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Dane Taylor

Publications and source records attributed to Dane Taylor.

At least 37 records · Page 2Linked to original sources

Noise-Response Analysis of Deep Neural Networks Quantifies Robustness and Fingerprints Structural Malware

The ubiquity of deep neural networks (DNNs), cloud-based training, and transfer learning is giving rise to a new cybersecurity frontier in which unsecure DNNs have `structural malware' (i.e., compromised weights and activation pathways). In particular, DNNs can be designed to have backdoors that allow an adversary to easily and reliably fool an image classifier by adding a pattern of pixels called a trigger. It is generally difficult to detect backdoors, and existing detection methods are computationally expensive and require extensive resources (e.g., access to the training data). Here, we propose a rapid feature-generation technique that quantifies the robustness of a DNN, `fingerprints' its nonlinearity, and allows us to detect backdoors (if present). Our approach involves studying how a DNN responds to noise-infused images with varying noise intensity, which we summarize with titration curves. We find that DNNs with backdoors are more sensitive to input noise and respond in a characteristic way that reveals the backdoor and where it leads (its `target'). Our empirical results demonstrate that we can accurately detect backdoors with high confidence orders-of-magnitude faster than existing approaches (seconds versus hours).

cs.LG↗

Impact of Community Structure on Consensus Machine Learning

Consensus dynamics support decentralized machine learning for data that is distributed across a cloud compute cluster or across the internet of things. In these and other settings, one seeks to minimize the time $τ_ε$ required to obtain consensus within some $ε>0$ margin of error. $τ_ε$ typically depends on the topology of the underlying communication network, and for many algorithms $τ_ε$ depends on the second-smallest eigenvalue $λ_2\in[0,1]$ of the network's normalized Laplacian matrix: $τ_ε\sim\mathcal{O}(λ_2^{-1})$. Here, we analyze the effect on $τ_ε$ of network community structure, which can arise when compute nodes/sensors are spatially clustered, for example. We study consensus machine learning over networks drawn from stochastic block models, which yield random networks that can contain heterogeneous communities with different sizes and densities. Using random matrix theory, we analyze the effects of communities on $λ_2$ and consensus, finding that $λ_2$ generally increases (i.e., $τ_ε$ decreases) as one decreases the extent of community structure. We further observe that there exists a critical level of community structure at which $τ_ε$ reaches a lower bound and is no longer limited by the presence of communities. We support our findings with empirical experiments for decentralized support vector machines.

cs.LG↗

Continuous-in-Depth Neural Networks

Recent work has attempted to interpret residual networks (ResNets) as one step of a forward Euler discretization of an ordinary differential equation, focusing mainly on syntactic algebraic similarities between the two systems. Discrete dynamical integrators of continuous dynamical systems, however, have a much richer structure. We first show that ResNets fail to be meaningful dynamical integrators in this richer sense. We then demonstrate that neural network models can learn to represent continuous dynamical systems, with this richer structure and properties, by embedding them into higher-order numerical integration schemes, such as the Runge Kutta schemes. Based on these insights, we introduce ContinuousNet as a continuous-in-depth generalization of ResNet architectures. ContinuousNets exhibit an invariance to the particular computational graph manifestation. That is, the continuous-in-depth model can be evaluated with different discrete time step sizes, which changes the number of layers, and different numerical integration schemes, which changes the graph connectivity. We show that this can be used to develop an incremental-in-depth training scheme that improves model quality, while significantly decreasing training time. We also show that, once trained, the number of units in the computational graph can even be decreased, for faster inference with little-to-no accuracy drop.

cs.LG↗

Tunable Eigenvector-Based Centralities for Multiplex and Temporal Networks

Characterizing the importances (i.e., centralities) of nodes in social, biological, and technological networks is a core topic in both network science and data science. We present a linear-algebraic framework that generalizes eigenvector-based centralities, including PageRank and hub/authority scores, to provide a common framework for two popular classes of multilayer networks: multiplex networks (which have layers that encode different types of relationships) and temporal networks (in which the relationships change over time). Our approach involves the study of joint, marginal, and conditional "supracentralities" that one can calculate from the dominant eigenvector of a supracentrality matrix [Taylor et al., 2017], which couples centrality matrices that are associated with individual network layers. We extend this prior work (which was restricted to temporal networks with layers that are coupled by adjacent-in-time coupling) by allowing the layers to be coupled through a (possibly asymmetric) interlayer-adjacency matrix $\tilde{\bf A}$, where the entry $\tilde{A}_{tt'} \geq 0$ encodes the coupling between layers $t$ and $t'$. Our framework provides a unifying foundation for centrality analysis of multiplex and temporal networks; it also illustrates a complicated dependency of the supracentralities on the topology and weights of interlayer coupling. By scaling $\tilde{\bf A}$ by an interlayer-coupling strength $ω\ge0$ and developing a singular perturbation theory for the limits of weak ($ω\to0^+$) and strong coupling ($ω\to\infty$), we also reveal an interesting dependence of supracentralities on the dominant left and right eigenvectors of $\tilde{\bf A}$.

cs.SI↗

Multiplex Markov Chains: Convection Cycles and Optimality

Multiplex networks are a common modeling framework for interconnected systems and multimodal data, yet we still lack fundamental insights for how multiplexity affects stochastic processes. We introduce a novel ``Markov chains of Markov chains'' model called multiplex Markov chains (MMCs) such that with probably $(1-ω)\in [0,1]$ random walkers remain in the same layer and follow (layer-specific) intralayer Markov chains, whereas with probability $ω$ they move to different layers following (node-specific) interlayer Markov chains. One main finding is the identification of multiplex convection, whereby a stationary distribution exhibits circulating flows that involve multiple layers. Convection cycles are well understood in fluids, but are insufficiently explored on networks. Our experiments reveal that one mechanism for convection is the existence of imbalances for the (intralayer) degrees of nodes in different layers. To gain further insight, we employ spectral perturbation theory to characterize the stationary distribution for the limits of small and large $ω$, and we show that MMCs inherently exhibit optimality for intermediate $ω$ in terms of their convergence rate and the extent of convection. As an application, we conduct an MMC-based analysis of brain-activity data, finding MMCs to differ between healthy persons and those with Alzheimer's disease. Overall, our work suggests MMCs and convection as two important new directions for network-related research.

physics.soc-ph↗

Supracentrality Analysis of Temporal Networks with Directed Interlayer Coupling

We describe centralities in temporal networks using a supracentrality framework to study centrality trajectories, which characterize how the importances of nodes change in time. We study supracentrality generalizations of eigenvector-based centralities, a family of centrality measures for time-independent networks that includes PageRank, hub and authority scores, and eigenvector centrality. We start with a sequence of adjacency matrices, each of which represents a time layer of a network at a different point or interval of time. Coupling centrality matrices across time layers with weighted interlayer edges yields a \emph{supracentrality matrix} $\mathbb{C}(ω)$, where $ω$ controls the extent to which centrality trajectories change over time. We can flexibly tune the weight and topology of the interlayer coupling to cater to different scientific applications. The entries of the dominant eigenvector of $\mathbb{C}(ω)$ represent \emph{joint centralities}, which simultaneously quantify the importance of every node in every time layer. Inspired by probability theory, we also compute \emph{marginal} and \emph{conditional centralities}. We illustrate how to adjust the coupling between time layers to tune the extent to which nodes' centrality trajectories are influenced by the oldest and newest time layers. We support our findings by analysis in the limits of small and large $ω$.

cs.SI↗

Transient crosslinking kinetics optimize gene cluster interactions

Our understanding of how chromosomes structurally organize and dynamically interact has been revolutionized through the lens of long-chain polymer physics. Major protein contributors to chromosome structure and dynamics are condensin and cohesin that stochastically generate loops within and between chains, and entrap proximal strands of sister chromatids. In this paper, we explore the ability of transient, protein-mediated, gene-gene crosslinks to induce clusters of genes, thereby dynamic architecture, within the highly repeated ribosomal DNA that comprises the nucleolus of budding yeast. We implement three approaches: live cell microscopy; computational modeling of the full genome during G1 in budding yeast, exploring four decades of timescales for transient crosslinks between 5k bp domains in the nucleolus on Chromosome XII; and, temporal network models with automated community detection algorithms applied to the full range of 4D modeling datasets. The data analysis tools detect and track gene clusters, their size, number, persistence time, and their plasticity. Of biological significance, our analysis reveals an optimal mean crosslink lifetime that promotes pairwise and cluster gene interactions through "flexible" clustering. In this state, large gene clusters self-assemble yet frequently interact, marked by gene exchanges between clusters, which in turn maximizes global gene interactions in the nucleolus. This regime stands between two limiting cases each with far less global gene interactions: with shorter crosslink lifetimes, "rigid" clustering emerges with clusters that interact infrequently; with longer crosslink lifetimes, there is a dissolution of clusters. These observations are compared with imaging experiments on a normal yeast strain and two condensin-modified mutant cell strains, applying the same image analysis pipeline to the experimental and simulated datasets.

q-bio.GN↗

Synchronization of Network-Coupled Oscillators with Uncertain Dynamics

Synchronization of network-coupled dynamical units is important to a variety of natural and engineered processes including circadian rhythms, cardiac function, neural processing, and power grids. Despite this ubiquity, it remains poorly understood how complex network structures and heterogeneous local dynamics combine to either promote or inhibit synchronization. Moreover, for most real-world applications it is impossible to obtain the exact specifications of the system, and there is a lack of theory for how uncertainty affects synchronization. We address this open problem by studying the Synchrony Alignment Function (SAF), which is an objective measure for the synchronization properties of a network of heterogeneous oscillators with given natural frequencies. We extend the SAF framework to analyze network-coupled oscillators with heterogeneous natural frequencies that are drawn as a multivariate random vector. Using probability theory for quadratic forms, we obtain expressions for the expectation and variance of the SAF for given network structures. We conclude with numerical experiments that illustrate how the incorporation of uncertainty yields a more robust theoretical framework for enhancing synchronization, and we provide new perspectives for why synchronization is generically promoted by network properties including degree-frequency correlations, link directedness, and link weight delocalization.

nlin.AO↗

Ensemble-based estimates of eigenvector error for empirical covariance matrices

Covariance matrices are fundamental to the analysis and forecast of economic, physical and biological systems. Although the eigenvalues $\{λ_i\}$ and eigenvectors $\{{\bf u}_i\}$ of a covariance matrix are central to such endeavors, in practice one must inevitably approximate the covariance matrix based on data with finite sample size $n$ to obtain empirical eigenvalues $\{\tildeλ_i\}$ and eigenvectors $\{\tilde{\bf u}_i\}$, and therefore understanding the error so introduced is of central importance. We analyze eigenvector error $\|{\bf u}_i - \tilde{\bf u}_i \|^2$ while leveraging the assumption that the true covariance matrix having size $p$ is drawn from a matrix ensemble with known spectral properties---particularly, we assume the distribution of population eigenvalues weakly converges as $p\to\infty$ to a spectral density $ρ(λ)$ and that the spacing between population eigenvalues is similar to that for the Gaussian orthogonal ensemble. Our approach complements previous analyses of eigenvector error that require the full set of eigenvalues to be known, which can be computationally infeasible when $p$ is large. To provide a scalable approach for uncertainty quantification of eigenvector error, we consider a fixed eigenvalue $λ$ and approximate the distribution of the expected square error $r= \mathbb{E}\left[\| {\bf u}_i - \tilde{\bf u}_i \|^2\right]$ across the matrix ensemble for all ${\bf u}_i$ associated with $λ_i=λ$. We find, for example, that for sufficiently large matrix size $p$ and sample size $n>p$, the probability density of $r$ scales as $1/nr^2$. This power-law scaling implies that eigenvector error is extremely heterogeneous---even if $r$ is very small for most eigenvectors, it can be large for others with non-negligible probability. We support this and further results with numerical experiments.

math.ST↗

Network-ensemble comparisons with stochastic rewiring and von Neumann entropy

Assessing whether a given network is typical or atypical for a random-network ensemble (i.e., network-ensemble comparison) has widespread applications ranging from null-model selection and hypothesis testing to clustering and classifying networks. We develop a framework for network-ensemble comparison by subjecting the network to stochastic rewiring. We study two rewiring processes, uniform and degree-preserved rewiring, which yield random-network ensembles that converge to the Erdos-Renyi and configuration-model ensembles, respectively. We study convergence through von Neumann entropy (VNE), a network summary statistic measuring information content based on the spectra of a Laplacian matrix, and develop a perturbation analysis for the expected effect of rewiring on VNE. Our analysis yields an estimate for how many rewires are required for a given network to resemble a typical network from an ensemble, offering a computationally efficient quantity for network-ensemble comparison that does not require simulation of the corresponding rewiring process.

physics.soc-ph↗

Rigid Graph Compression: Motif-based rigidity analysis for disordered fiber networks

Using particle-scale models to accurately describe property enhancements and phase transitions in macroscopic behavior is a major engineering challenge in composite materials science. To address some of these challenges, we use the graph theoretic property of rigidity to model me- chanical reinforcement in composites with stiff rod-like particles. We develop an efficient algorithmic approach called rigid graph compression (RGC) to describe the transition from floppy to rigid in disordered fiber networks ('rod-hinge systems'), which form the reinforcing phase in many composite systems. To establish RGC on a firm theoretical foundation, we adapt rigidity matroid theory to identify primitive topological network motifs that serve as rules for composing interacting rigid par- ticles into larger rigid components. This approach is computationally efficient and stable, because RGC requires only topological information about rod interactions (encoded by a sparse unweighted network) rather than geometrical details such as rod locations or pairwise distances (as required in rigidity matroid theory). We conduct numerical experiments on simulated two-dimensional rod-hinge systems to demonstrate that RGC closely approximates the rigidity percolation threshold for such systems, through comparison with the pebble game algorithm (which is exact in two dimensions). Importantly, whereas the pebble game is derived from Laman's condition and is only valid in two dimensions, the RGC approach naturally extends to higher dimensions.

cond-mat.dis-nn↗

Post-processing partitions to identify domains of modularity optimization

We introduce the Convex Hull of Admissible Modularity Partitions (CHAMP) algorithm to prune and prioritize different network community structures identified across multiple runs of possibly various computational heuristics. Given a set of partitions, CHAMP identifies the domain of modularity optimization for each partition ---i.e., the parameter-space domain where it has the largest modularity relative to the input set---discarding partitions with empty domains to obtain the subset of partitions that are "admissible" candidate community structures that remain potentially optimal over indicated parameter domains. Importantly, CHAMP can be used for multi-dimensional parameter spaces, such as those for multilayer networks where one includes a resolution parameter and interlayer coupling. Using the results from CHAMP, a user can more appropriately select robust community structures by observing the sizes of domains of optimization and the pairwise comparisons between partitions in the admissible subset. We demonstrate the utility of CHAMP with several example networks. In these examples, CHAMP focuses attention onto pruned subsets of admissible partitions that are 20-to-1785 times smaller than the sets of unique partitions obtained by community detection heuristics that were input into CHAMP.

cs.SI↗

Super-resolution community detection for layer-aggregated multilayer networks

Applied network science often involves preprocessing network data before applying a network-analysis method, and there is typically a theoretical disconnect between these steps. For example, it is common to aggregate time-varying network data into windows prior to analysis, and the tradeoffs of this preprocessing are not well understood. Focusing on the problem of detecting small communities in multilayer networks, we study the effects of layer aggregation by developing random-matrix theory for modularity matrices associated with layer-aggregated networks with $N$ nodes and $L$ layers, which are drawn from an ensemble of Erdős-Rényi networks. We study phase transitions in which eigenvectors localize onto communities (allowing their detection) and which occur for a given community provided its size surpasses a detectability limit $K^*$. When layers are aggregated via a summation, we obtain $K^*\varpropto \mathcal{O}(\sqrt{NL}/T)$, where $T$ is the number of layers across which the community persists. Interestingly, if $T$ is allowed to vary with $L$ then summation-based layer aggregation enhances small-community detection even if the community persists across a vanishing fraction of layers, provided that $T/L$ decays more slowly than $ \mathcal{O}(L^{-1/2})$. Moreover, we find that thresholding the summation can in some cases cause $K^*$ to decay exponentially, decreasing by orders of magnitude in a phenomenon we call super-resolution community detection. That is, layer aggregation with thresholding is a nonlinear data filter enabling detection of communities that are otherwise too small to detect. Importantly, different thresholds generally enhance the detectability of communities having different properties, illustrating that community detection can be obscured if one analyzes network data using a single threshold.

cs.SI↗

Case studies in network community detection

Community structure describes the organization of a network into subgraphs that contain a prevalence of edges within each subgraph and relatively few edges across boundaries between subgraphs. The development of community-detection methods has occurred across disciplines, with numerous and varied algorithms proposed to find communities. As we present in this Chapter via several case studies, community detection is not just an "end game" unto itself, but rather a step in the analysis of network data which is then useful for furthering research in the disciplinary domain of interest. These case-study examples arise from diverse applications, ranging from social and political science to neuroscience and genetics, and we have chosen them to demonstrate key aspects of community detection and to highlight that community detection, in practice, should be directed by the application at hand.

physics.soc-ph↗

Eigenvector-Based Centrality Measures for Temporal Networks

Numerous centrality measures have been developed to quantify the importances of nodes in time-independent networks, and many of them can be expressed as the leading eigenvector of some matrix. With the increasing availability of network data that changes in time, it is important to extend such eigenvector-based centrality measures to time-dependent networks. In this paper, we introduce a principled generalization of network centrality measures that is valid for any eigenvector-based centrality. We consider a temporal network with N nodes as a sequence of T layers that describe the network during different time windows, and we couple centrality matrices for the layers into a supra-centrality matrix of size NTxNT whose dominant eigenvector gives the centrality of each node i at each time t. We refer to this eigenvector and its components as a joint centrality, as it reflects the importances of both the node i and the time layer t. We also introduce the concepts of marginal and conditional centralities, which facilitate the study of centrality trajectories over time. We find that the strength of coupling between layers is important for determining multiscale properties of centrality, such as localization phenomena and the time scale of centrality changes. In the strong-coupling regime, we derive expressions for time-averaged centralities, which are given by the zeroth-order terms of a singular perturbation expansion. We also study first-order terms to obtain first-order-mover scores, which concisely describe the magnitude of nodes' centrality changes over time. As examples, we apply our method to three empirical temporal networks: the United States Ph.D. exchange in mathematics, costarring relationships among top-billed actors during the Golden Age of Hollywood, and citations of decisions from the United States Supreme Court.

physics.soc-ph↗

Synchronization of heterogeneous oscillators under network modifications: Perturbation and optimization of the synchrony alignment function

Synchronization is central to many complex systems in engineering physics (e.g., the power-grid, Josephson junction circuits, and electro-chemical oscillators) and biology (e.g., neuronal, circadian, and cardiac rhythms). Despite these widespread applications---for which proper functionality depends sensitively on the extent of synchronization---there remains a lack of understanding for how systems evolve and adapt to enhance or inhibit synchronization. We study how network modifications affect the synchronization properties of network-coupled dynamical systems that have heterogeneous node dynamics (e.g., phase oscillators with non-identical frequencies), which is often the case for real-world systems. Our approach relies on a synchrony alignment function (SAF) that quantifies the interplay between heterogeneity of the network and of the oscillators and provides an objective measure for a system's ability to synchronize. We conduct a spectral perturbation analysis of the SAF for structural network modifications including the addition and removal of edges, which subsequently ranks the edges according to their importance to synchronization. Based on this analysis, we develop gradient-descent algorithms to efficiently solve optimization problems that aim to maximize phase synchronization via network modifications. We support these and other results with numerical experiments.

nlin.AO↗

Optimal synchronization of directed complex networks

We study optimal synchronization of networks of coupled phase oscillators. We extend previous theory for optimizing the synchronization properties of undirected networks to the important case of directed networks. We derive a generalized synchrony alignment function that encodes the interplay between network structure and the oscillators' natural frequencies and serves as an objective measure for the network's degree of synchronization. Using the generalized synchrony alignment function, we show that a network's synchronization properties can be systematically optimized. This framework also allows us to study the properties of synchrony-optimized networks, and in particular, investigate the role of directed network properties such as nodal in- and out-degrees. For instance, we find that in optimally rewired networks the heterogeneity of the in-degree distribution roughly matches the heterogeneity of the natural frequency distribution, but no such relationship emerges for out-degrees. We also observe that a network's synchronization properties are promoted by a strong correlation between the nodal in-degrees and the natural frequencies of oscillators, whereas the relationship between the nodal out-degrees and the natural frequencies has comparatively little effect. This result is supported by our theory, which indicates that synchronization is promoted by a strong alignment of the natural frequencies with the left singular vectors corresponding to the largest singular values of the Laplacian matrix.

nlin.AO↗

Enhanced detectability of community structure in multilayer networks through layer aggregation

Many systems are naturally represented by a multilayer network in which edges exist in multiple layers that encode different, but potentially related, types of interactions, and it is important to understand limitations on the detectability of community structure in these networks. Using random matrix theory, we analyze detectability limitations for multilayer (specifically, multiplex) stochastic block models (SBMs) in which L layers are derived from a common SBM. We study the effect of layer aggregation on detectability for several aggregation methods, including summation of the layers' adjacency matrices for which we show the detectability limit vanishes as O(L^{-1/2}) with increasing number of layers, L. Importantly, we find a similar scaling behavior when the summation is thresholded at an optimal value, providing insight into the common - but not well understood - practice of thresholding pairwise-interaction data to obtain sparse network representations.

physics.soc-ph↗