@article{Carpi2011,
author = {Carpi, L. and Rosso, OA and Saco, PM and Ravetti, M.G.},
title = {Analyzing complex networks evolution through Information Theory Quantifiers.},
journal = {Physics Letters A},
year = {2011},
volume = {375},
pages = {801--804},
doi = {10.1016/j.physleta.2010.12.038},
owner = {martin},
timestamp = {2010.12.16},
url = {http://dx.doi.org/10.1016/j.physleta.2010.12.038}
}
@article{carpi2013,
author = {Carpi, L and Saco, P and Rosso, O.A. and Ravetti , MG},
title = {Structural evolution of the Tropical Pacific climate network},
journal = {The European Physical Journal B},
year = {2013},
note = {Accepted for Publication},
owner = {martin},
timestamp = {2012.09.21}
}
@article{Mateus00_JoS,
author = {Mateus, Geraldo and Ravetti, MG and de Souza, Maur\'icio and Valeriano,
Ta\'is},
title = {Capacitated lot sizing and sequence dependent setup scheduling: an
iterative approach for integration},
journal = {Journal of Scheduling},
year = {2010},
volume = {13},
pages = {245-259},
note = {10.1007/s10951-009-0156-2},
affiliation = {Universidade Federal de Minas Gerais Departamento de Ci�ncia da Computa��o
31270-901 Belo Horizonte MG Brazil},
issn = {1094-6136},
issue = {3},
owner = {martin},
publisher = {Springer Netherlands},
url = {http://dx.doi.org/10.1007/s10951-009-0156-2}
}
@article{de_Paula_2009COR,
author = {de Paula, Mateus Rocha and Mateus, Geraldo Robson and Ravetti, MG},
title = {A Non-Delayed Relax-and-Cut Algorithm for Scheduling Problems with
Parallel Machines, Due Dates and Sequence-Dependent Setup Times},
journal = {Computers \& Operations Research},
year = {2009},
volume = {37},
pages = {938-949},
number = {5},
month = {May},
doi = {10.1016/j.cor.2009.07.006},
owner = {martin},
timestamp = {2009.07.22},
url = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VC5-4WY6K2S-1&_user=915767&_coverDate=08%2F07%2F2009&_rdoc=1&_fmt=high&_orig=browse&_srch=doc-info(%23toc%235945%239999%23999999999%2399999%23FLA%23display%23Articles)&_cdi=5945&_sort=d&_docanchor=&_ct=118&_acct=C000047922&_version=1&_urlVersion=0&_userid=915767&md5=21fce4ff481b28009114e1ef44a6ecae#FCANote}
}
@article{dePaula:2011,
author = {de Paula, Mateus Rocha and Ravetti, MG and Berretta, Regina and Moscato,
Pablo},
title = {Differences in abundances of cell-signalling proteins in blood reveal
novel biomarkers for early detection of clinical Alzheimer's disease},
journal = {PLoS One},
year = {2011},
note = {Accepted for publication},
owner = {martin},
timestamp = {2011.02.26}
}
@article{Paula2007,
author = {de Paula, Mateus Rocha and Ravetti, MG and Mateus, Geraldo Robson
and Pardalos, Panos M.},
title = {Solving parallel machines scheduling problems with sequence-dependent
setup times using variable neighbourhood search},
journal = {IMA J Management Math},
year = {2007},
volume = {18},
pages = {101--115},
number = {2},
abstract = {Variable neighbourhood search (VNS) is a modern metaheuristic based
on systematic changes of the neighbourhood structure within a search
to solve optimization problems. The aim of this paper is to propose
and analyse a VNS algorithm to solve scheduling problems with parallel
machines and sequence-dependent setup times, which are of great importance
on the industrial context. Three versions of a greedy randomized
adaptive search procedure algorithm are used to compare with the
proposed VNS algorithm to highlight its advantages in terms of generality,
quality and speed for large instances.},
date = {April 1, 2007},
owner = {martin},
timestamp = {2009.07.20},
url = {http://imaman.oxfordjournals.org/cgi/content/abstract/18/2/101}
}
@article{Ravetti2007b,
author = {Ravetti, MG and Geraldo R. Mateus and Pedro L. Rocha and Panos M.
Pardalos},
title = {A scheduling problem with unrelated parallel machines and sequence
dependent setups},
journal = {International Journal of Operational Research},
year = {2007},
volume = {2},
pages = {380 - 399},
number = {4},
doi = {10.1504/IJOR.2007.014169},
owner = {martin},
review = {This paper addresses a scheduling problem with unrelated parallel
machines, sequence dependent setups and due dates. The problem is
based on a real case and the objective is to minimise the sum of
the makespan and the weighted delays. A mixed integer linear programming
model is proposed and since the model considers realistic constraints,
a metaheuristic based on GRASP is used as a solution method. Several
versions of the metaheuristic are tested and multiple instances of
the problem with different configurations are generated to test the
solution quality and the computational performance.},
timestamp = {2009.07.20},
url = {http://inderscience.metapress.com/app/home/contribution.asp?referrer=parent&backto=issue,2,9;journal,18,24;linkingpublicationresults,1:119736,1}
}
@article{Ravetti2008,
author = {Ravetti, MG AND Moscato, Pablo},
title = {Identification of a 5-Protein Biomarker Molecular Signature for Predicting
Alzheimer's Disease},
journal = {PLoS One},
year = {2008},
volume = {3},
pages = {e3111},
number = {9},
abstract = { Background Alzheimer's disease (AD) is a progressive
brain disease with a huge cost to human lives. The impact of the
disease is also a growing concern for the governments of developing
countries, in particular due to the increasingly high number of elderly
citizens at risk. Alzheimer's is the most common form of dementia,
a common term for memory loss and other cognitive impairments. There
is no current cure for AD, but there are drug and non-drug based
approaches for its treatment. In general the drug-treatments are
directed at slowing the progression of symptoms. They have proved
to be effective in a large group of patients but success is directly
correlated with identifying the disease carriers at its early stages.
This justifies the need for timely and accurate forms of diagnosis
via molecular means. We report here a 5-protein biomarker molecular
signature that achieves, on average, a 96% total accuracy in predicting
clinical AD. The signature is composed of the abundances of IL-1α,
IL-3, EGF, TNF-α and G-CSF.
Methodology/Principal
Findings Our results are based on a recent molecular dataset
that has attracted worldwide attention. Our paper illustrates that
improved results can be obtained with the abundance of only five
proteins. Our methodology consisted of the application of an integrative
data analysis method. This four step process included: a) abundance
quantization, b) feature selection, c) literature analysis, d) selection
of a classifier algorithm which is independent of the feature selection
process. These steps were performed without using any sample of the
test datasets. For the first two steps, we used the application of
Fayyad and Irani's discretization algorithm for selection and quantization,
which in turn creates an instance of the (alpha-beta)-k-Feature Set
problem; a numerical solution of this problem led to the selection
of only 10 proteins.
Conclusions/Significance
the previous study has provided an extremely useful dataset for
the identification of AD biomarkers. However, our subsequent analysis
also revealed several important facts worth reporting:
1.
A 5-protein signature (which is a subset of the 18-protein signature
of Ray et al. ) has the same overall performance
(when using the same classifier).
2. Using more than 20 different
classifiers available in the widely-used Weka software package, our
5-protein signature has, on average, a smaller prediction error indicating
the independence of the classifier and the robustness of this set
of biomarkers (i.e. 96% accuracy when predicting AD against non-demented
control).
3. Using very simple classifiers, like Simple Logistic
or Logistic Model Trees, we have achieved the following results on
92 samples: 100 percent success to predict Alzheimer's Disease and
92 percent to predict Non Demented Control on the AD dataset.
},
doi = {10.1371/journal.pone.0003111},
publisher = {Public Library of Science},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0003111}
}
@article{ravetti2012,
author = {Ravetti, Martín and Riveros, Carlos and Mendes, Alexandre and Resende,
Mauricio and Pardalos, Panos},
title = {Parallel hybrid heuristics for the permutation flow shop problem},
journal = {Annals of Operations Research},
year = {2012},
volume = {199},
pages = {269--284},
note = {10.1007/s10479-011-1056-3},
affiliation = {Departamento de Engenharia de Produção, Universidade Federal de Minas
Gerais (UFMG), Av. Antonio Carlos, 6627 Belo Horizonte, Brazil},
issn = {0254-5330},
issue = {1},
keyword = {Business and Economics},
publisher = {Springer Netherlands},
url = {http://dx.doi.org/10.1007/s10479-011-1056-3}
}
@article{Ravetti2010,
author = {Ravetti, MG and Rosso, Osvaldo A. and Berretta, Regina and Moscato,
Pablo},
title = {Uncovering Molecular Biomarkers That Correlate Cognitive Decline
with the Changes of Hippocampus' Gene Expression Profiles in Alzheimer's
Disease.},
journal = {Plos One},
year = {2010},
volume = {5},
pages = {e10153},
owner = {martin},
timestamp = {2010.12.16}
}
@article{Rocha2008,
author = {Pedro Leite Rocha and Ravetti, MG and Geraldo Robson Mateus and Panos
M. Pardalos},
title = {Exact algorithms for a scheduling problem with unrelated parallel
machines and sequence and machine-dependent setup times},
journal = {Computers \& Operations Research},
year = {2008},
volume = {35},
pages = {1250 - 1264},
number = {4},
abstract = {A scheduling problem with unrelated parallel machines, sequence and
machine-dependent setup times, due dates and weighted jobs is considered
in this work. A branch-and-bound algorithm (B&B) is developed and
a solution provided by the metaheuristic GRASP is used as an upper
bound. We also propose a set of instances for this type of problem.
The results are compared to the solutions provided by two mixed integer
programming models (MIP) with the solver CPLEX 9.0. We carry out
computational experiments and the algorithm performs extremely well
on instances with up to 30 jobs.},
doi = {DOI: 10.1016/j.cor.2006.07.015},
issn = {0305-0548},
url = {http://www.sciencedirect.com/science/article/B6VC5-4KSVGB9-1/2/7e608c81a94c4ad16d9162422e6df8dd}
}
@article{Rosso2013,
author = {Osvaldo A. Rosso and Laura C. Carpi and Patricia M. Saco and Martin
Gomez Ravetti and Angelo Plastino and Hilda A. Larrondo},
title = {The Amigo paradigm of forbidden/missing patterns: a detailed analysis},
journal = {The European Physical Journal B},
year = {2013},
note = {Accepted for Publication}
}
@article{Rosso2012,
author = {Osvaldo A. Rosso and Laura C. Carpi and Patricia M. Saco and Martín
Gómez Ravetti and Angelo Plastino and Hilda A. Larrondo},
title = {Causality and the entropy–complexity plane: Robustness and missing
ordinal patterns},
journal = {Physica A: Statistical Mechanics and its Applications},
year = {2012},
volume = {391},
pages = {42--55},
number = {1–2},
doi = {10.1016/j.physa.2011.07.030},
issn = {0378-4371},
keywords = {Time series analysis},
owner = {martin},
timestamp = {2012.09.21},
url = {http://www.sciencedirect.com/science/article/pii/S0378437111005772}
}
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