Artificial neural networks that can recover latent dynamics from recorded neural activity may provide a powerful avenue for identifying and interpreting the dynamical motifs underlying biological computation. Given that neural variance alone does not uniquely determine a latent dynamical system, interpretable architectures should prioritize accurate and low-dimensional latent dynamics. In this work, we evaluated the performance of sequential autoencoders (SAEs) in recovering latent chaotic attractors from simulated neural datasets. We found that SAEs with widely-used recurrent neural network (RNN)-based dynamics were unable to infer accurate firing rates at the true latent state dimensionality, and that larger RNNs relied upon dynamical features not present in the data. On the other hand, SAEs with neural ordinary differential equation (NODE)-based dynamics inferred accurate rates at the true latent state dimensionality, while also recovering latent trajectories and fixed point structure. Ablations reveal that this is mainly because NODEs (1) allow use of higher-capacity multi-layer perceptrons (MLPs) to model the vector field and (2) predict the derivative rather than the next state. Decoupling the capacity of the dynamics model from its latent dimensionality enables NODEs to learn the requisite low-D dynamics where RNN cells fail. Additionally, the fact that the NODE predicts derivatives imposes a useful autoregressive prior on the latent states. The suboptimal interpretability of widely-used RNN-based dynamics may motivate substitution for alternative architectures, such as NODE, that enable learning of accurate dynamics in low-dimensional latent spaces.
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Containers offer an array of advantages that benefit research reproducibility and portability across groups and systems. As container tools mature, container security improves, and High-performance computing (HPC) and cloud system tools converge, supercomputing centers are increasingly integrating containers in their workflows. The technology selection process requires sufficient information on the diverse tools available, yet the majority of research into containers still focuses on cloud environments. We consider an adaptive containerization approach, with a focus on accelerating the deployment of applications and workflows on HPC systems using containers. To this end, we discuss the specific HPC requirements regarding container tools, and analyze the entire containerization stack, including container engines and registries, in-depth. Finally, we consider various orchestrator and HPC workload manager integration scenarios.
The aim of this work is to perform a multitemporal analysis using the Google Earth Engine (GEE) platform for the detection of changes in urban areas using optical data and specific machine learning (ML) algorithms. As a case study, Cairo City has been identified, in Egypt country, as one of the five most populous megacities of the last decade in the world. Classification and change detection analysis of the region of interest (ROI) have been carried out from July 2013 to July 2021. Results demonstrate the validity of the proposed method in identifying changed and unchanged urban areas over the selected period. Furthermore, this work aims to evidence the growing significance of GEE as an efficient cloud-based solution for managing large quantities of satellite data.
We combine Kronecker products, and quantitative information flow, to give a novel formal analysis for the fine-grained verification of utility in complex privacy pipelines. The combination explains a surprising anomaly in the behaviour of utility of privacy-preserving pipelines -- that sometimes a reduction in privacy results also in a decrease in utility. We use the standard measure of utility for Bayesian analysis, introduced by Ghosh at al., to produce tractable and rigorous proofs of the fine-grained statistical behaviour leading to the anomaly. More generally, we offer the prospect of formal-analysis tools for utility that complement extant formal analyses of privacy. We demonstrate our results on a number of common privacy-preserving designs.
Graph algorithms play an important role in many computer science areas. In order to solve problems that can be modeled using graphs, it is necessary to use a data structure that can represent those graphs in an efficient manner. On top of this, an infrastructure should be build that will assist in implementing common algorithms or developing specialized ones. Here, a new Java library is introduced, called Graph4J, that uses a different approach when compared to existing, well-known Java libraries such as JGraphT, JUNG and Guava Graph. Instead of using object-oriented data structures for graph representation, a lower-level model based on arrays of primitive values is utilized, that drastically reduces the required memory and the running times of the algorithm implementations. The design of the library, the space complexity of the graph structures and the time complexity of the most common graph operations are presented in detail, along with an experimental study that evaluates its performance, when compared to the other libraries. Emphasis is given to infrastructure related aspects, that is graph creation, inspection, alteration and traversal. The improvements obtained for other implemented algorithms are also analyzed and it is shown that the proposed library significantly outperforms the existing ones.
The VALERIE tool pipeline is a synthetic data generator developed with the goal to contribute to the understanding of domain-specific factors that influence perception performance of DNNs (deep neural networks). This work was carried out under the German research project KI Absicherung in order to develop a methodology for the validation of DNNs in the context of pedestrian detection in urban environments for automated driving. The VALERIE22 dataset was generated with the VALERIE procedural tools pipeline providing a photorealistic sensor simulation rendered from automatically synthesized scenes. The dataset provides a uniquely rich set of metadata, allowing extraction of specific scene and semantic features (like pixel-accurate occlusion rates, positions in the scene and distance + angle to the camera). This enables a multitude of possible tests on the data and we hope to stimulate research on understanding performance of DNNs. Based on performance metric a comparison with several other publicly available datasets is provided, demonstrating that VALERIE22 is one of best performing synthetic datasets currently available in the open domain.
Modeling complex systems that consist of different types of objects leads to multilayer networks, in which vertices are connected by both inter-layer and intra-layer edges. In this paper, we investigate multiplex networks, in which vertices in different layers are identified with each other, and the only inter-layer edges are those that connect a vertex with its copy in other layers. Let the third-order adjacency tensor $\mathcal{A}\in\R^{N\times N\times L}$ and the parameter $\gamma\geq 0$, which is associated with the ease of communication between layers, represent a multiplex network with $N$ vertices and $L$ layers. To measure the ease of communication in a multiplex network, we focus on the average inverse geodesic length, which we refer to as the multiplex global efficiency $e_\mathcal{A}(\gamma)$ by means of the multiplex path length matrix $P\in\R^{N\times N}$. This paper generalizes the approach proposed in \cite{NR23} for single-layer networks. We describe an algorithm based on min-plus matrix multiplication to construct $P$, as well as variants $P^K$ that only take into account multiplex paths made up of at most $K$ intra-layer edges. These matrices are applied to detect redundant edges and to determine non-decreasing lower bounds $e_\mathcal{A}^K(\gamma)$ for $e_\mathcal{A}(\gamma)$, for $K=1,2,\dots,N-2$. Finally, the sensitivity of $e_\mathcal{A}^K(\gamma)$ to changes of the entries of the adjacency tensor $\mathcal{A}$ is investigated to determine edges that should be strengthened to enhance the multiplex global efficiency the most.
The forecasting and computation of the stability of chaotic systems from partial observations are tasks for which traditional equation-based methods may not be suitable. In this computational paper, we propose data-driven methods to (i) infer the dynamics of unobserved (hidden) chaotic variables (full-state reconstruction); (ii) time forecast the evolution of the full state; and (iii) infer the stability properties of the full state. The tasks are performed with long short-term memory (LSTM) networks, which are trained with observations (data) limited to only part of the state: (i) the low-to-high resolution LSTM (LH-LSTM), which takes partial observations as training input, and requires access to the full system state when computing the loss; and (ii) the physics-informed LSTM (PI-LSTM), which is designed to combine partial observations with the integral formulation of the dynamical system's evolution equations. First, we derive the Jacobian of the LSTMs. Second, we analyse a chaotic partial differential equation, the Kuramoto-Sivashinsky (KS), and the Lorenz-96 system. We show that the proposed networks can forecast the hidden variables, both time-accurately and statistically. The Lyapunov exponents and covariant Lyapunov vectors, which characterize the stability of the chaotic attractors, are correctly inferred from partial observations. Third, the PI-LSTM outperforms the LH-LSTM by successfully reconstructing the hidden chaotic dynamics when the input dimension is smaller or similar to the Kaplan-Yorke dimension of the attractor. This work opens new opportunities for reconstructing the full state, inferring hidden variables, and computing the stability of chaotic systems from partial data.
We consider two classes of natural stochastic processes on finite unlabeled graphs. These are Euclidean stochastic optimization algorithms on the adjacency matrix of weighted graphs and a modified version of the Metropolis MCMC algorithm on stochastic block models over unweighted graphs. In both cases we show that, as the size of the graph goes to infinity, the random trajectories of the stochastic processes converge to deterministic limits. These deterministic limits are curves on the space of measure-valued graphons. Measure-valued graphons, introduced by Lov\'{a}sz and Szegedy, are a refinement of the concept of graphons that can distinguish between two infinite exchangeable arrays that give rise to the same graphon limit. We introduce new metrics on this space which provide us with a natural notion of convergence for our limit theorems. This notion is equivalent to the convergence of infinite-exchangeable arrays. Under a suitable time-scaling, the Metropolis chain admits a diffusion limit as the number of vertices go to infinity. We then demonstrate that, in an appropriately formulated zero-noise limit, the stochastic process of adjacency matrices of this diffusion converge to a deterministic gradient flow curve on the space of graphons introduced in arXiv:2111.09459 [math.PR]. Under suitable assumptions, this allows us to estimate an exponential convergence rate for the Metropolis chain in a certain limiting regime. To the best of our knowledge, both the actual rate and the connection between a natural Metropolis chain commonly used in exponential random graph models and gradient flows on graphons are new in the literature.
Optimal transport has gained much attention in image processing field, such as computer vision, image interpolation and medical image registration. Recently, Bredies et al. (ESAIM:M2AN 54:2351-2382, 2020) and Schmitzer et al. (IEEE T MED IMAGING 39:1626-1635, 2019) established the framework of optimal transport regularization for dynamic inverse problems. In this paper, we incorporate Wasserstein distance, together with total variation, into static inverse problems as a prior regularization. The Wasserstein distance formulated by Benamou-Brenier energy measures the similarity between the given template and the reconstructed image. Also, we analyze the existence of solutions of such variational problem in Radon measure space. Moreover, the first-order primal-dual algorithm is constructed for solving this general imaging problem in a specific grid strategy. Finally, numerical experiments for undersampled MRI reconstruction are presented which show that our proposed model can recover images well with high quality and structure preservation.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
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