Computing Temporal Reachability Under Waiting-Time Constraints in Linear Time

This paper proposes a simple algorithm for computing single-source reachability in a temporal graph under waiting-time constraints, that is when waiting at each node is bounded by some time constraints. Given a space-time representation of a temporal graph, and a source node, the algorithm computes in linear-time which nodes and temporal edges are reachable through a constrained temporal walk from the source

Minimum-Cost Temporal Walks under Waiting-Time Constraints in Linear Time

In a temporal graph, each edge is available at specific points in time. Such an availability point is often represented by a ''temporal edge'' that can be traversed from its tail only at a specific departure time, for arriving in its head after a specific travel time. In such a graph, the connectivity from one node to another is naturally captured by the existence of a temporal path where temporal edges can be traversed one after the other. When imposing constraints on how much time it is possible to wait at a node in-between two temporal edges, it then becomes interesting to consider temporal walks where it is allowed to visit several times the same node, possibly at different times. We study the complexity of computing minimum-cost temporal walks from a single source under waiting-time constraints in a temporal graph, and ask under which conditions this problem can be solved in linear time. Our main result is a linear time algorithm when temporal edges are provided in input by non-decreasing departure time and also by non-decreasing arrival time. We use an algebraic framework for manipulating abstract costs, enabling the optimization of a large variety of criteria or even combinations of these. It allows to improve previous results for several criteria such as number of edges or overall waiting time. This result is somehow optimal: a logarithmic factor in the time complexity appears to be necessary if the input contains only one ordering of the temporal edges (either by arrival times or departure times)

Finding Temporal Paths Under Waiting Time Constraints

Computing a (short) path between two vertices is one of the most fundamental primitives in graph algorithmics. In recent years, the study of paths in temporal graphs, that is, graphs where the vertex set is fixed but the edge set changes over time, gained more and more attention. A path is time-respecting, or temporal, if it uses edges with non-decreasing time stamps. We investigate a basic constraint for temporal paths, where the time spent at each vertex must not exceed a given duration ?, referred to as ?-restless temporal paths. This constraint arises naturally in the modeling of real-world processes like packet routing in communication networks and infection transmission routes of diseases where recovery confers lasting resistance. While finding temporal paths without waiting time restrictions is known to be doable in polynomial time, we show that the "restless variant" of this problem becomes computationally hard even in very restrictive settings. For example, it is W[1]-hard when parameterized by the feedback vertex number or the pathwidth of the underlying graph. The main question thus is whether the problem becomes tractable in some natural settings. We explore several natural parameterizations, presenting FPT algorithms for three kinds of parameters: (1) output-related parameters (here, the maximum length of the path), (2) classical parameters applied to the underlying graph (e.g., feedback edge number), and (3) a new parameter called timed feedback vertex number, which captures finer-grained temporal features of the input temporal graph, and which may be of interest beyond this work

As Time Goes By: Adding a Temporal Dimension Towards Resolving Delegations in Liquid Democracy

In recent years, the study of various models and questions related to Liquid Democracy has been of growing interest among the community of Computational Social Choice. A concern that has been raised, is that current academic literature focuses solely on static inputs, concealing a key characteristic of Liquid Democracy: the right for a voter to change her mind as time goes by, regarding her options of whether to vote herself or delegate her vote to other participants, till the final voting deadline. In real life, a period of extended deliberation preceding the election-day motivates voters to adapt their behaviour over time, either based on observations of the remaining electorate or on information acquired for the topic at hand. By adding a temporal dimension to Liquid Democracy, such adaptations can increase the number of possible delegation paths and reduce the loss of votes due to delegation cycles or delegating paths towards abstaining agents, ultimately enhancing participation. Our work takes a first step to integrate a time horizon into decision-making problems in Liquid Democracy systems. Our approach, via a computational complexity analysis, exploits concepts and tools from temporal graph theory which turn out to be convenient for our framework

Betweenness centrality for temporal multiplexes

Betweenness centrality quantifies the importance of a vertex for the information flow in a network. We propose a flexible definition of betweenness for temporal multiplexes, where geodesics are determined accounting for the topological and temporal structure and the duration of paths. We propose an algorithm to compute the new metric via a mapping to a static graph. We show the importance of considering the temporal multiplex structure and an appropriate distance metric comparing the results with those obtained with static or single-layer metrics on a dataset of $\sim 20$k European flights

Complexity of the Temporal Shortest Path Interdiction Problem

In the shortest path interdiction problem, an interdictor aims to remove arcs of total cost at most a given budget from a directed graph with given arc costs and traversal times such that the length of a shortest s-t-path is maximized. For static graphs, this problem is known to be strongly NP-hard, and it has received considerable attention in the literature. While the shortest path problem is one of the most fundamental and well-studied problems also for temporal graphs, the shortest path interdiction problem has not yet been formally studied on temporal graphs, where common definitions of a "shortest path" include: latest start path (path with maximum start time), earliest arrival path (path with minimum arrival time), shortest duration path (path with minimum traveling time including waiting times at nodes), and shortest traversal path (path with minimum traveling time not including waiting times at nodes). In this paper, we analyze the complexity of the shortest path interdiction problem on temporal graphs with respect to all four definitions of a shortest path mentioned above. Even though the shortest path interdiction problem on static graphs is known to be strongly NP-hard, we show that the latest start and the earliest arrival path interdiction problems on temporal graphs are polynomial-time solvable. For the shortest duration and shortest traversal path interdiction problems, however, we show strong NP-hardness, but we obtain polynomial-time algorithms for these problems on extension-parallel temporal graphs

The impact of temporal sampling resolution on parameter inference for biological transport models

Imaging data has become widely available to study biological systems at various scales, for example the motile behaviour of bacteria or the transport of mRNA, and it has the potential to transform our understanding of key transport mechanisms. Often these imaging studies require us to compare biological species or mutants, and to do this we need to quantitatively characterise their behaviour. Mathematical models offer a quantitative description of a system that enables us to perform this comparison, but to relate these mechanistic mathematical models to imaging data, we need to estimate the parameters of the models. In this work, we study the impact of collecting data at different temporal resolutions on parameter inference for biological transport models by performing exact inference for simple velocity jump process models in a Bayesian framework. This issue is prominent in a host of studies because the majority of imaging technologies place constraints on the frequency with which images can be collected, and the discrete nature of observations can introduce errors into parameter estimates. In this work, we avoid such errors by formulating the velocity jump process model within a hidden states framework. This allows us to obtain estimates of the reorientation rate and noise amplitude for noisy observations of a simple velocity jump process. We demonstrate the sensitivity of these estimates to temporal variations in the sampling resolution and extent of measurement noise. We use our methodology to provide experimental guidelines for researchers aiming to characterise motile behaviour that can be described by a velocity jump process. In particular, we consider how experimental constraints resulting in a trade-off between temporal sampling resolution and observation noise may affect parameter estimates.Comment: Published in PLOS Computational Biolog

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing