Temporal graphs are graphs that evolve over time. Many problems which are polynomial-time solvable in standard graphs become NP -hard when appropriately defined in the realm of temporal graphs. This suggested the definition of several parameters for temporal graphs and to prove the fixed-parameter tractability of several problems with respect to these parameters. In this paper, we introduce a hierarchy of parameters based on the previously defined interval membership width and on the temporal evolution of the connected components of the underlying static graph. We then show that the Eulerian trail problem and the temporal 2-coloring problem are both fixed-parameter tractable (in short, FPT ) with respect to any of the parameters in the hierarchy. We also introduce a vertex-variant of the parameters and we show that the firefighter problem (which was known to be FPT with respect to the vertex-variant of the interval membership width) is also FPT with respect to one of the parameters in the second level of the hierarchy.

Abstract. A temporal graph is a graph whose edges appear only at certain points in time. Recently, the second and the last three authors proposed a natural temporal analog of the Erdős–Rényi random graph model. The proposed model is obtained by randomly permuting the edges of an Erdős–Rényi random graph and interpreting this permutation as an ordering of presence times. It was shown that the connectivity threshold in the Erdős–Rényi model fans out into multiple phase transitions for several distinct notions of reachability in the temporal setting. In the present paper, we identify a sharp threshold for the emergence of a giant temporally connected component. We show that at [Formula: see text] the size of the largest temporally connected component increases from [Formula: see text] to [Formula: see text]. This threshold holds for both open and closed connected components, i.e., components that allow (respectively, forbid) their connecting paths to use external nodes.

Bu{\ss} et al [KDD 2020] recently proved that the problem of computing the betweenness of all nodes of a temporal graph is computationally hard in the case of foremost and fastest paths, while it is solvable in time O(n 3 T 2 ) in the case of shortest and shortest foremost paths, where n is the number of nodes and T is the number of distinct time steps. A new algorithm for temporal betweenness computation is introduced in this paper. In the case of shortest and shortest foremost paths, it requires O(n + M ) space and runs in time where M is the number of temporal edges, thus significantly improving the algorithm of Bu{\ss} et al in terms of time complexity (note that T is usually large). Experimental evidence is provided that our algorithm performs between twice and almost 250 times better than the algorithm of Bu{\ss} et al. Moreover, we were able to compute the exact temporal betweenness values of several large temporal graphs with over a million of temporal edges. For such size, only approximate computation was possible by using the algorithm of Santoro and Sarpe [WWW 2022]. Maybe more importantly, our algorithm extends to the case of restless walks (that is, walks with waiting constraints in each node), thus providing a polynomial-time algorithm (with complexity O(nM )) for computing the temporal betweenness in the case of several different optimality criteria. Such restless computation was known only for the shortest criterion (Rymar et al [JGAA 2023]), with complexity O(n 2 M T 2 ). We performed an extensive experimental validation by comparing different waiting constraints and different optimisation criteria. Moreover, as a case study, we investigate six public transit networks including Berlin, Rome, and Paris. Overall we find a general consistency between the different variants of betweenness centrality. However, we do measure a sensible influence of waiting constraints, and note some cases of low correlation for certain pairs of criteria in some networks.

We consider the problem of assigning appearing times to the edges of a digraph in order to maximize the (average) temporal reachability between pairs of nodes. Motivated by the application to public transit networks, where edges cannot be scheduled independently one of another, we consider the setting where the edges are grouped into certain walks (called trips) in the digraph and where assigning the appearing time to the first edge of a trip forces the appearing times of the subsequent edges. In this setting, we show that, quite surprisingly, it is NP-complete to decide whether there exists an assignment of times connecting a given pair of nodes. This result allows us to prove that the problem of maximising the temporal reachability cannot be approximated within a factor better than some polynomial term in the size of the graph. We thus focus on the case where, for each pair of nodes, there exists an assignment of times such that one node is reachable from the other. We call this property strong temporalisability. It is a very natural assumption for the application to public transit networks. On the negative side, the problem of maximising the temporal reachability remains hard to approximate within a factor $\sqrt$ n/12 in that setting. Moreover, we show the existence of collections of trips that are strongly temporalisable but for which any assignment of starting times to the trips connects at most an O(1/ $\sqrt$ n) fraction of all pairs of nodes. On the positive side, we show that there must exist an assignment of times that connects a constant fraction of all pairs in the strongly temporalisable and symmetric case, that is, when the set of trips to be scheduled is such that, for each trip, there is a symmetric trip visiting the same nodes in reverse order. Keywords:edge labeling edge scheduled network network optimisation temporal graph temporal path temporal reachability time assignment

We revisit the planning problem in the blocks world, and we implement a known heuristic for this task. Importantly, our implementation is biologically plausible, in the sense that it is carried out exclusively through the spiking of neurons. Even though much has been accomplished in the blocks world over the past five decades, we believe that this is the first algorithm of its kind. The input is a sequence of symbols encoding an initial set of block stacks as well as a target set, and the output is a sequence of motion commands such as "put the top block in stack 1 on the table". The program is written in the Assembly Calculus, a recently proposed computational framework meant to model computation in the brain by bridging the gap between neural activity and cognitive function. Its elementary objects are assemblies of neurons (stable sets of neurons whose simultaneous firing signifies that the subject is thinking of an object, concept, word, etc.), its commands include project and merge, and its execution model is based on widely accepted tenets of neuroscience. A program in this framework essentially sets up a dynamical system of neurons and synapses that eventually, with high probability, accomplishes the task. The purpose of this work is to establish empirically that reasonably large programs in the Assembly Calculus can execute correctly and reliably; and that rather realistic --- if idealized --- higher cognitive functions, such as planning in the blocks world, can be implemented successfully by such programs.

A weighted link stream is a pair (V,𝔼) comprising V, the set of nodes, and 𝔼, the list of temporal edges (u,v,t,λ), where u,v are two nodes in V, t is the starting time of the temporal edge, and λ is its travel time. By making use of this model, different notions of diameter can be defined, which refer to the following distances: earliest arrival time, latest departure time, fastest time, and shortest time. After proving that any of these diameters cannot be computed in time sub-quadratic with respect to the number of temporal edges, we propose different algorithms (inspired by the approach used for computing the diameter of graphs) which allow us to compute, in practice very efficiently, the diameter of quite large real-world weighted link stream for several definitions of the diameter. Indeed, all the proposed algorithms require very often a very low number of single source (or target) best path computations. We verify the effectiveness of our approach by means of an extensive set of experiments on real-world link streams. We also experimentally prove that the temporal version of the well-known 2-sweep technique, for computing a lower bound on the diameter of a graph, is quite effective in the case of weighted link stream, by returning very often tight bounds.

Betweenness centrality is a graph parameter that has been successfully applied to network analysis. In the context of computer networks, it was considered for various objectives, ranging from routing to service placement. However, as observed by Maccari et al. [INFOCOM 2018], research on betweenness centrality for improving protocols was hampered by the lack of a usable, fully distributed algorithm for computing this parameter. We resolve this issue by designing an efficient algorithm for computing betweenness centrality, which can be implemented by minimal modifications to any distance-vector routing protocol based on Bellman-Ford. The convergence time of our implementation is shown to be proportional to the diameter of the network.

Temporal graphs are graphs in which arcs have temporal labels, specifying at which time they can be traversed. Motivated by recent results concerning the reliability analysis of a temporal graph through the enumeration of minimal cutsets in the corresponding line graph, in this paper we attack the problem of enumerating minimal s-d separators in s-d directed acyclic graphs (in short, s-d DAGs), also known as 2-terminal DAGs or s-t digraphs. Our main result is an algorithm for enumerating all the minimal s-d separators in a DAG with O(nm) delay, where n and m are respectively the number of nodes and arcs, and the delay is the time between the output of two consecutive solutions. To this aim, we give a characterization of the minimal s-d separators in a DAG through vertex cuts of an expanded version of the DAG itself. As a consequence of our main result, we provide an algorithm for enumerating all the minimal s-d cutsets in a temporal graph with delay O(m³), where m is the number of temporal arcs.

The study of interactive proofs in the context of distributed network computing is a novel topic, recently introduced by Kol, Oshman, and Saxena [PODC 2018]. In the spirit of sequential interactive proofs theory, we study the power of distributed interactive proofs. This is achieved via a series of results establishing trade-offs between various parameters impacting the power of interactive proofs, including the number of interactions, the certificate size, the communication complexity, and the form of randomness used. Our results also connect distributed interactive proofs with the established field of distributed verification. In general, our results contribute to providing structure to the landscape of distributed interactive proofs.

Given a connected graph G =( V , E ), where V denotes the set of nodes and E the set of edges of the graph, the length (that is, the number of edges) of the shortest path between two nodes v and w is denoted by d ( v , w ). The closeness centrality of a vertex v is then defined as n =1/Σ w ∈ V d ( v , w ), where n =| V |. This measure is widely used in the analysis of real-world complex networks, and the problem of selecting the k most central vertices has been deeply analyzed in the last decade. However, this problem is computationally not easy, especially for large networks: in the first part of the article, we prove that it is not solvable in time O (| E | 2=ϵ ) on directed graphs, for any constant ϵ > 0, under reasonable complexity assumptions. Furthermore, we propose a new algorithm for selecting the k most central nodes in a graph: we experimentally show that this algorithm improves significantly both the textbook algorithm, which is based on computing the distance between all pairs of vertices, and the state of the art. For example, we are able to compute the top k nodes in few dozens of seconds in real-world networks with millions of nodes and edges. Finally, as a case study, we compute the 10 most central actors in the Internet Movie Database (IMDB) collaboration network, where two actors are linked if they played together in a movie, and in the Wikipedia citation network, which contains a directed edge from a page p to a page q if p contains a link to q .

In recent years, researchers proposed several algorithms that compute metric quantities of real-world complex networks, and that are very efficient in practice, although there is no worst-case guarantee. In this work, we propose an axiomatic framework to analyze the performances of these algorithms, by proving that they are efficient on the class of graphs satisfying certain properties. Furthermore, we prove that these properties are verified asymptotically almost surely by several probabilistic models that generate power law random graphs, such as the Configuration Model, the Chung-Lu model, and the Norros-Reittu model. Thus, our results imply average-case analyses in these models. For example, in our framework, existing algorithms can compute the diameter and the radius of a graph in subquadratic time, and sometimes even in time n1+o(1). Moreover, in some regimes, it is possible to compute the k most central vertices according to closeness centrality in subquadratic time, and to design a distance oracle with sublinear query time and subquadratic space occupancy. In the worst case, it is impossible to obtain comparable results for any of these problems, unless widely- believed conjectures are false.

Centrality indices are widely used analytic measures for the importance of nodes in a network. Closeness centrality is very popular among these measures. For a single node v, it takes the sum of the distances of v to all other nodes into account. The currently best algorithms in practical applications for computing the closeness for all nodes exactly in unweighted graphs are based on breadth-first search (BFS) from every node. Thus, even for sparse graphs, these algorithms require quadratic running time in the worst case, which is prohibitive for large networks. In many relevant applications, however, it is unnecessary to compute closeness values for all nodes. Instead, one requires only the k nodes with the highest closeness values in descending order. Thus, we present a new algorithm for computing this top-k ranking in unweighted graphs. Following the rationale of previous work, our algorithm significantly reduces the number of traversed edges. It does so by computing upper bounds on the closeness and stopping the current BFS search when k nodes already have higher closeness than the bounds computed for the other nodes. In our experiments with real-world and synthetic instances of various types, one of these new bounds is good for small-world graphs with low diameter (such as social networks), while the other one excels for graphs with high diameter (such as road networks). Combining them yields an algorithm that is faster than the state of the art for top-k computations for all test instances, by a wide margin for high-diameter graphs. Finally, we prove that the quadratic worst-case complexity cannot be improved on directed, disconnected graphs, under reasonable complexity assumptions.

In this paper we analyse the core-periphery clustering properties of collaboration networks, where the core of a network is formed by the nodes with highest degree. In particular, we first observe that, even for random graph models aiming at matching the degree-distribution and/or the clustering coefficient of real networks, these models produce synthetic graphs which have a spatial distribution of the triangles with respect to the core and to the periphery which does not match the spatial distribution of the triangles in the real networks. We therefore propose a new model, called CPCL, whose aim is to distribute the triangles in a way fitting with their real core-periphery distribution, and thus producing graphs matching the core-periphery clustering of real networks.

The closeness centrality is a well-known measure of importance of a vertex within a given complex network. Having high closeness centrality can have positive impact on the vertex itself: hence, in this paper we consider the optimization problem of determining how much a vertex can increase its centrality by creating a limited amount of new edges incident to it. We will consider both the undirected and the directed graph cases. In both cases, we first prove that the optimization problem does not admit a polynomial-time approximation scheme (unless P = NP ), and then propose a greedy approximation algorithm (with an almost tight approximation ratio), whose performance is then tested on synthetic graphs and real-world networks.

Abstract Motivation: Completing the genome sequence of an organism is an important task in comparative, functional and structural genomics. However, this remains a challenging issue from both a computational and an experimental viewpoint. Genome scaffolding (i.e. the process of ordering and orientating contigs) of de novo assemblies usually represents the first step in most genome finishing pipelines. Results: In this article we present MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalizes the scaffolding problem by means of a combinatorial optimization formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries. This makes usability and running time two additional important features of our method. Moreover, benchmarks and tests on real bacterial datasets showed that MeDuSa is highly accurate and, in most cases, outperforms traditional scaffolders. The possibility to use MeDuSa on eukaryotic datasets has also been evaluated, leading to interesting results. Availability and implementation: MeDuSa web server: http://combo.dbe.unifi.it/medusa. A stand-alone version of the software can be downloaded from https://github.com/combogenomics/medusa/releases. All results presented in this work have been obtained with MeDuSa v. 1.3. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

MOTIVATION: The increasing availability of metabolomics data enables to better understand the metabolic processes involved in the immediate response of an organism to environmental changes and stress. The data usually come in the form of a list of metabolites whose concentrations significantly changed under some conditions, and are thus not easy to interpret without being able to precisely visualize how such metabolites are interconnected. RESULTS: We present a method that enables to organize the data from any metabolomics experiment into metabolic stories. Each story corresponds to a possible scenario explaining the flow of matter between the metabolites of interest. These scenarios may then be ranked in different ways depending on which interpretation one wishes to emphasize for the causal link between two affected metabolites: enzyme activation, enzyme inhibition or domino effect on the concentration changes of substrates and products. Equally probable stories under any selected ranking scheme can be further grouped into a single anthology that summarizes, in a unique subnetwork, all equivalently plausible alternative stories. An anthology is simply a union of such stories. We detail an application of the method to the response of yeast to cadmium exposure. We use this system as a proof of concept for our method, and we show that we are able to find a story that reproduces very well the current knowledge about the yeast response to cadmium. We further show that this response is mostly based on enzyme activation. We also provide a framework for exploring the alternative pathways or side effects this local response is expected to have in the rest of the network. We discuss several interpretations for the changes we see, and we suggest hypotheses that could in principle be experimentally tested. Noticeably, our method requires simple input data and could be used in a wide variety of applications. AVAILABILITY AND IMPLEMENTATION: The code for the method presented in this article is available at http://gobbolino.gforge.inria.fr.

NP-completeness is one of the most central concepts in computer science, and has been extensively applied in many diverse application areas. Despite this, students have problems grasping the concept and, more specifically, applying it to new problems. Independently, we have identified these problems at our universities in different countries and cultures. In an action research approach we have modified our courses and studied the effects. We here present some promising results. Our approach is mainly based on the idea of making more evident the fact that proving a new NP-completeness result is not at all different from designing a new algorithm. Based on this idea, we used tools typically used to teach algorithms (such as automatic program assessment and algorithm visualization systems), accompanied by other activities mainly devoted to augmenting the motivation to study computational complexity and forcing students to think and adopt a standpoint.

In this paper we describe how we tried to make the well-known JFLAP Turing machine simulator accessible to blind students taking a theoretical computer science course. Software accessibility is an important topic for both legal and ethical reasons: in our case, however, we also wanted to make the accessible software usable by blind students in cooperation with the other students, in order to encourage the integration of the blind students within the rest of the class. For this reason, the accessible version of the JFLAP Turing machine simulator that we developed is as much similar as possible to and fully compatible with the original one. In the paper, we also report some very satisfactory preliminary validation results that indicate how the new software can really make Turing machines accessible to blind students.

We argue that algorithm visualization techniques can be usefully applied to the teaching of NP-completeness results. On the ground of this opinion and of a quite positive preliminary student evaluation, we have thus included the visualization of four well-known NP-completeness proofs into the distribution of the AlViE algorithm visualization environment.

An edge-Markovian process with birth-rate p and death-rate q generates sequences of graphs (G0,G1,G2,…) with the same node set [n] such that Gt is obtained from Gt−1 as follows: if e ∉ E(Gt−1) then e ∈ E(Gt) with probability p, and if e ∈ E(Gt−1) then e ∉ E(Gt) with probability q. Clementi et al. (PODC 2008) analyzed thoroughly information dissemination in such dynamic graphs, by establishing bounds on their flooding time--flooding is the basic mechanism in which every node becoming aware of an information at step t forwards this information to all its neighbors at all forthcoming steps t∦ > t. In this paper, we establish tight bounds on the complexity of flooding for all possible birth rates and death rates, completing the previous results by Clementi et al. Moreover, we note that despite its many advantages in term of simplicity and robustness, flooding suffers from its high bandwidth consumption. Hence we also show that flooding in dynamic graphs can be implemented in a more parsimonious manner, so that to save bandwidth, yet preserving efficiency in term of simplicity and completion time.

Abstract We study the connectivity properties of a family of random graphs that closely model the Bluetooth's device discovery process, where each device tries to connect to other devices within its visibility range in order to establish reliable communication channels yielding a connected topology. Specifically, we provide both analytical and experimental evidence that when the visibility range of each node (i.e. device) is limited to a vanishing function ofn, the total number of nodes in the system, full connectivity can still be achieved with high probability by letting each node connect only to a ‘small’ number of visible neighbors. Our results extend previous studies, where connectivity properties were analyzed only for the case of a constant visibility range, and provide evidence that Bluetooth can indeed be used for establishing largead hocnetworks. Copyright © 2008 John Wiley & Sons, Ltd.

We propose an extension of the Teaching Machine project, called Quiz Generator, that allows instructors to produce assessment quizzes in the field of algorithm and data structures quite easily. This extension makes use of visualization techniques and is based on new features of the Teaching Machine that allow third-party visualizers to be added as plugins and on new scripting capabilities. Using these new capabilities, five quiz types have already been produced, which can be applied to any algorithm and/or data structure for which the necessary visualizer plugins exist.

We describe a two-year experience of fully integrating algorithm visualization technology into a CS2 course on data structures and algorithms. Our integration methodology was based on the engagement taxonomy proposed by the working group on Improving the Educational Impact of Algorithm Visualization: in particular, we used five forms of engagement of this taxonomy, that is, the no-viewing, the viewing, the changing, the constructing and the presenting forms. The integration of algorithm visualization technology into the course culminated in the writing of a textbook on the design, analysis and visualization of data structures and algorithms, whose reading is strictly dependent on the use of an algorithm visualization tool, called Alvie, which has been developed by the authors.

We describe the approach that has been followed by the authors while teaching the CS1 laboratory course on Java programming at the University of Florence. In particular, we focus on the assessment method that has been utilized: by making use of specific software developed by the teachers themselves, the method allowed them to automatically obtain a preliminary evaluation of the students' performance, which could subsequently be analyzed and modified after a manual exploration of the students' work.

In this paper we present NetPrIDE, an integrated development environment for designing, implementing and visualizing computer network protocols, which has primarily been used for teaching computer networks. NetPrIDE makes use of an abstract and formal notation to clearly and firmly specify a protocol: once the protocol has been specified and the network topology has been fixed, the implementation and the visualization of the protocol is performed in a completely automated way.

In this paper we propose a new environment for allowing students of a first programming undergraduate course to test their Java code. This environment allows the student to learn the basics of the Java language without necessarily knowing the object-oriented features of the language itself, and the teacher to propose new tests by making use of a graphical test editor. Moreover, the client-server architecture of the Web-based version of the environment is designed so that the student does not even need a Java virtual machine on its computing device, but only a Web browser. This latter feature makes our environment a useful tool for ubiquitous testing of Java programming skills.

An electronic course book (ECB in short) is a learning module consisting of hyperdocuments with a functional use of interactivity and multimedia, presented on the WWW and/or CDROM [1]. In this paper we propose an ECB producer application, which can assist any author in the development of an ECB based on WWW usability criteria and which presents a collection of several multimedia elements which can enhance the process of learning and which differentiate an electronic course book from a classical paper book. The ECB, which represents an electronic form of classroom support, will turn out to be useful both to teachers, since they will take advantage of the slide-based presentation of the text and of the several simulation tools included in the ECB, and to students, since they will be able to learn by reading, by doing and by answering.

According to Baas, van den Eijnde, and Junger (2001) an electronic course book (ECB) is a learning module consisting of menu-driven hyperdocuments with a functional use of interactivity and multimedia, presented on the WWW and/or CDROM. The main purpose of this paper is to propose a model for the development of a computer network ECB based on (a) the integration of several tools, which are dispersed in the WWW as university course materials and that for their multimedia nature could not be inserted in a paper book, and (b) on WWW usability criteria, which make the design of the book very different from that of a printed book. The ECB will be useful both to teachers (while giving their lectures) since they will take advantage of the slide-based presentation of the text and of the several simulation tools included in the ECB, and to students (while studying the material) since they will be able to learn by reading, by doing and by answering.

The study of the approximability properties of NP-hard optimization problems has recently made great advances mainly due to the results obtained in the field of proof checking. The last important breakthrough proves the APX-completeness of several important optimization problems and thus reconciles "two distinct views of approximation classes: syntactic and computational" [S. Khanna et al., in Proc. 35th IEEE Symp. on Foundations of Computer Science, IEEE Computer Society Press, Los Alamitos, CA, 1994, pp. 819--830]. In this paper we obtain new results on the structure of several computationally-defined approximation classes. In particular, after defining a new approximation preserving reducibility to be used for asmany approximation classes as possible, we give the first examples of natural NPO-complete problems and the first examples of natural APX-intermediate problems. Moreover, we state new connections between the approximability properties and the query complexity of NPO problems.

No abstract available.

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Comparing the complexity of different combinatorial optimization problems has been an extremely active research area during the last 23 years. This has led to the definition of several approximation preserving reducibilities and to the development of powerful reduction techniques. We first review the main approximation preserving reducibilities that have appeared in the literature and suggest which one of them should be used. Successively, we give some hints on how to prove new non-approximability results by emphasizing the most interesting techniques among the new ones that have been developed in the last few years.

The study of the approximability properties of NP-hard optimization problems has recently made great advances mainly due to the results obtained in the field of proof checking. The last important breakthrough proves the APX-completeness of several important optimization problems and thus reconciles "two distinct views of approximation classes: syntactic and computational" [S. Khanna et al., in Proc. 35th IEEE Symp. on Foundations of Computer Science, IEEE Computer Society Press, Los Alamitos, CA, 1994, pp. 819--830]. In this paper we obtain new results on the structure of several computationally-defined approximation classes. In particular, after defining a new approximation preserving reducibility to be used for asmany approximation classes as possible, we give the first examples of natural NPO-complete problems and the first examples of natural APX-intermediate problems. Moreover, we state new connections between the approximability properties and the query complexity of NPO problems.