Small Graphs Research Articles

Neuronal network inference and membrane potential model using multivariate Hawkes processes

BackgroundIn this work, we propose to catch the complexity of the membrane potential’s dynamic of a motoneuron between its spikes, taking into account the spikes from other neurons around. Our approach relies on two types of data: extracellular recordings of multiple spikes trains and intracellular recordings of the membrane potential of a central neuron. New methodWe provide a unified framework and a complete pipeline to analyze neuronal activity from data extraction to statistical inference. To the best of our knowledge, this is the first time that a Hawkes-diffusion model is investigated on such complex data. The first step of the proposed procedure is to select a subnetwork of neurons impacting the central neuron using a multivariate Hawkes process. Then we infer a jump-diffusion dynamic in which jumps are driven from a Hawkes process, the occurrences of which correspond to the spike trains of the aforementioned subset of neurons that interact with the central neuron. ResultsFrom the Hawkes estimation step we recover a small connectivity graph which contains the central neuron, and we show that taking into account this information improves the inference of membrane potential through the proposed jump-diffusion model. A goodness of fit test is applied to validate the relevance of the Hawkes model in such context. Comparison with existing methodsWe compare an empirical inference method and two sparse estimation procedures based on the Hawkes assumption for the reconstruction of the connectivity graph using the spike-trains. Then, the Hawkes-diffusion model is competed with the simple diffusion in terms of best fit to describe the behavior of the membrane potential of a central neuron surrounded by a network. ConclusionsThe present method takes advantage of both spike trains and membrane potential to understand the behavior of a fixed neuron. The entire code has been developed and is freely available on GitHub.

Discovering association rules from big graphs

This paper tackles two challenges to discovery of graph rules. Existing discovery methods often (a) return an excessive number of rules, and (b) do not scale with large graphs given the intractability of the discovery problem. We propose an application-driven strategy to cut back rules and data that are irrelevant to users' interests, by training a machine learning (ML) model to identify data pertaining to a given application. Moreover, we introduce a sampling method to reduce a big graph G to a set H of small sample graphs. Given expected support and recall bounds, the method is able to deduce samples in H and mine rules from H to satisfy the bounds in the entire G . As proof of concept, we develop an algorithm to discover Graph Association Rules (GARs), which are a combination of graph patterns and attribute dependencies, and may embed ML classifiers as predicates. We show that the algorithm is parallelly scalable, i.e. , it guarantees to reduce runtime when more machines are used. We experimentally verify that the method is able to discover rules with recall above 91% when using sample ratio 10%, with speedup of 61 times.

Corona product of signed graphs and its application to modeling signed networks

The notion of corona of two graphs was introduced by Frucht and Harary in 1970. In this paper, we generalize their definition of corona product of two graphs and introduce corona product of two signed graphs by utilizing the framework of marked graphs, which was introduced by Beineke and Harary in 1978. We study structural and spectral properties of corona product of signed graphs. Further, we define signed corona graphs by considering corona product of a fixed small signed graph with itself iteratively, and we call the small graph as the seed graph for the corresponding corona product graphs. Signed corona graphs can be employed as a signed network generative model for large growing signed networks. We study structural properties of corona graphs that include statistics of signed links, all types of signed triangles and degree distribution. Besides we analyze algebraic conflict of signed corona graphs generated by specially structured seed graphs. Finally, we show that a suitable choice of a seed graph can produce corona graphs which preserve properties of real signed networks.

Making graphs compact by lossless contraction

This paper proposes a scheme to reduce big graphs to small graphs. It contracts obsolete parts and regular structures into supernodes. The supernodes carry a synopsis S_mathcal {Q} for each query class mathcal {Q} in use, to abstract key features of the contracted parts for answering queries of mathcal {Q}. Moreover, for various types of graphs, we identify regular structures to contract. The contraction scheme provides a compact graph representation and prioritizes up-to-date data. Better still, it is generic and lossless. We show that the same contracted graph is able to support multiple query classes at the same time, no matter whether their queries are label based or not, local or non-local. Moreover, existing algorithms for these queries can be readily adapted to compute exact answers by using the synopses when possible and decontracting the supernodes only when necessary. As a proof of concept, we show how to adapt existing algorithms for subgraph isomorphism, triangle counting, shortest distance, connected component and clique decision to contracted graphs. We also provide a bounded incremental contraction algorithm in response to updates, such that its cost is determined by the size of areas affected by the updates alone, not by the entire graphs. We experimentally verify that on average, the contraction scheme reduces graphs by 71.9% and improves the evaluation of these queries by 1.69, 1.44, 1.47, 2.24 and 1.37 times, respectively.

An analysis of the parameterized complexity of periodic timetabling

Public transportation networks are typically operated with a periodic timetable. The periodic event scheduling problem (PESP) is the standard mathematical modeling tool for periodic timetabling. PESP is a computationally very challenging problem: For example, solving the instances of the benchmarking library PESPlib to optimality seems out of reach. Since PESP can be solved in linear time on trees, and the treewidth is a rather small graph parameter in the networks of the PESPlib, it is a natural question to ask whether there are polynomial-time algorithms for input networks of bounded treewidth, or even better, fixed-parameter tractable algorithms. We show that deciding the feasibility of a PESP instance is NP-hard even when the treewidth is 2, the branchwidth is 2, or the carvingwidth is 3. Analogous results hold for the optimization of reduced PESP instances, where the feasibility problem is trivial. Moreover, we show W[1]-hardness of the general feasibility problem with respect to treewidth, which means that we can most likely only accomplish pseudo-polynomial-time algorithms on input networks with bounded tree- or branchwidth. We present two such algorithms based on dynamic programming. We further analyze the parameterized complexity of PESP with bounded cyclomatic number, diameter, or vertex cover number. For event-activity networks with a special—but standard—structure, we give explicit and sharp bounds on the branchwidth in terms of the maximum degree and the carvingwidth of an underlying line network. Finally, we investigate several parameters on the smallest instance of the benchmarking library PESPlib.

Bringing Your Own View: Graph Contrastive Learning without Prefabricated Data Augmentations.

Self-supervision is recently surging at its new frontier of graph learning. It facilitates graph representations beneficial to downstream tasks; but its success could hinge on domain knowledge for handcraft or the often expensive trials and errors. Even its state-of-the-art representative, graph contrastive learning (GraphCL), is not completely free of those needs as GraphCL uses a prefabricated prior reflected by the ad-hoc manual selection of graph data augmentations. Our work aims at advancing GraphCL by answering the following questions: How to represent the space of graph augmented views? What principle can be relied upon to learn a prior in that space? And what framework can be constructed to learn the prior in tandem with contrastive learning? Accordingly, we have extended the prefabricated discrete prior in the augmentation set, to a learnable continuous prior in the parameter space of graph generators, assuming that graph priors per se, similar to the concept of image manifolds, can be learned by data generation. Furthermore, to form contrastive views without collapsing to trivial solutions due to the prior learnability, we have leveraged both principles of information minimization (InfoMin) and information bottleneck (InfoBN) to regularize the learned priors. Eventually, contrastive learning, InfoMin, and InfoBN are incorporated organically into one framework of bi-level optimization. Our principled and automated approach has proven to be competitive against the state-of-the-art graph self-supervision methods, including GraphCL, on benchmarks of small graphs; and shown even better generalizability on large-scale graphs, without resorting to human expertise or downstream validation. Our code is publicly released at https://github.com/Shen-Lab/GraphCL_Automated.

Wasserstein-Based Graph Alignment

A novel method for comparing non-aligned graphs of various sizes is proposed, based on the Wasserstein distance between graph signal distributions induced by the respective graph Laplacian matrices. Specifically, a new formulation for the one-to-many graph alignment problem is casted, which aims at matching a node in the smaller graph with one or more nodes in the larger graph. By incorporating optimal transport into our graph comparison framework, a structurally-meaningful graph distance, and a signal transportation plan that models the structure of graph data are generated. The resulting alignment problem is solved with stochastic gradient descent, where a novel Dykstra operator is used to ensure that the solution is a one-to-many (soft) assignment matrix. The performance of our novel framework is demonstrated on graph alignment, graph classification and graph signal transportation. Our method is shown to lead to significant improvements with respect to the state-of-the-art algorithms on each ofthese tasks.

OblivGM: Oblivious Attributed Subgraph Matching as a Cloud Service

In recent years there has been growing popularity of leveraging cloud computing for storing and querying attributed graphs, which have been widely used to model complex structured data in various applications. Such trend of outsourced graph analytics, however, is accompanied with critical privacy concerns regarding the information-rich and proprietary attributed graph data. In light of this, we design, implement, and evaluate OblivGM, a new system aimed at oblivious graph analytics services outsourced to the cloud. OblivGM focuses on the support for attributed subgraph matching, one popular and fundamental graph query functionality aiming to retrieve from a large attributed graph subgraphs isomorphic to a small query graph. Built from a delicate synergy of insights from attributed graph modelling and advanced lightweight cryptography, OblivGM protects the confidentiality of data content associated with attributed graphs and queries, conceals the connections among vertices in attributed graphs, and hides search access patterns. Meanwhile, OblivGM flexibly supports oblivious evaluation of varying subgraph queries, which may contain equality and/or range predicates. Extensive experiments over a real-world attributed graph dataset demonstrate that while providing strong security guarantees, OblivGM achieves practically affordable performance (with query latency on the order of a few seconds).

Properties of Large 2-Crossing-Critical Graphs

A $c$-crossing-critical graph is one that has crossing number at least $c$ but each of its proper subgraphs has crossing number less than $c$. Recently, a set of explicit construction rules was identified by Bokal, Oporowski, Richter, and Salazar to generate all large $2$-crossing-critical graphs (i.e., all apart from a finite set of small sporadic graphs). They share the property of containing a generalized Wagner graph $V_{10}$ as a subdivision. In this paper, we study these graphs and establish their order, simple crossing number, edge cover number, clique number, maximum degree, chromatic number, chromatic index, and treewidth. We also show that the graphs are linear-time recognizable and that all our proofs lead to efficient algorithms for the above measures. Keywords. Crossing number, crossing-critical graph, chromatic number, chromatic index, treewidth.

Strategic robustness in bi-level system-of-systems design

Abstract Robust designs protect system utility in the presence of uncertainty in technical and operational outcomes. Systems-of-systems, which lack centralized managerial control, are vulnerable to strategic uncertainty from coordination failures between partially or completely independent system actors. This work assesses the suitability of a game-theoretic equilibrium selection criterion to measure system robustness to strategic uncertainty and investigates the effect of strategically robust designs on collaborative behavior. The work models interactions between agents in a thematic representation of a mobile computing technology transition using an evolutionary game theory framework. Strategic robustness and collaborative solutions are assessed over a range of conditions by varying agent payoffs. Models are constructed on small world, preferential attachment and random graph topologies and executed in batch simulations. Results demonstrate that systems designed to reduce the impacts of coordination failure stemming from strategic uncertainty also increase the stability of the collaborative strategy by increasing the probability of collaboration by partners; a form of robustness by environment shaping that has not been previously investigated in design literature. The work also demonstrates that strategy selection follows the risk dominance equilibrium selection criterion and that changes in robustness to coordination failure can be measured with this criterion.

New Graphical Software Tool for Creating Cause-Effect Graph Specifications

Cause-effect graphing is a commonly used black-box technique with many applications in practice. It is important to be able to create accurate cause-effect graph specifications from system requirements before converting them to test case tables used for black-box testing. In this paper, a new graphical software tool for creating cause-effect graph specifications is presented. The tool uses standardized graphical notation for describing different types of nodes, logical relations and constraints, resulting in a visual representation of the desired cause-effect graph which can be exported for later usage and imported in the tool. The purpose of this work is to make the cause-effect graph specification process easier for users in order to solve some of the problems which arise due to the insufficient amount of understanding of cause-effect graph elements. The proposed tool was successfully used for creating cause-effect graph specifications for small, medium and large graphs. It was also successfully used for performing different types of tasks by users without any prior knowledge of the functionalities of the tool, indicating that the tool is easy to use, helpful and intuitive. The results indicate that the usage of standardized notation is easier to understand than non-standardized approaches from other tools.

Practical Near-Data-Processing Architecture for Large-Scale Distributed Graph Neural Network

Graph Neural Networks have drawn tremendous attention in the past few years due to their convincing performance and high interpretability in various graph-based tasks like link prediction and node classification. With the ever-growing graph size in the real world, especially for industrial graphs at a billion-level, the storage of graphs can easily consume Terabytes so that the process of GNNs has to be processed in a distributed manner. As a result, the execution could be inefficient due to the expensive cross-node communication and irregular memory access. Various GNN accelerators have been proposed for efficient GNN processing. They, however, mainly focused on small and medium-size graphs, which is not applicable to large-scale distributed graphs. In this paper, we present a practical Near-Data-Processing architecture based on a memory-pool system for large-scale distributed GNNs. We propose a customized memory fabric interface to construct the memory pool for low-latency and high throughput cross-node communication, which can provide flexible memory allocation and strong scalability. A practical Near-Data-Processing design is proposed for efficient work offloading and bandwidth utilization improvement. Moreover, we also introduce a partition and scheduling scheme to further improve performance and achieve workload balance. Comprehensive evaluations demonstrate that the proposed architecture can achieve up to <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$27\times $ </tex-math></inline-formula> and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$8\times $ </tex-math></inline-formula> higher training speed compared to two state-of-the-art distributed GNN frameworks: Deep Graph Library and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$P^{3}$ </tex-math></inline-formula> , respectively.

Multicriteria Scalable Graph Drawing via Stochastic Gradient Descent, (SGD)2.

Readability criteria, such as distance or neighborhood preservation, are often used to optimize node-link representations of graphs to enable the comprehension of the underlying data. With few exceptions, graph drawing algorithms typically optimize one such criterion, usually at the expense of others. We propose a layout approach, Multicriteria Scalable Graph Drawing via Stochastic Gradient Descent, (SGD)2, that can handle multiple readability criteria. (SGD)2 can optimize any criterion that can be described by a differentiable function. Our approach is flexible and can be used to optimize several criteria that have already been considered earlier (e.g., obtaining ideal edge lengths, stress, neighborhood preservation) as well as other criteria which have not yet been explicitly optimized in such fashion (e.g., node resolution, angular resolution, aspect ratio). The approach is scalable and can handle large graphs. A variation of the underlying approach can also be used to optimize many desirable properties in planar graphs, while maintaining planarity. Finally, we provide quantitative and qualitative evidence of the effectiveness of (SGD)2: we analyze the interactions between criteria, measure the quality of layouts generated from (SGD)2 as well as the runtime behavior, and analyze the impact of sample sizes. The source code is available on github and we also provide an interactive demo for small graphs.

Computing some role assignments of Cartesian product of graphs

In social networks, a role assignment is such that individuals play the same role, if they relate in the same way to other individuals playing counterpart roles. When a smaller graph models the social roles in a network, this gives rise to the decision problem called r-Role Assignment whether it exists such an assignment of r distinct roles to the vertices of the graph. This problem is known to be NP-complete for any fixed r ≥ 2. The Cartesian product of graphs is one of the most studied operation on graphs and has numerous applications in diverse areas, such as Mathematics, Computer Science, Chemistry and Biology. In this paper, we determine the computational complexity of r-Role Assignment restricted to Cartesian product of graphs, for r = 2, 3. In fact, we show that the Cartesian product of graphs is always 2-role assignable, however the problem of 3-Role Assignment is still NP-complete for this class.

Phase transition in random intersection graphs with communities

AbstractThe “random intersection graph with communities” (RIGC) models networks with communities, assuming an underlying bipartite structure of groups and individuals. Each group has its own internal structure described by a (small) graph, while groups may overlap. The group memberships are generated by a bipartite configuration model. The model generalizes the classical random intersection graph model, a special case where each community is a complete graph. The RIGC model is analytically tractable. We prove a phase transition in the size of the largest connected component in terms of the model parameters. We prove that percolation on RIGC produces a graph within the RIGC family, also undergoing a phase transition with respect to size of the largest component. Our proofs rely on the connection to the bipartite configuration model. Our related results on the bipartite configuration model are of independent interest, since they shed light on interesting differences from the unipartite case.

Latency, capacity, and distributed minimum spanning trees

We study the cost of distributed MST construction in the setting where each edge has a latency and a capacity, along with the weight. Edge latencies capture the delay on the links of the communication network, while capacity captures their throughput (in this case, the rate at which messages can be sent). Depending on how the edge latencies relate to the edge weights, we provide several tight bounds on the time and messages required to construct an MST. When edge weights exactly correspond with the latencies, we show that, perhaps interestingly, the bottleneck parameter in determining the running time of an algorithm is the total weight W of the MST (rather than the total number of nodes n, as in the standard CONGEST model). That is, we show a tight bound of Θ˜(D+W/c) rounds, where D refers to the latency diameter of the graph, W refers to the total weight of the constructed MST and edges have capacity c. The proposed algorithm sends O˜(m+W) messages, where m, the total number of edges in the network graph under consideration, is a known lower bound on message complexity for MST construction. We also show that Ω(W) is a lower bound for fast MST constructions. When the edge latencies and the corresponding edge weights are unrelated, and either can take arbitrary values, we show that (unlike the sub-linear time algorithms in the standard CONGEST model, on small diameter graphs), the best time complexity that can be achieved is Θ˜(D+n/c). However, if we restrict all edges to have equal latency ℓ and capacity c while having possibly different weights (weights could deviate arbitrarily from ℓ), we give an algorithm that constructs an MST in O˜(D+nℓ/c) time. In each case, we provide nearly matching upper and lower bounds.

The secure domination number of Cartesian products of small graphs with paths and cycles

The secure domination numbers of the Cartesian products of two small graphs with paths or cycles is determined, as well as for Möbius ladder graphs. Prior to this work, in all cases where the secure domination number has been determined, the proof has either been trivial, or has been derived from lower bounds established by considering different forms of domination. However, the latter mode of proof is not applicable for most graphs, including those considered here. Hence, this work represents the first attempt to determine secure domination numbers via the properties of secure domination itself, and it is expected that these methods may be used to determine further results in the future.

A Polynomial Kernel for Diamond-Free Editing

Given a fixed graph H, the H-free editing problem asks whether we can edit at most k edges to make a graph contain no induced copy of H. We obtain a polynomial kernel for this problem when H is a diamond. The incompressibility dichotomy for H being a 3-connected graph and the classical complexity dichotomy suggest that except for H being a complete/empty graph, H-free editing problems admit polynomial kernels only for a few small graphs H. Therefore, we believe that our result is an essential step toward a complete dichotomy on the compressibility of H-free editing. Additionally, we give a cubic-vertex kernel for the diamond-free edge deletion problem, which is far simpler than the previous kernel of the same size for the problem.

The minimality of the Georges–Kelmans graph

In 1971, Tutte wrote in an article that it is tempting to conjecture that every 3-connected bipartite cubic graph is hamiltonian. Motivated by this remark, Horton constructed a counterexample on 96 96 vertices. In a sequence of articles by different authors several smaller counterexamples were presented. The smallest of these graphs is a graph on 50 vertices which was discovered independently by Georges and Kelmans. In this article we show that there is no smaller counterexample. As all non-hamiltonian 3-connected bipartite cubic graphs in the literature have cyclic 4-cuts—even if they have girth 6—it is natural to ask whether this is a necessary prerequisite. In this article we answer this question in the negative and give a construction of an infinite family of non-hamiltonian cyclically 5-connected bipartite cubic graphs. In 1969 Barnette gave a weaker version of the conjecture stating that 3-connected planar bipartite cubic graphs are hamiltonian. We show that Barnette’s conjecture is true up to at least 90 vertices. We also report that a search of small non-hamiltonian 3-connected bipartite cubic graphs did not find any with genus less than 4.

Vertex-Based Topological Indices of Double and Strong Double Graph of Dutch Windmill Graph

A measurement of the molecular topology of graphs is known as a topological index, and several physical and chemical properties such as heat formation, boiling point, vaporization, enthalpy, and entropy are used to characterize them. Graph theory is useful in evaluating the relationship between various topological indices of some graphs derived by applying certain graph operations. Graph operations play an important role in many applications of graph theory because many big graphs can be obtained from small graphs. Here, we discuss two graph operations, i.e., double graph and strong double graph. In this article, we will compute the topological indices such as geometric arithmetic index GA , atom bond connectivity index ABC , forgotten index F , inverse sum indeg index ISI , general inverse sum indeg index ISI α , β , first multiplicative-Zagreb index PM 1 and second multiplicative-Zagreb index PM 2 , fifth geometric arithmetic index GA 5 , fourth atom bond connectivity index ABC 4 of double graph, and strong double graph of Dutch Windmill graph D 3 p .