On Temporal Graph Exploration

A temporal graph is a graph in which the edge set can change from step to step. The temporal graph exploration problem TEXP is the problem of computing a foremost exploration schedule for a temporal graph, i.e., a temporal walk that starts at a given start node, visits all nodes of the graph, and has the smallest arrival time. In the first part of the paper, we consider only temporal graphs that are connected at each step. For such temporal graphs with $n$ nodes, we show that it is NP-hard to approximate TEXP with ratio $O(n^{1-\epsilon})$ for any $\epsilon>0$. We also provide an explicit construction of temporal graphs that require $\Theta(n^2)$ steps to be explored. We then consider TEXP under the assumption that the underlying graph (i.e. the graph that contains all edges that are present in the temporal graph in at least one step) belongs to a specific class of graphs. Among other results, we show that temporal graphs can be explored in $O(n^{1.5} k^2 \log n)$ steps if the underlying graph has treewidth $k$ and in $O(n \log^3 n)$ steps if the underlying graph is a $2\times n$ grid. In the second part of the paper, we replace the connectedness assumption by a weaker assumption and show that $m$-edge temporal graphs with regularly present edges and with random edges can always be explored in $O(m)$ steps and $O(m \log n)$ steps with high probability, respectively. We finally show that the latter result can be used to obtain a distributed algorithm for the gossiping problem.Comment: This is an extended version of an ICALP 2015 pape

Focus: A Graph Approach for Data-Mining and Domain-Specific Assembly of Next Generation Sequencing Data

Next Generation Sequencing (NGS) has emerged as a key technology leading to revolutionary breakthroughs in numerous biomedical research areas. These technologies produce millions to billions of short DNA reads that represent a small fraction of the original target DNA sequence. These short reads contain little information individually but are produced at a high coverage of the original sequence such that many reads overlap. Overlap relationships allow for the reads to be linearly ordered and merged by computational programs called assemblers into long stretches of contiguous sequence called contigs that can be used for research applications. Although the assembly of the reads produced by NGS remains a difficult task, it is the process of extracting useful knowledge from these relatively short sequences that has become one of the most exciting and challenging problems in Bioinformatics. The assembly of short reads is an aggregative process where critical information is lost as reads are merged into contigs. In addition, the assembly process is treated as a black box, with generic assembler tools that do not adapt to input data set characteristics. Finally, as NGS data throughput continues to increase, there is an increasing need for smart parallel assembler implementations. In this dissertation, a new assembly approach called Focus is proposed. Unlike previous assemblers, Focus relies on a novel hybrid graph constructed from multiple graphs at different levels of granularity to represent the assembly problem, facilitating information capture and dynamic adjustment to input data set characteristics. This work is composed of four specific aims: 1) The implementation of a robust assembly and analysis tool built on the hybrid graph platform 2) The development and application of graph mining to extract biologically relevant features in NGS data sets 3) The integration of domain specific knowledge to improve the assembly and analysis process. 4) The construction of smart parallel computing approaches, including the application of energy-aware computing for NGS assembly and knowledge integration to improve algorithm performance. In conclusion, this dissertation presents a complete parallel assembler called Focus that is capable of extracting biologically relevant features directly from its hybrid assembly graph

LIPIcs, Volume 261, ICALP 2023, Complete Volume

LIPIcs, Volume 261, ICALP 2023, Complete Volum

LIPIcs, Volume 258, SoCG 2023, Complete Volume

LIPIcs, Volume 258, SoCG 2023, Complete Volum

Complexity and algorithms related to two classes of graph problems

This thesis addresses the problems associated with conversions on graphs and editing by removing a matching. We study the f-reversible processes, which are those associated with a threshold value for each vertex, and whose dynamics depends on the number of neighbors with different state for each vertex. We set a tight upper bound for the period and transient lengths, characterize all trees that reach the maximum transient length for 2-reversible processes, and we show that determining the size of a minimum conversion set is NP-hard. We show that the AND-OR model defines a convexity on graphs. We show results of NP-completeness and efficient algorithms for certain convexity parameters for this new one, as well as approximate algorithms. We introduce the concept of generalized threshold processes, where the results are NP-completeness and efficient algorithms for both non relaxed and relaxed versions. We study the problem of deciding whether a given graph admits a removal of a matching in order to destroy all cycles. We show that this problem is NP-hard even for subcubic graphs, but admits efficient solution for several graph classes. We study the problem of deciding whether a given graph admits a removal of a matching in order to destroy all odd cycles. We show that this problem is NP-hard even for planar graphs with bounded degree, but admits efficient solution for some graph classes. We also show parameterized results.Esta tese aborda problemas associados a conversões em grafos e de edição pela remoção de um emparelhamento. Estudamos processos f-reversíveis, que são aqueles associados a um valor de limiar para cada vértice e cuja dinâmica depende da quantidade de vizinhos com estado contrário para cada vértice. Estabelecemos um limite superior justo para o tamanho do período e transiente, caracterizamos todas as árvores que alcançam o transiente máximo em processos 2-reversíveis e mostramos que determinar o tamanho de um conjunto conversor mínimo é NP-difícil. Mostramos que o modelo AND-OR define uma convexidade sobre grafos. Mostramos resultados de NP-completude e algoritmos eficientes para certos parâmetros de convexidade para esta nova, assim como algoritmos aproximativos. Introduzimos o conceito de processos de limiar generalizados, onde mostramos resultados de NP-completude e algoritmos eficientes para ambas as versões não relaxada e relaxada. Estudamos o problema de decidir se um dado grafo admite uma remoção de um emparelhamento de modo a remover todos os ciclos. Mostramos que este problema é NP-difícil mesmo para grafos subcúbicos, mas admite solução eficiente para várias classes de grafos. Estudamos o problema de decidir se um dado grafo admite uma remoção de um emparelhamento de modo a remover todos os ciclos ímpares. Mostramos que este problema é NP-difícil mesmo para grafos planares com grau limitado, mas admite solução eficiente para algumas classes de grafos. Mostramos também resultados parametrizados

Proceedings of the 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization

International audienceThe 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, Ecole Polytechnique and CEDRIC, CNAM