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In this paper, we propose to regularize ill-posed inverse problems using a deep hierarchical variational autoencoder (HVAE) as an image prior. The proposed method synthesizes the advantages of i) denoiser-based Plug \& Play approaches and ii) generative model based approaches to inverse problems. First, we exploit VAE properties to design an efficient algorithm that benefits from convergence guarantees of Plug-and-Play (PnP) methods. Second, our approach is not restricted to specialized datasets and the proposed PnP-HVAE model is able to solve image restoration problems on natural images of any size. Our experiments show that the proposed PnP-HVAE method is competitive with both SOTA denoiser-based PnP approaches, and other SOTA restoration methods based on generative models.

This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of the root and reticulation vertices, can be oriented as a directed nonbinary phylogenetic network. Moreover, we characterize when this is possible and show that, in such instances, the resulting directed nonbinary phylogenetic network is unique. In addition, without being given the location of the root and the reticulation vertices, we describe an algorithm for deciding whether an undirected binary phylogenetic network $N$ can be oriented as a directed binary phylogenetic network of a certain class. The algorithm is fixed-parameter tractable (FPT) when the parameter is the level of $N$ and is applicable to classes of directed phylogenetic networks that satisfy certain conditions. As an example, we show that the well-studied class of binary tree-child networks satisfies these conditions.

In this paper, we propose the unfitted spectral element method for solving elliptic interface and corresponding eigenvalue problems. The novelty of the proposed method lies in its combination of the spectral accuracy of the spectral element method and the flexibility of the unfitted Nitsche's method. We also use tailored ghost penalty terms to enhance its robustness. We establish optimal $hp$ convergence rates for both elliptic interface problems and interface eigenvalue problems. Additionally, we demonstrate spectral accuracy for model problems in terms of polynomial degree.

Biological structural designs in nature, like hoof walls, horns, and antlers, can be used as inspiration for generating structures with excellent mechanical properties. A common theme in these designs is the small percent porosity in the structure ranging from 1 - 5\%. In this work, the sheep horn was used as an inspiration due to its higher toughness when loaded in the radial direction compared to the longitudinal direction. Under dynamic transverse compression, we investigated the structure-property relations in low porosity structures characterized by their two-dimensional (2D) cross-sections. A diverse design space was created by combining polygonal tubules with different numbers of sides placed on a grid with varying numbers of rows and columns. The volume fraction and the orientation angle of the tubules were also varied. The finite element (FE) method was used with a rate-dependent elastoplastic material model to generate the stress-strain curves under plane strain conditions. A gated recurrent unit (GRU) model was trained to predict the structures' stress-strain response and energy absorption under different strain rates and applied strains. The parameter-based model uses eight discrete parameters to characterize the design space and as inputs to the model. The trained GRU model can efficiently predict the response of a new design in as little as 0.16 ms and allows rapid performance evaluation of 128000 designs in the design space. The GRU predictions identified high-performance structures, and four design trends that affect the specific energy absorption were extracted and discussed.

In this paper, we revisit McFadden (1978)'s correction factor for sampling of alternatives in multinomial logit (MNL) and mixed multinomial logit (MMNL) models. McFadden (1978) proved that consistent parameter estimates are obtained when estimating MNL models using a sampled subset of alternatives, including the chosen alternative, in combination with a correction factor. We decompose this correction factor into i) a correction for overestimating the MNL choice probability due to using a smaller subset of alternatives, and ii) a correction for which a subset of alternatives is contrasted through utility differences and thereby the extent to which we learn about the parameters of interest in MNL. Keane and Wasi (2016) proved that the overall expected positive information divergence - comprising the above two elements - is minimised between the true and sampled likelihood when applying a sampling protocol satisfying uniform conditioning. We generalise their result to the case of positive conditioning and show that whilst McFadden (1978)'s correction factor may not minimise the overall expected information divergence, it does minimise the expected information loss with respect to the parameters of interest. We apply this result in the context of Bayesian analysis and show that McFadden (1978)'s correction factor minimises the expected information loss regarding the parameters of interest across the entire posterior density irrespective of sample size. In other words, McFadden (1978)'s correction factor has desirable small and large sample properties. We also show that our results for Bayesian MNL models transfer to MMNL and that only McFadden (1978) correction factor is sufficient to minimise the expected information loss in the parameters of interest. Monte Carlo simulations illustrate the successful application of sampling of alternatives in Bayesian MMNL models.

This brief addresses the design of a Nonlinear Model Predictive Control (NMPC) strategy for exponentially incremental Input-to-State Stable (ISS) systems. In particular, a novel formulation is devised, which does not necessitate the onerous computation of terminal ingredients, but rather relies on the explicit definition of a minimum prediction horizon ensuring closed-loop stability. The designed methodology is particularly suited for the control of systems learned by Recurrent Neural Networks (RNNs), which are known for their enhanced modeling capabilities and for which the incremental ISS properties can be studied thanks to simple algebraic conditions. The approach is applied to Gated Recurrent Unit (GRU) networks, providing also a method for the design of a tailored state observer with convergence guarantees. The resulting control architecture is tested on a benchmark system, demonstrating its good control performances and efficient applicability.

Including information from additional spectral bands (e.g., near-infrared) can improve deep learning model performance for many vision-oriented tasks. There are many possible ways to incorporate this additional information into a deep learning model, but the optimal fusion strategy has not yet been determined and can vary between applications. At one extreme, known as "early fusion," additional bands are stacked as extra channels to obtain an input image with more than three channels. At the other extreme, known as "late fusion," RGB and non-RGB bands are passed through separate branches of a deep learning model and merged immediately before a final classification or segmentation layer. In this work, we characterize the performance of a suite of multispectral deep learning models with different fusion approaches, quantify their relative reliance on different input bands and evaluate their robustness to naturalistic image corruptions affecting one or more input channels.

Nowadays, the Convolutional Neural Networks (CNNs) have achieved impressive performance on many computer vision related tasks, such as object detection, image recognition, image retrieval, etc. These achievements benefit from the CNNs outstanding capability to learn the input features with deep layers of neuron structures and iterative training process. However, these learned features are hard to identify and interpret from a human vision perspective, causing a lack of understanding of the CNNs internal working mechanism. To improve the CNN interpretability, the CNN visualization is well utilized as a qualitative analysis method, which translates the internal features into visually perceptible patterns. And many CNN visualization works have been proposed in the literature to interpret the CNN in perspectives of network structure, operation, and semantic concept. In this paper, we expect to provide a comprehensive survey of several representative CNN visualization methods, including Activation Maximization, Network Inversion, Deconvolutional Neural Networks (DeconvNet), and Network Dissection based visualization. These methods are presented in terms of motivations, algorithms, and experiment results. Based on these visualization methods, we also discuss their practical applications to demonstrate the significance of the CNN interpretability in areas of network design, optimization, security enhancement, etc.

Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.