Operations research: from computational biology to sensor network

In this dissertation we discuss the deployment of combinatorial optimization methods for modeling and solve real life problemS, with a particular emphasis to two biological problems arising from a common scenario: the reconstruction of the three-dimensional shape of a biological molecule from Nuclear Magnetic Resonance (NMR) data. The fi rst topic is the 3D assignment pathway problem (APP) for a RNA molecule. We prove that APP is NP-hard, and show a formulation of it based on edge-colored graphs. Taking into account that interactions between consecutive nuclei in the NMR spectrum are diff erent according to the type of residue along the RNA chain, each color in the graph represents a type of interaction. Thus, we can represent the sequence of interactions as the problem of fi nding a longest (hamiltonian) path whose edges follow a given order of colors (i.e., the orderly colored longest path). We introduce three alternative IP formulations of APP obtained with a max flow problem on a directed graph with packing constraints over the partitions, which have been compared among themselves. Since the last two models work on cyclic graphs, for them we proposed an algorithm based on the solution of their relaxation combined with the separation of cycle inequalities in a Branch & Cut scheme. The second topic is the discretizable distance geometry problem (DDGP), which is a formulation on discrete search space of the well-known distance geometry problem (DGP). The DGP consists in seeking the embedding in the space of a undirected graph, given a set of Euclidean distances between certain pairs of vertices. DGP has two important applications: (i) fi nding the three dimensional conformation of a molecule from a subset of interatomic distances, called Molecular Distance Geometry Problem, and (ii) the Sensor Network Localization Problem. We describe a Branch & Prune (BP) algorithm tailored for this problem, and two versions of it solving the DDGP both in protein modeling and in sensor networks localization frameworks. BP is an exact and exhaustive combinatorial algorithm that examines all the valid embeddings of a given weighted graph G=(V,E,d), under the hypothesis of existence of a given order on V. By comparing the two version of BP to well-known algorithms we are able to prove the e fficiency of BP in both contexts, provided that the order imposed on V is maintained

Distances and Domination in Graphs

This book presents a compendium of the 10 articles published in the recent Special Issue “Distance and Domination in Graphs”. The works appearing herein deal with several topics on graph theory that relate to the metric and dominating properties of graphs. The topics of the gathered publications deal with some new open lines of investigations that cover not only graphs, but also digraphs. Different variations in dominating sets or resolving sets are appearing, and a review on some networks’ curvatures is also present

The bidimensionality theory and its algorithmic applications

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mathematics, 2005.Includes bibliographical references (p. 201-219).Our newly developing theory of bidimensional graph problems provides general techniques for designing efficient fixed-parameter algorithms and approximation algorithms for NP- hard graph problems in broad classes of graphs. This theory applies to graph problems that are bidimensional in the sense that (1) the solution value for the k x k grid graph (and similar graphs) grows with k, typically as Q(k²), and (2) the solution value goes down when contracting edges and optionally when deleting edges. Examples of such problems include feedback vertex set, vertex cover, minimum maximal matching, face cover, a series of vertex- removal parameters, dominating set, edge dominating set, r-dominating set, connected dominating set, connected edge dominating set, connected r-dominating set, and unweighted TSP tour (a walk in the graph visiting all vertices). Bidimensional problems have many structural properties; for example, any graph embeddable in a surface of bounded genus has treewidth bounded above by the square root of the problem's solution value. These properties lead to efficient-often subexponential-fixed-parameter algorithms, as well as polynomial-time approximation schemes, for many minor-closed graph classes. One type of minor-closed graph class of particular relevance has bounded local treewidth, in the sense that the treewidth of a graph is bounded above in terms of the diameter; indeed, we show that such a bound is always at most linear. The bidimensionality theory unifies and improves several previous results.(cont.) The theory is based on algorithmic and combinatorial extensions to parts of the Robertson-Seymour Graph Minor Theory, in particular initiating a parallel theory of graph contractions. The foundation of this work is the topological theory of drawings of graphs on surfaces and our results regarding the relation (the linearity) of the size of the largest grid minor in terms of treewidth in bounded-genus graphs and more generally in graphs excluding a fixed graph H as a minor. In this thesis, we also develop the algorithmic theory of vertex separators, and its relation to the embeddings of certain metric spaces. Unlike in the edge case, we show that embeddings into L₁ (and even Euclidean embeddings) are insufficient, but that the additional structure provided by many embedding theorems does suffice for our purposes. We obtain an O[sq. root( log n)] approximation for min-ratio vertex cuts in general graphs, based on a new semidefinite relaxation of the problem, and a tight analysis of the integrality gap which is shown to be [theta][sq. root(log n)]. We also prove various approximate max-flow/min-vertex- cut theorems, which in particular give a constant-factor approximation for min-ratio vertex cuts in any excluded-minor family of graphs. Previously, this was known only for planar graphs, and for general excluded-minor families the best-known ratio was O(log n). These results have a number of applications. We exhibit an O[sq. root (log n)] pseudo-approximation for finding balanced vertex separators in general graphs.(cont.) Furthermore, we obtain improved approximation ratios for treewidth: In any graph of treewidth k, we show how to find a tree decomposition of width at most O(k[sq. root(log k)]), whereas previous algorithms yielded O(k log k). For graphs excluding a fixed graph as a minor, we give a constant-factor approximation for the treewidth; this via the bidimensionality theory can be used to obtain the first polynomial-time approximation schemes for problems like minimum feedback vertex set and minimum connected dominating set in such graphs.by MohammadTaghi Hajiaghayi.Ph.D

Symmetry in Graph Theory

This book contains the successful invited submissions to a Special Issue of Symmetry on the subject of ""Graph Theory"". Although symmetry has always played an important role in Graph Theory, in recent years, this role has increased significantly in several branches of this field, including but not limited to Gromov hyperbolic graphs, the metric dimension of graphs, domination theory, and topological indices. This Special Issue includes contributions addressing new results on these topics, both from a theoretical and an applied point of view

Mining and Managing User-Generated Content and Preferences

Ιn this thesis, we present techniques to manage the results of expressive queries, such as skyline, and mine online content that has been generated by users. Given the numerous scenarios and applications where content mining can be applied, we focus, in particular, to two cases: review mining and social media analysis. More specifically, we focus on preference queries, where users can query a set of items, each associated with an attribute set. For each of the attributes, users can specify their preference on whether to minimize or maximize it, e.g., "minimize price", "maximize performance", etc. Such queries are also know as "pareto optimal", or "skyline queries". A drawback of this query type is that the result may become too large for the user to inspect manually. We propose an approach that addresses this issue, by selecting a set of diverse skyline results. We provide a formal definition of skyline diversification and present efficient techniques to return such a set of points. The result can then be ranked according to established quality criteria. We also propose an alternative scheme for ranking skyline results, following an information retrieval approach

Congress UPV Proceedings of the 21ST International Conference on Science and Technology Indicators

This is the book of proceedings of the 21st Science and Technology Indicators Conference that took place in València (Spain) from 14th to 16th of September 2016. The conference theme for this year, ‘Peripheries, frontiers and beyond’ aimed to study the development and use of Science, Technology and Innovation indicators in spaces that have not been the focus of current indicator development, for example, in the Global South, or the Social Sciences and Humanities. The exploration to the margins and beyond proposed by the theme has brought to the STI Conference an interesting array of new contributors from a variety of fields and geographies. This year’s conference had a record 382 registered participants from 40 different countries, including 23 European, 9 American, 4 Asia-Pacific, 4 Africa and Near East. About 26% of participants came from outside of Europe. There were also many participants (17%) from organisations outside academia including governments (8%), businesses (5%), foundations (2%) and international organisations (2%). This is particularly important in a field that is practice-oriented. The chapters of the proceedings attest to the breadth of issues discussed. Infrastructure, benchmarking and use of innovation indicators, societal impact and mission oriented-research, mobility and careers, social sciences and the humanities, participation and culture, gender, and altmetrics, among others. We hope that the diversity of this Conference has fostered productive dialogues and synergistic ideas and made a contribution, small as it may be, to the development and use of indicators that, being more inclusive, will foster a more inclusive and fair world

Proceedings of the International Congress on Interdisciplinarity in Social and Human Sciences

Interdisciplinarity is the main topic and the main goal of this conference. Since the sixteen century with the creation of the first Academy of Sciences, in Napoles (Italy) (1568), and before that with the creation of the Fine Arts Academies, the world of science and arts began to work independently, on the contrary of the Academy of Plato, in Classical Antiquity, where science, art and sport went interconnected. Over time, specific sciences began to be independent, and the specificity of sciences caused an increased difficulty in mutual understanding. The same trend has affected the Human and Social Sciences. Each of the specific sciences gave rise to a wide range of particular fields. This has the advantage of allowing the deepening of specialised knowledge, but it means that there is often only a piecemeal approach of the research object, not taking into account the its overall complexity. So, it is important to work for a better understanding of the scientific phenomena with the complementarity of the different sciences, in an interdisciplinary perspective. With this growing specialisation of sciences, Interdisciplinarity acquired more relevance for scientists to find moreencompassing and useful answers for their research questions.info:eu-repo/semantics/publishedVersio