Papers by Fabien Tarissan
We propose a method employing mathematical programming and global optimization techniques for sol... more We propose a method employing mathematical programming and global optimization techniques for solving inverse problems arising in biological regulatory network (BRN) reconstruction. This problem consists in estimating unknown parameters of a model that describe the structure and dynamics of a biological system from a set of experimental observations and can be naturally cast as an optimization problem: choose the parameter values minimizing a given distance between the observed and estimated values of some observable variables. This minimization is subject to constraints derived from the models.
We propose a method employing mathematical programming and global optimization techniques for sol... more We propose a method employing mathematical programming and global optimization techniques for solving inverse problems arising in biological regulatory network (BRN) reconstruction. This problem consists in estimating unknown parameters of a model that describe the structure and dynamics of a biological system from a set of experimental observations and can be naturally cast as an optimization problem: choose the parameter values minimizing a given distance between the observed and estimated values of some observable variables. This minimization is subject to constraints derived from the models.
Emergence, Complexity and Computation, 2015
Cologne Twente Workshop on Graphs and Combinatorical Optimization, 2009
This paper employs mathematical programming and mixed integer linear programming techniques for s... more This paper employs mathematical programming and mixed integer linear programming techniques for solving a problem arising in the study of genetic regulatory networks. More precisely, we solve the inverse problem consisting in the determination of the arc weights in the digraph representing the network in such a way that the number of fixed points is minimized.
We propose a method employing mathematical programming and global optimization techniques for sol... more We propose a method employing mathematical programming and global optimization techniques for solving inverse problems arising in biological regulatory network (BRN) reconstruction. This problem consists in esti- mating unknown parameters of a model that describe the structure and dynamics of a biological system from a set of experimental observations and can be naturally cast as an optimization problem: choose the
The Cologne-Twente Workshop (CTW) on Graphs and Combinatorial Optimization started off as a serie... more The Cologne-Twente Workshop (CTW) on Graphs and Combinatorial Optimization started off as a series of workshops organized bi-annually by either Köln University or Twente University. As its importance grew over time, it re-centered its geographical focus by including northern Italy (CTW04 in Menaggio, on the lake Como and CTW08 in Gargnano, on the Garda lake). This year, CTW (in its eighth edition) will be staged in France for the first time: more precisely in the heart of Paris, at the Conservatoire National d’Arts et Métiers (CNAM), between 2nd and 4th June 2009, by a mixed organizing committee with members from LIX, École Polytechnique and CEDRIC, CNAM. As tradition warrants, a special issue of Discrete Applied Mathematics (DAM) will be devoted to CTW09, containing full-length versions of selected presentations given at the workshop and possibly other contributions related to the workshop topics. The deadline for submission to this issue will be posted in due time on the
We propose a method employing mathematical programming and global optimization techniques for sol... more We propose a method employing mathematical programming and global optimization techniques for solving inverse problems arising in biological regulatory network (BRN) reconstruction. This problem consists in estimating unknown parameters of a model that describe the structure and dynamics of a biological system from a set of experimental observations and can be naturally cast as an optimization problem: choose the parameter values minimizing a given distance between the observed and estimated values of some observable variables. This minimization is subject to constraints derived from the models. Two significant examples are presented on how to handle different kinds of dynamics: pattern formation occurring from diffusable and nondiffusable gene products in the drosophila melanogaster morphogenesis and reconstruction of the gene regulatory network of arabidospsis thaliana based on the identification of stable sub-networks during morphogenesis. 1
Understanding the spread of information on complex networks is a key issue from a theoretical and... more Understanding the spread of information on complex networks is a key issue from a theoretical and applied perspective. Despite the large effort in developing models for this phenomenon, gauging them with large-scale real-world data remains an important obstacle in the field. In this work we assess the relevance of the classic SIR model to capture key properties of spreading phenomena in real communication networks. We use a real file spreading trace in a P2P network to calibrate the model and to simulate similar diffusions. Comparing spreading cascades of real and simulated traces we observe sharp topological differences and conclude that this model fail to mimic key properties of such cascades.
Analysis of real datasets to characterize the local stability properties of the Internet routing ... more Analysis of real datasets to characterize the local stability properties of the Internet routing paths suggests that extending the route selection criteria to account for such property would not increase the routing path length. Nevertheless, even if selecting a more stable routing path could be considered as valuable from a routing perspective, it does not necessarily imply that the associated forwarding path would be more stable. Hence, if the dynamics of the Internet routing and forwarding system show different properties, then one can not straightforwardly derive the one from the other. If this assumption is verified, then the relationship between the stability of the forwarding path (followed by the traffic) and the corresponding routing path as selected by the path-vector routing algorithm requires further characterization. For this purpose, we locally relate, i.e., at the router level, the stability properties of routing path with the corresponding forwarding path. The propos...
Emergence, Complexity and Computation, 2014
2012 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, 2012
Understanding the spread of information on complex networks is a key issue from a theoretical and... more Understanding the spread of information on complex networks is a key issue from a theoretical and applied perspective. Despite the effort in developing theoretical models for this phenomenon, gauging them with large-scale real-world data remains an important challenge due to the scarcity of open, extensive and detailed data. In this paper, we explain how traces of peer-to-peer file sharing may be used to this goal. We also perform simulations to assess the relevance of the standard SIR model to mimic key properties of spreading cascade. We examine the impact of the network topology on observed properties and finally turn to the evaluation of two heterogeneous versions of the SIR model. We conclude that all the models tested failed to reproduce key properties of such cascades: typically real spreading cascades are relatively "elongated" compared to simulated ones. We have also observed some interesting similarities common to all SIR models tested.
2014 IEEE 22nd International Symposium on Modelling, Analysis & Simulation of Computer and Telecommunication Systems, 2014
ABSTRACT The classical approach for Internet topology measurement consists in distributively coll... more ABSTRACT The classical approach for Internet topology measurement consists in distributively collecting as much data as possible and merging it into one single piece of topology on which are conducted subsequent analysis. Although this approach may seem reasonable, in most cases network measurements performed in this way suffer from some or all of the following limitations: they give only partial views of the networks under concern, these views may be intrinsically biased, and they contain erroneous data due to the measurement tools. Here we present a new tool, named UDP Ping , that relies on a very different approach for the measurement of the Internet topology. Its basic principle is to measure the interface of a given target directed toward a monitor which sends the measurement probe. We demonstrate how to use it to deploy real world-wide measurements that provide reliable (i.e. bias and error free) knowledge of the Internet topology, namely the degree distribution of routers in the core Internet in our example.
2014 IFIP Networking Conference, 2014
ABSTRACT Most current models of the internet rely on knowledge of the degree distribution of its ... more ABSTRACT Most current models of the internet rely on knowledge of the degree distribution of its core routers, which plays a key role for simulation purposes. In practice, this distribution is usually observed directly on maps known to be partial, biased and erroneous. This raises serious concerns on the true knowledge one may have of this key property. Here, we design an original measurement approach targeting reliable estimation of the degree distribution of core routers, without resorting to any map. It consists in sampling random core routers and precisely estimate their degree thanks to probes sent from many distributed monitors. We run and assess a large-scale measurement following this approach, carefully controlling and correcting bias and errors encountered in practice. The estimate we obtain is much more reliable than previous knowledge, and it shows that the true degree distribution is very different from all current assumptions.
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Papers by Fabien Tarissan