Brunel N, Zecchina R.

Proc Natl Acad Sci U S A. 2007 Jun 26;104(26):11079-84. Epub 2007 Jun 20.

34.

Statistical mechanics of combinatorial auctions.

Galla T, Leone M, Marsili M, Sellitto M, Weigt M, Zecchina R.

Phys Rev Lett. 2006 Sep 22;97(12):128701. Epub 2006 Sep 20.

PMID:
17026006
35.

Learning by message passing in networks of discrete synapses.

Braunstein A, Zecchina R.

Phys Rev Lett. 2006 Jan 27;96(3):030201. Epub 2006 Jan 25.

PMID:
16486667
36.

Core percolation and onset of complexity in boolean networks.

Correale L, Leone M, Pagnani A, Weigt M, Zecchina R.

Phys Rev Lett. 2006 Jan 13;96(1):018101. Epub 2006 Jan 4.

PMID:
16486521
37.

Lossy data compression with random gates.

Ciliberti S, Mézard M, Zecchina R.

Phys Rev Lett. 2005 Jul 15;95(3):038701. Epub 2005 Jul 14.

PMID:
16090781
38.

Clustering of solutions in the random satisfiability problem.

Mézard M, Mora T, Zecchina R.

Phys Rev Lett. 2005 May 20;94(19):197205. Epub 2005 May 19.

PMID:
16090207
39.

Source coding by efficient selection of ground-state clusters.

Battaglia D, Braunstein A, Chavas J, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jul;72(1 Pt 2):015103. Epub 2005 Jul 18.

PMID:
16090025
40.

Minimizing energy below the glass thresholds.

Battaglia D, Kolár M, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Sep;70(3 Pt 2):036107. Epub 2004 Sep 15.

PMID:
15524587
41.

Polynomial iterative algorithms for coloring and analyzing random graphs.

Braunstein A, Mulet R, Pagnani A, Weigt M, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Sep;68(3 Pt 2):036702. Epub 2003 Sep 3.

PMID:
14524921
42.

Random K-satisfiability problem: from an analytic solution to an efficient algorithm.

Mézard M, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Nov;66(5 Pt 2):056126. Epub 2002 Nov 26.

PMID:
12513575
43.

Coloring random graphs.

Mulet R, Pagnani A, Weigt M, Zecchina R.

Phys Rev Lett. 2002 Dec 23;89(26):268701. Epub 2002 Dec 9.

PMID:
12484862
44.

Analytic and algorithmic solution of random satisfiability problems.

Mézard M, Parisi G, Zecchina R.

Science. 2002 Aug 2;297(5582):812-5. Epub 2002 Jun 27.

45.

Optimizing searches via rare events.

Montanari A, Zecchina R.

Phys Rev Lett. 2002 Apr 29;88(17):178701. Epub 2002 Apr 10.

PMID:
12005788
46.

Hiding solutions in random satisfiability problems: a statistical mechanics approach.

Barthel W, Hartmann AK, Leone M, Ricci-Tersenghi F, Weigt M, Zecchina R.

Phys Rev Lett. 2002 May 6;88(18):188701. Epub 2002 Apr 18.

PMID:
12005728
47.

Learning to coordinate in a complex and nonstationary world.

Marsili M, Mulet R, Ricci-Tersenghi F, Zecchina R.

Phys Rev Lett. 2001 Nov 12;87(20):208701. Epub 2001 Oct 24.

PMID:
11690517
48.

Exact solutions for diluted spin glasses and optimization problems.

Franz S, Leone M, Ricci-Tersenghi F, Zecchina R.

Phys Rev Lett. 2001 Sep 17;87(12):127209. Epub 2001 Aug 31.

PMID:
11580554
49.

Simplest random K-satisfiability problem.

Ricci-Tersenghi F, Weigt M, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Feb;63(2 Pt 2):026702. Epub 2001 Jan 23.

PMID:
11308607
50.

Glassy dynamics near zero temperature

Ricci-Tersenghi F, Zecchina R.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Dec;62(6 Pt A):R7567-70.

PMID:
11138102

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