LIPIcs, Volume 274, ESA 2023, Complete Volume

LIPIcs, Volume 274, ESA 2023, Complete Volum

LIPIcs, Volume 258, SoCG 2023, Complete Volume

LIPIcs, Volume 258, SoCG 2023, Complete Volum

Analyse des graphes de reactions biochimiques avec une application au réseau metabolique de la cellule de plante

Nowadays, systems biology are facing the challenges of analysing the huge amount of biological data and large-scale metabolic networks. Although several methods have been developed in recent years to solve this problem, it is existing hardness in studying these data and interpreting the obtained results comprehensively. This thesis focuses on analysis of structural properties, computation of elementary flux modes and determination of minimal cut sets of the heterotrophic plant cellmetabolic network. In our research, we have collaborated with biologists to reconstructa mid-size metabolic network of this heterotrophic plant cell. This network contains about 90 nodes and 150 edges. First step, we have done the analysis of structural properties by using graph theory measures, with the aim of finding its owned organisation. The central points orhub reactions found in this step do not explain clearly the network structure. The small-world or scale-free attributes have been investigated, but they do not give more useful information. In the second step, one of the promising analysis methods, named elementary flux modes, givesa large number of solutions, around hundreds of thousands of feasible metabolic pathways that is difficult to handle them manually. In the third step, minimal cut sets computation, a dual approach of elementary flux modes, has been used to enumerate all minimal and unique sets of reactions stopping the feasible pathways found in the previous step. The number of minimal cut sets has a decreasing trend in large-scale networks in the case of growing the network size. We have also combined elementary flux modes analysis and minimal cut sets computation to find the relationship among the two sets of results. The findings reveal the importance of minimal cut sets in use of seeking the hierarchical structure of this network through elementary flux modes. We have set up the circumstance that what will be happened if glucose entry is absent. Bi analysis of small minimal cut sets we have been able to found set of reactions which has to be present to produce the different sugars or metabolites of interest in absence of glucose entry. Minimal cut sets of size 2 have been used to identify 8 reactions which play the role of the skeleton/core of our network. In addition to these first results, by using minimal cut sets of size 3, we have pointed out five reactions as the starting point of creating a new branch in creationof feasible pathways. These 13 reactions create a hierarchical classification of elementary flux modes set. It helps us understanding more clearly the production of metabolites of interest inside the plant cell metabolism.Aujourd’hui, la biologie des systèmes est confrontée aux défis de l’analyse de l’énorme quantité de données biologiques et à la taille des réseaux métaboliques pour des analyses à grande échelle. Bien que plusieurs méthodes aient été développées au cours des dernières années pour résoudre ce problème, ce sujet reste un domaine de recherche en plein essor. Cette thèse se concentre sur l’analyse des propriétés structurales, le calcul des modes élémentaires de flux et la détermination d’ensembles de coupe minimales du graphe formé par ces réseaux. Dans notre recherche, nous avons collaboré avec des biologistes pour reconstruire un réseau métabolique de taille moyenne du métabolisme cellulaire de la plante, environ 90 noeuds et 150 arêtes. En premier lieu, nous avons fait l’analyse des propriétés structurelles du réseau dans le but de trouver son organisation. Les réactions points centraux de ce réseau trouvés dans cette étape n’expliquent pas clairement la structure du réseau. Les mesures classiques de propriétés des graphes ne donnent pas plus d’informations utiles. En deuxième lieu, nous avons calculé les modes élémentaires de flux qui permettent de trouver les chemins uniques et minimaux dans un réseau métabolique, cette méthode donne un grand nombre de solutions, autour des centaines de milliers de voies métaboliques possibles qu’il est difficile de gérer manuellement. Enfin, les coupes minimales de graphe, ont été utilisés pour énumérer tous les ensembles minimaux et uniques des réactions qui stoppent les voies possibles trouvées à la précédente étape. Le nombre de coupes minimales a une tendance à ne pas croître exponentiellement avec la taille du réseau a contrario des modes élémentaires de flux. Nous avons combiné l’analyse de ces modes et les ensembles de coupe pour améliorer l’analyse du réseau. Les résultats montrent l’importance d’ensembles de coupe pour la recherche de la structure hiérarchique du réseau à travers modes de flux élémentaires. Nous avons étudié un cas particulier : qu’arrive-t-il si on stoppe l’entrée de glucose ? En utilisant les coupes minimales de taille deux, huit réactions ont toujours été trouvés dans les modes élémentaires qui permettent la production des différents sucres et métabolites d’intérêt au cas où le glucose est arrêté. Ces huit réactions jouent le rôle du squelette / coeur de notre réseau. En élargissant notre analyse aux coupes minimales de taille 3, nous avons identifié cinq réactions comme point de branchement entre différent modes. Ces 13 réactions créent une classification hiérarchique des modes de flux élémentaires fixés et nous ont permis de réduire considérablement le nombre de cas à étudier (approximativement divisé par 10) dans l’analyse des chemins réalisables dans le réseau métabolique. La combinaison de ces deux outils nous a permis d’approcher plus efficacement l’étude de la production des différents métabolites d’intérêt par la cellule de plante hétérotrophique

Approximation Algorithms for Geometric Clustering and Touring Problems

Clustering and touring are two fundamental topics in optimization that have been studied extensively and have ``launched a thousand ships''. In this thesis, we study variants of these problems for Euclidean instances, in which clusters often correspond to sensors that are required to cover, measure or localize targets and tours need to visit locations for the purpose of item delivery or data collection. In the first part of the thesis, we focus on the task of sensor placement for environments in which localization is a necessity and in which its quality depends on the relative angle between the target and the pair of sensors observing it. We formulate a new coverage constraint that bounds this angle and consider the problem of placing a small number of sensors that satisfy it in addition to classical ones such as proximity and line-of-sight visibility. We present a general framework that chooses a small number of sensors and approximates the coverage constraint to arbitrary precision. In the second part of the thesis, we consider the task of collecting data from a set of sensors by getting close to them. This corresponds to a well-known generalization of the Traveling Salesman Problem (TSP) called TSP with Neighborhoods, in which we want to compute a shortest tour that visits at least one point from each unit disk centered at a sensor. One approach is based on an observation that relates the optimal solution with the optimal TSP on the sensors. We show that the associated bound can be improved unless we are in certain exceptional circumstances for which we can get better algorithms. Finally, we discuss Maximum Scatter TSP, which asks for a tour that maximizes the length of the shortest edge. While the Euclidean version admits an efficient approximation scheme and the problem is known to be NP-hard in three dimensions or higher, the question of getting a polynomial time algorithm for two dimensions remains open. To this end, we develop a general technique for the case of points concentrated around the boundary of a circle that we believe can be extended to more general cases

LIPIcs, Volume 261, ICALP 2023, Complete Volume

LIPIcs, Volume 261, ICALP 2023, Complete Volum

Fuzzy Techniques for Decision Making 2018

Zadeh's fuzzy set theory incorporates the impreciseness of data and evaluations, by imputting the degrees by which each object belongs to a set. Its success fostered theories that codify the subjectivity, uncertainty, imprecision, or roughness of the evaluations. Their rationale is to produce new flexible methodologies in order to model a variety of concrete decision problems more realistically. This Special Issue garners contributions addressing novel tools, techniques and methodologies for decision making (inclusive of both individual and group, single- or multi-criteria decision making) in the context of these theories. It contains 38 research articles that contribute to a variety of setups that combine fuzziness, hesitancy, roughness, covering sets, and linguistic approaches. Their ranges vary from fundamental or technical to applied approaches