Observing and tracking bandlimited graph processes from sampled measurements

A critical challenge in graph signal processing is the sampling of bandlimited graph signals; signals that are sparse in a well-defined graph Fourier domain. Current works focused on sampling time-invariant graph signals and ignored their temporal evolution. However, time can bring new insights on sampling since sensor, biological, and financial network signals are correlated in both domains. Hence, in this work, we develop a sampling theory for time varying graph signals, named graph processes, to observe and track a process described by a linear state-space model. We provide a mathematical analysis to highlight the role of the graph, process bandwidth, and sample locations. We also propose sampling strategies that exploit the coupling between the topology and the corresponding process. Numerical experiments corroborate our theory and show the proposed methods trade well the number of samples with accuracy

Rapid spatio-temporal flood modelling via hydraulics-based graph neural networks

Numerical modelling is a reliable tool for flood simulations, but accurate solutions are computationally expensive. In recent years, researchers have explored data-driven methodologies based on neural networks to overcome this limitation. However, most models are only used for a specific case study and disregard the dynamic evolution of the flood wave. This limits their generalizability to topographies that the model was not trained on and in time-dependent applications. In this paper, we introduce shallow water equation–graph neural network (SWE–GNN), a hydraulics-inspired surrogate model based on GNNs that can be used for rapid spatio-temporal flood modelling. The model exploits the analogy between finite-volume methods used to solve SWEs and GNNs. For a computational mesh, we create a graph by considering finite-volume cells as nodes and adjacent cells as being connected by edges. The inputs are determined by the topographical properties of the domain and the initial hydraulic conditions. The GNN then determines how fluxes are exchanged between cells via a learned local function. We overcome the time-step constraints by stacking multiple GNN layers, which expand the considered space instead of increasing the time resolution. We also propose a multi-step-ahead loss function along with a curriculum learning strategy to improve the stability and performance. We validate this approach using a dataset of two-dimensional dike breach flood simulations in randomly generated digital elevation models generated with a high-fidelity numerical solver. The SWE–GNN model predicts the spatio-temporal evolution of the flood for unseen topographies with mean average errors in time of 0.04 m for water depths and 0.004 m2 s−1 for unit discharges. Moreover, it generalizes well to unseen breach locations, bigger domains, and longer periods of time compared to those of the training set, outperforming other deep-learning models. On top of this, SWE–GNN has a computational speed-up of up to 2 orders of magnitude faster than the numerical solver. Our framework opens the doors to a new approach to replace numerical solvers in time-sensitive applications with spatially dependent uncertainties.</p

In Vitro Transformation of Primary Human CD34+ Cells by AML Fusion Oncogenes: Early Gene Expression Profiling Reveals Possible Drug Target in AML

Different fusion oncogenes in acute myeloid leukemia (AML) have distinct clinical and laboratory features suggesting different modes of malignant transformation. Here we compare the in vitro effects of representatives of 4 major groups of AML fusion oncogenes on primary human CD34+ cells. As expected from their clinical similarities, MLL-AF9 and NUP98-HOXA9 had very similar effects in vitro. They both caused erythroid hyperplasia and a clear block in erythroid and myeloid maturation. On the other hand, AML1-ETO and PML-RARA had only modest effects on myeloid and erythroid differentiation. All oncogenes except PML-RARA caused a dramatic increase in long-term proliferation and self-renewal. Gene expression profiling revealed two distinct temporal patterns of gene deregulation. Gene deregulation by MLL-AF9 and NUP98-HOXA9 peaked 3 days after transduction. In contrast, the vast majority of gene deregulation by AML1-ETO and PML-RARA occurred within 6 hours, followed by a dramatic drop in the numbers of deregulated genes. Interestingly, the p53 inhibitor MDM2 was upregulated by AML1-ETO at 6 hours. Nutlin-3, an inhibitor of the interaction between MDM2 and p53, specifically inhibited the proliferation and self-renewal of primary human CD34+ cells transduced with AML1-ETO, suggesting that MDM2 upregulation plays a role in cell transformation by AML1-ETO. These data show that differences among AML fusion oncogenes can be recapitulated in vitro using primary human CD34+ cells and that early gene expression profiling in these cells can reveal potential drug targets in AML

Graph-time signal processing: Filtering and sampling strategies

The necessity to process signals living in non-Euclidean domains, such as signals defined on the top of a graph, has led to the extension of signal processing techniques to the graph setting. Among different approaches, graph signal processing distinguishes itself by providing a Fourier analysis of these signals. Analogously to the Fourier transform for time and image signals, the graph Fourier transform decomposes the graph signals decomposes in terms of the harmonics provided by the underlying topology. For instance, a graph signal characterized by a slow variation between adjacent nodes has a low frequency content.Along with the graph Fourier transform, graph filters are the key tool to alter the graph frequency content of a graph signal. This thesis focuses on graph filters that are performed distributively in the node domain–that is, each node needs to exchange information only within its neighbor to perform a given filtering operation. Similarly to the classical filters, we propose ways to design and implement distributed finite impulse response and infinite impulse response graph filters.One of the key contributions of this thesis is to bring the temporal dimension to graph signal processing and build upon a graph-time signal processing framework. This is done in different ways. First, we analyze the effects that the temporal variations on the graph signal and graph topology have on the filtering output. Second, we introduce the notion of joint graph-time filtering. Third, we presentpr a statistical analysis of the distributed graph filtering when the graph signal and the graph topology change randomly in time. Finally, we extend the sampling framework from the reconstruction of graph signals to the observation and tracking of time-varying graph processes.We characterize the behavior of the distributed autoregressivemoving average (ARMA) graph filters when the graph signal and the graph topology are time-varying. The latter analysis is exploited in two ways: i ) to quantify the limitations of graph filters in a dynamic environment, such as a moving sensors processing a time-varying signal in a sensor network; and i i ) to provide ways for filtering with low computation and communication complexity time-varying graph signals.We develop the notion of distributed graph-time filtering, which is an operation that jointly processes the graph frequencies of a time-varying graph signal on one hand and its temporal frequencies on the other hand. We propose distributed finite impulse response and infinite impulse response recursions to implement a two-dimensional graphtime filtering operation. Finally, we propose design strategies to find the filter coefficients that approximate a desired two-dimensional frequency response.We extend the analysis of graph filters to a stochastic environment, i.e., when the graph topology and the graph signal change randomly over time. By characterizing the first and second order moments of the filter output, we quantify the impact of the graph signal and the graph topology randomness into the distributed filtering operation. The latter allows us to develop the notion of graph filtering in the mean, which is also used to ease the computational burden of classical graph filters.Finally, we propose a sampling framework for time-varying graph signals. Particularly, when the graph signal changes over time following a state-space model, we extend the graph signal sampling theory to the tasks of observing and tracking the time-varying graph signal froma few relevant nodes. The latter theory considers the graph signal sampling as a particular case and shows that tools from sparse sensing and sensor selection can be used for sampling.Circuits and System

Towards Finite-Time Consensus with Graph Convolutional Neural Networks

Atrial electrograms are often used to gain understanding on the development of atrial fibrillation (AF). Using such electrograms, cardiologists can reconstruct how the depolarization wave-front propagates across the atrium. Knowing the exact moment at which the depolarization wavefront in the tissue reaches each electrode is an important aspect of such reconstruction. A common way to determine the LAT is based on the steepest deflection (SD) of the individual electrograms. However, the SD annotates each electrogram individually and is expected to be more prone to errors compared to approaches that would employ the data from the surrounding electrodes to estimate the LAT. As electrograms from neighboring electrodes tend to have rather similar morphology up to a delay, we propose in this paper to use the cross-correlation to find the pair-wise relative delays between electrograms. Instead of only using the direct neighbors we consider the array as a graph and involve higher order neighbors as well. Using a least-squares method, the absolute LATs can then be estimated from the calculated pair-wise relative delays. Simulated and clinically recorded electrograms are used to evaluate the proposed approach. From the simulated data it follows that the proposed approach outperforms the SD approach

Graph-Time Convolutional Neural Networks: Architecture and Theoretical Analysis

Devising and analysing learning models for spatiotemporal network data is of importance for tasks including forecasting, anomaly detection, and multi-agent coordination, among others. Graph Convolutional Neural Networks (GCNNs) are an established approach to learn from time-invariant network data. The graph convolution operation offers a principled approach to aggregate information and offers mathematical analysis by exploring tools from graph signal processing. This analysis provides insights into the equivariance properties of GCNNs; spectral behaviour of the learned filters; and the stability to graph perturbations, which arise from support perturbations or uncertainties. However, extending the convolutional learning and respective analysis to the spatiotemporal domain is challenging because spatiotemporal data have more intrinsic dependencies. Hence, a higher flexibility to capture jointly the spatial and temporal dependencies is required to learn meaningful higher-order representations. Here, we leverage product graphs to represent the spatiotemporal dependencies in the data and introduce Graph-Time Convolutional Neural Networks (GTCNNs) as a principled architecture. We also introduce a parametric product graph to learn the spatiotemporal coupling. The convolution principle further allows a similar mathematical tractability as for GCNNs. In particular, the stability result shows GTCNNs are stable to spatial perturbations. owever, there is an implicit trade-off between discriminability and robustness; i.e., the more complex the model, the less stable. Extensive numerical results on benchmark datasets corroborate our findings and show the GTCNN compares favorably with state-of-the-art solutions. We anticipate the GTCNN to be a starting point for more sophisticated models that achieve good performance but are also fundamentally grounded.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Multimedia Computin

Learning Stochastic Graph Neural Networks With Constrained Variance

Stochastic graph neural networks (SGNNs) are information processing architectures that learn representations from data over random graphs. SGNNs are trained with respect to the expected performance, which comes with no guarantee about deviations of particular output realizations around the optimal expectation. To overcome this issue, we propose a variance-constrained optimization problem for SGNNs, balancing the expected performance and the stochastic deviation. An alternating primal-dual learning procedure is undertaken that solves the problem by updating the SGNN parameters with gradient descent and the dual variable with gradient ascent. To characterize the explicit effect of the variance-constrained learning, we analyze theoretically the variance of the SGNN output and identify a trade-off between the stochastic robustness and the discrimination power. We further analyze the duality gap of the variance-constrained optimization problem and the converging behavior of the primal-dual learning procedure. The former indicates the optimality loss induced by the dual transformation and the latter characterizes the limiting error of the iterative algorithm, both of which guarantee the performance of the variance-constrained learning. Through numerical simulations, we corroborate our theoretical findings and observe a strong expected performance with a controllable variance.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Multimedia Computin

Graph-Time Trend Filtering and Unrolling Network

Reconstructing missing values and removing noise from network-based multivariate time series requires developing graph-time regularizers capable of capturing their spatiotemporal behavior. However, current approaches based on joint spatiotemporal smoothness, diffusion, or variations thereof may not be effective for time series with discontinuities across the graph or time. To address this challenge, we propose a joint graph-time trend filter operating over a product graph representing spatiotemporal relations. Additionally, we develop a graph-time unrolled neural network to learn the prior from the data, which is based on the alternating direction method of multipliers iterations of the graph-time trend filter and on graph-time convolutional filters. Numerical tests with two synthetic and four real datasets corroborate the effectiveness of both approaches, highlight their inherent trade-offs, and show they compare well with state-of-the-art alternatives.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Multimedia Computin

Convolutional Filtering in Simplicial Complexes

This paper proposes convolutional filtering for data whose structure can be modeled by a simplicial complex (SC). SCs are mathematical tools that not only capture pairwise relationships as graphs but account also for higher-order network structures. These filters are built by following the shift-and-sum principle of the convolution operation and rely on the Hodge-Laplacians to shift the signal within the simplex. But since in SCs we have also inter-simplex coupling, we use the incidence matrices to transfer the signal in adjacent simplices and build a filter bank to jointly filter signals from different levels. We prove some interesting properties for the proposed filter bank, including permutation and orientation equivariance, a computational complexity that is linear in the SC dimension, and a spectral interpretation using the simplicial Fourier transform. We illustrate the proposed approach with numerical experiments.Accepted author manuscriptMultimedia Computin

Graph-time convolutional neural networks

Spatiotemporal data can be represented as a process over a graph, which captures their spatial relationships either explicitly or implicitly. How to leverage such a structure for learning representations is one of the key challenges when working with graphs. In this paper, we represent the spatiotemporal relationships through product graphs and develop a first principle graph-time convolutional neural network (GTCNN). The GTCNN is a compositional architecture with each layer comprising a graph-time convolutional module, a graphtime pooling module, and a nonlinearity. We develop a graph-time convolutional filter by following the shift-and-sum principles of the convolutional operator to learn higher-level features over the product graph. The product graph itself is parametric so that we can learn also the spatiotemporal coupling from data. We develop a zero-pad pooling that preserves the spatial graph (the prior about the data) while reducing the number of active nodes and the parameters. Experimental results with synthetic and real data corroborate the different components and compare with baseline and state-of-the-art solutions.Accepted author manuscriptMultimedia Computin