Constrained information flows in temporal networks reveal intermittent communities

Many real-world networks represent dynamic systems with interactions that change over time, often in uncoordinated ways and at irregular intervals. For example, university students connect in intermittent groups that repeatedly form and dissolve based on multiple factors, including their lectures, interests, and friends. Such dynamic systems can be represented as multilayer networks where each layer represents a snapshot of the temporal network. In this representation, it is crucial that the links between layers accurately capture real dependencies between those layers. Often, however, these dependencies are unknown. Therefore, current methods connect layers based on simplistic assumptions that do not capture node-level layer dependencies. For example, connecting every node to itself in other layers with the same weight can wipe out dependencies between intermittent groups, making it difficult or even impossible to identify them. In this paper, we present a principled approach to estimating node-level layer dependencies based on the network structure within each layer. We implement our node-level coupling method in the community detection framework Infomap and demonstrate its performance compared to current methods on synthetic and real temporal networks. We show that our approach more effectively constrains information inside multilayer communities so that Infomap can better recover planted groups in multilayer benchmark networks that represent multiple modes with different groups and better identify intermittent communities in real temporal contact networks. These results suggest that node-level layer coupling can improve the modeling of information spreading in temporal networks and better capture intermittent community structure.Comment: 10 pages, 10 figures, published in PR

Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures.

The microbiota of the built environment is an amalgamation of both human and environmental sources. While human sources have been examined within single-family households or in public environments, it is unclear what effect a large number of cohabitating people have on the microbial communities of their shared environment. We sampled the public and private spaces of a college dormitory, disentangling individual microbial signatures and their impact on the microbiota of common spaces. We compared multiple methods for marker gene sequence clustering and found that minimum entropy decomposition (MED) was best able to distinguish between the microbial signatures of different individuals and was able to uncover more discriminative taxa across all taxonomic groups. Further, weighted UniFrac- and random forest-based graph analyses uncovered two distinct spheres of hand- or shoe-associated samples. Using graph-based clustering, we identified spheres of interaction and found that connection between these clusters was enriched for hands, implicating them as a primary means of transmission. In contrast, shoe-associated samples were found to be freely interacting, with individual shoes more connected to each other than to the floors they interact with. Individual interactions were highly dynamic, with groups of samples originating from individuals clustering freely with samples from other individuals, while all floor and shoe samples consistently clustered together.IMPORTANCE Humans leave behind a microbial trail, regardless of intention. This may allow for the identification of individuals based on the "microbial signatures" they shed in built environments. In a shared living environment, these trails intersect, and through interaction with common surfaces may become homogenized, potentially confounding our ability to link individuals to their associated microbiota. We sought to understand the factors that influence the mixing of individual signatures and how best to process sequencing data to best tease apart these signatures

A framework for the construction of generative models for mesoscale structure in multilayer networks

Multilayer networks allow one to represent diverse and coupled connectivity patterns—such as time-dependence, multiple subsystems, or both—that arise in many applications and which are difficult or awkward to incorporate into standard network representations. In the study of multilayer networks, it is important to investigate mesoscale (i.e., intermediate-scale) structures, such as dense sets of nodes known as communities, to discover network features that are not apparent at the microscale or the macroscale. The ill-defined nature of mesoscale structure and its ubiquity in empirical networks make it crucial to develop generative models that can produce the features that one encounters in empirical networks. Key purposes of such models include generating synthetic networks with empirical properties of interest, benchmarking mesoscale-detection methods and algorithms, and inferring structure in empirical multilayer networks. In this paper, we introduce a framework for the construction of generative models for mesoscale structures in multilayer networks. Our framework provides a standardized set of generative models, together with an associated set of principles from which they are derived, for studies of mesoscale structures in multilayer networks. It unifies and generalizes many existing models for mesoscale structures in fully ordered (e.g., temporal) and unordered (e.g., multiplex) multilayer networks. One can also use it to construct generative models for mesoscale structures in partially ordered multilayer networks (e.g., networks that are both temporal and multiplex). Our framework has the ability to produce many features of empirical multilayer networks, and it explicitly incorporates a user-specified dependency structure between layers. We discuss the parameters and properties of our framework, and we illustrate examples of its use with benchmark models for community-detection methods and algorithms in multilayer networks

Flow stability for dynamic community detection

Many systems exhibit complex temporal dynamics due to the presence of different processes taking place simultaneously. An important task in these systems is to extract a simplified view of their time-dependent network of interactions. Community detection in temporal networks usually relies on aggregation over time windows or consider sequences of different stationary epochs. For dynamics-based methods, attempts to generalize static-network methodologies also face the fundamental difficulty that a stationary state of the dynamics does not always exist. Here, we derive a method based on a dynamical process evolving on the temporal network. Our method allows dynamics that do not reach a steady state and uncovers two sets of communities for a given time interval that accounts for the ordering of edges in forward and backward time. We show that our method provides a natural way to disentangle the different dynamical scales present in a system with synthetic and real-world examples

Restless Temporal Path Parameterized Above Lower Bounds

Reachability questions are one of the most fundamental algorithmic primitives in temporal graphs - graphs whose edge set changes over discrete time steps. A core problem here is the NP-hard Short Restless Temporal Path: given a temporal graph G, two distinct vertices s and z, and two numbers ? and k, is there a ?-restless temporal s-z path of length at most k? A temporal path is a path whose edges appear in chronological order and a temporal path is ?-restless if two consecutive path edges appear at most ? time steps apart from each other. Among others, this problem has applications in neuroscience and epidemiology. While Short Restless Temporal Path is known to be computationally hard, e.g., it is NP-hard even if the temporal graph consists of three discrete time steps and it is W[1]-hard when parameterized by the feedback vertex number of the underlying graph, it is fixed-parameter tractable when parameterized by the path length k. We improve on this by showing that Short Restless Temporal Path can be solved in (randomized) 4^(k-d)|G|^O(1) time, where d is the minimum length of a temporal s-z path

The Complexity of Finding Small Separators in Temporal Graphs

Temporal graphs are graphs with time-stamped edges. We study the problem of finding a small vertex set (the separator) with respect to two designated terminal vertices such that the removal of the set eliminates all temporal paths connecting one terminal to the other. Herein, we consider two models of temporal paths: paths that pass through arbitrarily many edges per time step (non-strict) and paths that pass through at most one edge per time step (strict). Regarding the number of time steps of a temporal graph, we show a complexity dichotomy (NP-hardness versus polynomial-time solvability) for both problem variants. Moreover we prove both problem variants to be NP-complete even on temporal graphs whose underlying graph is planar. We further show that, on temporal graphs with planar underlying graph, if additionally the number of time steps is constant, then the problem variant for strict paths is solvable in quasi-linear time. Finally, we introduce and motivate the notion of a temporal core (vertices whose incident edges change over time). We prove that the non-strict variant is fixed-parameter tractable when parameterized by the size of the temporal core, while the strict variant remains NP-complete, even for constant-size temporal cores

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