Papers by Philippe Vismara
Discrete Mathematical Chemistry
The design of a synthesis strategy in Organic Chemistry rests on the perception of the target mol... more The design of a synthesis strategy in Organic Chemistry rests on the perception of the target molecule. This one has to be perceived from several viewpoints: topology, stereochemistry, functionality... We propose an abstract representation of molecules which describes the topological viewpoint (cycles, carbon chains and their structural relationships). This representation is based on a polynomial algorithm that computes the set of relevant cycles in the molecular graph. This set is equal to the union of all the minimum cycle bases of the graph. The abstract representation is integrated in RESYN, a system for computer-aided organic synthesis planning.

Lecture Notes in Computer Science
Routing problems appear in many practical applications. In the context of Constraint Programming,... more Routing problems appear in many practical applications. In the context of Constraint Programming, circuit constraints have been successfully developed to handle problems like the well-known Traveling Salesman Problem or the Vehicle Routing Problem. These kind of constraints are linked to the search for a Hamiltonian circuit in a graph. In this paper we consider a more general multiple tour problem that consists in covering a part of the graph with a set of minimal cost circuits. We define a new global constraint WeightedSubCircuits that generalizes the WeightedCircuit constraint by releasing the need to obtain a Hamiltonian circuit. It enforces multiple disjoint circuits of bounded total cost to partially cover a weighted graph, the subsets of vertices to be covered being induced by external constraints. We show that enforcing Bounds Consistency for WeightedSubCircuits is NP-hard. We propose an incomplete but polynomial filtering method based on the search for a lower bound of a weighted Steiner circuit.
Constrained optimization of landscape indices in conservation planning to support ecological restoration in New Caledonia
Journal of Applied Ecology

OENO One
Aim: This short communication aims at providing insights to verify whether common yield sampling ... more Aim: This short communication aims at providing insights to verify whether common yield sampling protocols (i.e., one round trip within the fields over two representative rows) are optimal whatever the considered fields. In addition, it aims to show how factors like the spatial organisation of the within-field yield variability, the length of the rows, the erratic variance, etc. may affect the optimal sampling route and the error of the yield estimation.Methods and Material: A new algorithm based on constraint programming and stochastic approaches was used to provide optimal sampling routes for vineyards. This algorithm guarantees the representativeness of the measurement sites and a minimization of the walking distance. Practical constraints (trellised structure, starting point, etc.) are considered by the algorithm to optimise the walking distance and the resulting sampling route. The algorithm has been applied to 60 simulated vineyards with known yield variability. Characteristic...
Journal of Chemical Information and Modeling, Feb 22, 2010
The formability of a bond in a target molecule is a bond property related to the problem of findi... more The formability of a bond in a target molecule is a bond property related to the problem of finding a reaction that synthesizes the target by forming the bond: the easier this problem, the higher the formability. Bond formability provides an interesting piece of information that might be used for selecting strategic bonds during a retrosynthesic analysis or for assessing synthetic accessibility in virtual screening. The article describes a graph-mining algorithm called GemsBond that evaluates formability of bonds by mining structural environments contained in several thousand molecular graphs of reaction products. When tested on reaction databases, GemsBond recognizes most formed bonds in reaction products and provides explanations consistent with knowledge in organic synthesis.
Q-Intersection Algorithms for Constraint-Based Robust Parameter Estimation
Twenty Eighth Aaai Conference on Artificial Intelligence, Jun 21, 2014
Appariements dirig�s pour le raisonnement par classification sur des hi�rarchies de graphes
Lmo, 1996

Constraints, 2015
Assemblage consists in blending base wines in order to create target wines. Recent developments i... more Assemblage consists in blending base wines in order to create target wines. Recent developments in aroma analysis allow us to measure chemical compounds impacting the taste of wines. This chemical analysis makes it possible to design a decision tool for the following problem: given a set of target wines, determine which volumes must be extracted from each base wine to produce wines that satisfy constraints on aroma concentration, volumes, alcohol contents and price. This paper describes the modeling of wine assemblage as a mixed constrained optimization problem, where the main goal is to minimize the gap to the desired concentrations for every aromatic criterion. The deterministic branch and bound solvers Couenne and IbexOpt behave well on the wine blending problem thanks to their interval constraint propagation/programming and polyhedral relaxation methods. We also study the performance of other optimization goals that could be embedded in a configuration tool, where the different possible interactions amount to solving the same constraints with different objective functions. We finally show on a recent generic wine blending instance that the proposed optimization process scales up well with the number of base wines.
Appariements dirigés pour le raisonnement par classification sur des hiérarchies de graphes
Langages et Modèles à Objets, 1996
A Constraint-Based Approach to the Differential Harvest Problem
Lecture Notes in Computer Science, 2015
Reconnaissance et repr esentation d'el ements structuraux pour la description d'objets complexes. Application al'elaboration de strat effigies de synth ese en …
lirmm.fr
... Je remercie Claude Lauren co qui a dirig e cette th ese dans le domaine de la chimie et m&... more ... Je remercie Claude Lauren co qui a dirig e cette th ese dans le domaine de la chimie et m'a appris tout ce que je sais en synth ese organique et beaucoup plus encore. Son soutien ... en utilisant le th eor eme de Menger (1926): ((un graphe est k-connexe si l'on peut Page 17. 10 ...

The Electronic Journal of Combinatorics, 1997
The perception of cyclic structures is a crucial step in the analysis of graphs. To describe the ... more The perception of cyclic structures is a crucial step in the analysis of graphs. To describe the cycle vector space of a graph, a minimum cycle basis can be computed in polynomial time using an algorithm of Horton, 1987]. But the set of cycles corresponding to a minimum basis is not always relevant for analyzing the cyclic structure of a graph. This restriction is due to the fact that a minimum cycle basis is generally not unique for a given graph. Therefore, the smallest canonical set of cycles which describes the cyclic structure of a graph is the union of all the minimum cycle bases. This set of cycles is called the set of relevant cycles and denoted by C R. A relevant cycle can also be de ned as a cycle which is not the sum of shorter cycles. A polynomial algorithm is presented that computes a compact representation of the potentially exponential-sized set C R in O(m 3) (where denotes the cyclomatic number). This compact representation consists of a polynomial number of relevant cycle prototypes from which all the relevant cycles can be listed in O(n jC R j). A polynomial method is also given that computes the number of relevant cycles without listing all of them.
Finding Maximum Common Connected Subgraphs Using Clique Detection or Constraint Satisfaction Algorithms
Communications in Computer and Information Science, 2008
This paper investigates the problem of Maximum Common Connected Subgraph (MCCS) which is not nece... more This paper investigates the problem of Maximum Common Connected Subgraph (MCCS) which is not necessarily an induced subgraph. This problem has so far been neglected by the literature which is mainly devoted to the MCIS problem. Two reductions of the MCCS problem to a MCCIS problem are explored: a classic method based on linegraphs and an original approach using subdivision

Breaking Variable Symmetry in Almost Injective Problems
Lecture Notes in Computer Science, 2012
ABSTRACT Lexicographic constraints are commonly used to break variable symmetries. In the general... more ABSTRACT Lexicographic constraints are commonly used to break variable symmetries. In the general case, the number of constraint to be posted is potentially exponential in the number of variables. For injective problems (AllDiff), Puget's method[12] breaks all variable symmetries with a linear number of constraints. In this paper we assess the number of constraints for "almost" injective problems. We propose to characterize them by a parameter μ based on Global Cardinality Constraint as a generalization of the AllDiff constraint. We show that for almost injective problems, variable symmetries can be broken with no more than $\binom{n}{\mu}$ constraints which is XP in the framework of parameterized complexity. When only ν variables can take duplicated values, the number of constraints is FPT in μ and ν.
Constrained Wine Blending
Lecture Notes in Computer Science, 2013
Journal of Chemical Information and Modeling, 2010
The formability of a bond in a target molecule is a bond property related to the problem of findi... more The formability of a bond in a target molecule is a bond property related to the problem of finding a reaction that synthesizes the target by forming the bond: the easier this problem, the higher the formability. Bond formability provides an interesting piece of information that might be used for selecting strategic bonds during a retrosynthesic analysis or for assessing synthetic accessibility in virtual screening. The article describes a graph-mining algorithm called GemsBond that evaluates formability of bonds by mining structural environments contained in several thousand molecular graphs of reaction products. When tested on reaction databases, GemsBond recognizes most formed bonds in reaction products and provides explanations consistent with knowledge in organic synthesis.

Journal of Chemical Information and Modeling, 2005
Whereas the potential symmetry of a molecule may be a feature of importance in synthesis design, ... more Whereas the potential symmetry of a molecule may be a feature of importance in synthesis design, this one is often difficult to detect visually in the structural formula. In the present article we describe an efficient algorithm for the perception of this molecular property. We have addressed this problem in terms of graph theory and defined it as the Maximum Symmetrical Split of a molecular graph. A solution is obtained by deleting in such a graph a minimum number of edges and vertices so that the resulting subgraph consists of exactly two isomorphic connected components that correspond to a pair of synthetically equivalent synthons. In view to reduce the search space of the problem, we have based our algorithm on CSP techniques. In this study we have found that the maximum symmetrical split is an original kind of Constraint Satisfaction Problem. The algorithm has been implemented into the RESYN_Assistant system and its performance has been tested on a set of varied molecules which were the targets of previously published synthetic studies. The results show that potential symmetry is perceived quickly and efficiently by the program. The graphical display of this perception information may help a chemist to design reflexive or highly convergent syntheses.
The Journal of Object Technology, 2012
Many design guidelines state that a software system architecture should avoid cycles between its ... more Many design guidelines state that a software system architecture should avoid cycles between its packages. Yet such cycles appear again and again in many programs. We believe that the existing approaches for cycle detection are too coarse to assist the developers to remove cycles from their programs. In this paper, we describe an efficient algorithm that performs a fine-grained analysis of the cycles among the packages of an application. In addition, we define a metric to rank cycles by their level of undesirability, prioritizing the cycles that seems the more undesired by the developers. Our approach is validated on two large and mature software systems in Java and Smalltalk.
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Papers by Philippe Vismara