A Bayesian Deep CNN Framework for Reconstructing K-T-Undersampled Resting-fMRI

Karan Taneja, Prachi Kulkarni, Shabbir Merchant, Suyash Awate

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Auto-TLDR; K-t undersampled R-fMRI Reconstruction using Deep Convolutional Neural Networks

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Undersampled reconstruction in resting functional magnetic resonance imaging (R-fMRI) holds the potential to enable higher spatial resolution in brain R-fMRI without increasing scan duration. We propose a novel framework to reconstruct k-t undersampled R-fMRI relying on a deep convolutional neural network (CNN) framework that leverages the insight that R-fMRI measurements are in k-space (frequency domain) and explicitly models the Fourier transformation from the frequency domain to the spatial domain. The architecture of our CNN framework comprises a multi-stage scheme that jointly learns two multilayer CNN components for (i)~filling in missing k-space data using acquired data in frequency-temporal neighborhoods and (ii)~image quality enhancement in the spatiotemporal domain. We propose four methods within our framework, including a Bayesian CNN that produces uncertainty maps indicating the per-voxel (and per-timepoint) confidence in the blood oxygenation level dependent (BOLD) time-series reconstruction. Results on brain R-fMRI show that our CNN framework improves over the state of the art, quantitatively and qualitatively, in terms of the connectivity maps for three cerebral functional networks.

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Auto-TLDR; Bayesian Neural Networks for Inverse Reconstruction via Bayesian Knowledge-Aided Computation

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Auto-TLDR; Clustering Task-Specific Fiber Pathways in Functional MRI using BOLD Signals

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Auto-TLDR; Unsupervised Deep Neural Network for Semantic Image Inpainting

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Auto-TLDR; Semi-supervised Deep Neural Networks for Generative Mixture Modeling and Clustering

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Auto-TLDR; A Novel method to estimate static and dynamic brain networks using Kulback- Leibler divergence using fMRI data

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Representing the brain activities by networks is very crucial to understand the human brain and design brain-computer interfaces. This study proposes a novel method to estimate static and dynamic brain networks using Kulback- Leibler divergence. The suggested brain networks are based on the probability distributions of voxel intensity values measured by functional Magnetic Resonance Images (fMRI) recorded while the subjects perform a predefined cognitive task, namely complex problem-solving. We investigate the validity of the estimated brain networks by modeling and analyzing the different phases of the complex problem-solving processes of the human brain, namely planning and execution phases. The suggested computational network model is tested by Support Vector Machines. We observe that the network models can successfully discriminate the planning and execution phases of the complex problem-solving process with more than 90% accuracy, when the suggested dynamic networks, extracted from the fMRI data, are classified by Support Vector Machines.

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Auto-TLDR; Conditional Generative Adversarial Networks for Phase Retrieval

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Auto-TLDR; Two-dimensional Convolutional Neural Networks for Gravitational Wave Detection from Time Series with Background Noise

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Auto-TLDR; Intimate Relationship Prediction by Attention-enhanced Cascade Convolutional Recurrent Neural Network Using Functional Near-Infrared Spectroscopy

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The detection of intimacy plays a crucial role in the improvement of intimate relationship, which contributes to promote the family and social harmony. Previous studies have shown that different degrees of intimacy have significant differences in brain imaging. Recently, a few of work has emerged to recognise intimacy automatically by using machine learning technique. Moreover, considering the temporal dynamic characteristics of intimacy relationship on neural mechanism, how to model spatio-temporal dynamics for intimacy prediction effectively is still a challenge. In this paper, we propose a novel method to explore deep spatial-temporal representations for intimacy prediction by Attention-enhanced Cascade Convolutional Recurrent Neural Network (ACCRNN). Given the advantages of time-frequency resolution in complex neuronal activities analysis, this paper utilizes functional near-infrared spectroscopy (fNIRS) to analyse and infer to intimate relationship. We collect a fNIRS-based dataset for the analysis of intimate relationship. Forty-two-channel fNIRS signals are recorded from the 44 subjects' prefrontal cortex when they watched a total of 18 photos of lovers, friends and strangers for 30 seconds per photo. The experimental results show that our proposed method outperforms the others in terms of accuracy with the precision of 96.5%. To the best of our knowledge, this is the first time that such a hybrid deep architecture has been employed for fNIRS-based intimacy prediction.

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Auto-TLDR; Image Denoising with Deep Convolutional Neural Networks

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Auto-TLDR; Geodesic Clustering of Connectivity Matrices for Multiple Sclerosis Classification

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Auto-TLDR; Trainable and Spectrally Initializable Matrix Transformations for Neural Networks

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In this work, we introduce a new architectural component to Neural Networks (NN), i.e., trainable and spectrally initializable matrix transformations on feature maps. While previous literature has already demonstrated the possibility of adding static spectral transformations as feature processors, our focus is on more general trainable transforms. We study the transforms in various architectural configurations on four datasets of different nature: from medical (ColorectalHist, HAM10000) and natural (Flowers) images to historical documents (CB55). With rigorous experiments that control for the number of parameters and randomness, we show that networks utilizing the introduced matrix transformations outperform vanilla neural networks. The observed accuracy increases appreciably across all datasets. In addition, we show that the benefit of spectral initialization leads to significantly faster convergence, as opposed to randomly initialized matrix transformations. The transformations are implemented as auto-differentiable PyTorch modules that can be incorporated into any neural network architecture. The entire code base is open-source.

Neural Machine Registration for Motion Correction in Breast DCE-MRI

Federica Aprea, Stefano Marrone, Carlo Sansone

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Auto-TLDR; A Neural Registration Network for Dynamic Contrast Enhanced-Magnetic Resonance Imaging

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Cancer is one of the leading causes of death in the western world, with medical imaging playing a key role for early diagnosis. Focusing on breast cancer, one of the emerging imaging methodologies is Dynamic Contrast Enhanced-Magnetic Resonance Imaging (DCE-MRI). The flip side of using DCE-MRI is in its long acquisition times, often causing the patient to move, resulting in motion artefacts, namely distortions in the acquired image that can affect DCE-MRI analysis. A possible solution consists in the use of Motion Correction Techniques (MCTs), i.e. procedures intended to re-align the post-contrast image to the corresponding pre-contrast (reference) one. This task is particularly critic in DCE-MRI, due to brightness variations introduced in post-contrast images by the contrast-agent flowing. To face this problem, in this work we introduce a new MCT for breast DCE-MRI leveraging Physiologically Based PharmacoKinetic (PBPK) modelling and Artificial Neural Networks (ANN) to determine the most suitable physiologically-compliant transformation. To this aim, we propose a Neural Registration Network relying on a very task-specific loss function explicitly designed to take into account the contrast agent flowing while enforcing a correct re-alignment. We compared the obtained results against some conventional motion correction techniques, evaluating the performance on a patient-by-patient basis. Results clearly show the effectiveness of the proposed approach, resulting as the best performing even when compares against other techniques designed to take into account for brightness variations.

Planar 3D Transfer Learning for End to End Unimodal MRI Unbalanced Data Segmentation

Martin Kolarik, Radim Burget, Carlos M. Travieso-Gonzalez, Jan Kocica

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Auto-TLDR; Planar 3D Res-U-Net Network for Unbalanced 3D Image Segmentation using Fluid Attenuation Inversion Recover

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We present a novel approach of 2D to 3D transfer learning based on mapping pre-trained 2D convolutional neural network weights into planar 3D kernels. The method is validated by proposed planar 3D res-u-net network with encoder transferred from the 2D VGG-16 which is applied for a single-stage unbalanced 3D image data segmentation. In particular, we evaluate the method on the MICCAI 2016 MS lesion segmentation challenge dataset utilizing solely Fluid Attenuation Inversion Recover (FLAIR) sequence without brain extraction for training and inference to simulate real medical praxis. The planar 3D res-u-net network performed the best both in sensitivity and Dice score amongst end to end methods processing raw MRI scans and achieved comparable Dice score to a state-of-the-art unimodal not end to end approach. Complete source code was released under the open-source license and this paper is in compliance with the Machine learning Reproducibility Checklist. By implementing practical transfer learning for 3D data representation we were able to successfully segment heavily unbalanced data without selective sampling and achieved more reliable results using less training data in single modality. From medical perspective, the unimodal approach gives an advantage in real praxis as it does not require co-registration nor additional scanning time during examination. Although modern medical imaging methods capture high resolution 3D anatomy scans suitable for computer aided detection system processing, deployment of automatic systems for interpretation of radiology imaging is still rather theoretical in many medical areas. Our work aims to bridge the gap offering solution for partial research questions.

MedZip: 3D Medical Images Lossless Compressor Using Recurrent Neural Network (LSTM)

Omniah Nagoor, Joss Whittle, Jingjing Deng, Benjamin Mora, Mark W. Jones

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Auto-TLDR; Recurrent Neural Network for Lossless Medical Image Compression using Long Short-Term Memory

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As scanners produce higher-resolution and more densely sampled images, this raises the challenge of data storage, transmission and communication within healthcare systems. Since the quality of medical images plays a crucial role in diagnosis accuracy, medical imaging compression techniques are desired to reduce scan bitrate while guaranteeing lossless reconstruction. This paper presents a lossless compression method that integrates a Recurrent Neural Network (RNN) as a 3D sequence prediction model. The aim is to learn the long dependencies of the voxel's neighbourhood in 3D using Long Short-Term Memory (LSTM) network then compress the residual error using arithmetic coding. Experiential results reveal that our method obtains a higher compression ratio achieving 15% saving compared to the state-of-the-art lossless compression standards, including JPEG-LS, JPEG2000, JP3D, HEVC, and PPMd. Our evaluation demonstrates that the proposed method generalizes well to unseen modalities CT and MRI for the lossless compression scheme. To the best of our knowledge, this is the first lossless compression method that uses LSTM neural network for 16-bit volumetric medical image compression.

Classification of Spatially Enriched Pixel Time Series with Convolutional Neural Networks

Mohamed Chelali, Camille Kurtz, Anne Puissant, Nicole Vincent

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Auto-TLDR; Spatio-Temporal Features Extraction from Satellite Image Time Series Using Random Walk

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Satellite Image Time Series (SITS), MRI sequences, and more generally image time series, constitute 2D+t data providing spatial and temporal information about an observed scene. Given a pattern recognition task such as image classification, considering jointly such rich information is crucial during the decision process. Nevertheless, due to the complex representation of the data-cube, spatio-temporal features extraction from 2D+t data remains difficult to handle. We present in this article an approach to learn such features from this data, and then to proceed to their classification. Our strategy consists in enriching pixel time series with spatial information. It is based on Random Walk to build a novel segment-based representation of the data, passing from a 2D+t dimension to a 2D one, without loosing too much spatial information. Such new representation is then involved in an end-to-end learning process with a classical 2D Convolutional Neural Network (CNN) in order to learn spatio-temporal features for the classification of image time series. Our approach is evaluated on a remote sensing application for the mapping of agricultural crops. Thanks to a visual attention mechanism, the proposed $2D$ spatio-temporal representation makes also easier the interpretation of a SITS to understand spatio-temporal phenomenons related to soil management practices.

Improved anomaly detection by training an autoencoder with skip connections on images corrupted with Stain-shaped noise

Anne-Sophie Collin, Christophe De Vleeschouwer

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Auto-TLDR; Autoencoder with Skip Connections for Anomaly Detection

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In industrial vision, the anomaly detection problem can be addressed with an autoencoder trained to map an arbitrary image, i.e. with or without any defect, to a clean image, i.e. without any defect. In this approach, anomaly detection relies conventionally on the reconstruction residual or, alternatively, on the reconstruction uncertainty. To improve the sharpness of the reconstruction, we consider an autoencoder architecture with skip connections. In the common scenario where only clean images are available for training, we propose to corrupt them with a synthetic noise model to prevent the convergence of the network towards the identity mapping, and introduce an original Stain noise model for that purpose. We show that this model favors the reconstruction of clean images from arbitrary real-world images, regardless of the actual defects appearance. In addition to demonstrating the relevance of our approach, our validation provides the first consistent assessment of reconstruction-based methods, by comparing their performance over the MVTec AD dataset [ref.], both for pixel- and image-wise anomaly detection.

Graph Convolutional Neural Networks for Power Line Outage Identification

Jia He, Maggie Cheng

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Auto-TLDR; Graph Convolutional Networks for Power Line Outage Identification

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In this paper, we consider the power line outage identification problem as a graph signal classification problem, where the signal at each vertex is given as a time series. We propose graph convolutional networks (GCNs) for the task of classifying signals supported on graphs. An important element of the GCN design is filter design. We consider filtering signals in either the vertex (spatial) domain, or the frequency (spectral) domain. Two basic architectures are proposed. In the spatial GCN architecture, the GCN uses a graph shift operator as the basic building block to incorporate the underlying graph structure into the convolution layer. The spatial filter directly utilizes the graph connectivity information. It defines the filter to be a polynomial in the graph shift operator to obtain the convolved features that aggregate neighborhood information of each node. In the spectral GCN architecture, a frequency filter is used instead. A graph Fourier transform operator first transforms the raw graph signal from the vertex domain to the frequency domain, and then a filter is defined using the graph's spectral parameters. The spectral GCN then uses the output from the graph Fourier transform to compute the convolved features. There are additional challenges to classify the time-evolving graph signal as the signal value at each vertex changes over time. The GCNs are designed to recognize different spatiotemporal patterns from high-dimensional data defined on a graph. The application of the proposed methods to power line outage identification shows that these GCN architectures can successfully classify abnormal signal patterns and identify the outage location.

Robust Skeletonization for Plant Root Structure Reconstruction from MRI

Jannis Horn

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Auto-TLDR; Structural reconstruction of plant roots from MRI using semantic root vs shoot segmentation and 3D skeletonization

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Temporal Pattern Detection in Time-Varying Graphical Models

Federico Tomasi, Veronica Tozzo, Annalisa Barla

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Auto-TLDR; A dynamical network inference model that leverages on kernels to consider general temporal patterns

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Tensor Factorization of Brain Structural Graph for Unsupervised Classification in Multiple Sclerosis

Berardino Barile, Marzullo Aldo, Claudio Stamile, Françoise Durand-Dubief, Dominique Sappey-Marinier

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Auto-TLDR; A Fully Automated Tensor-based Algorithm for Multiple Sclerosis Classification based on Structural Connectivity Graph of the White Matter Network

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Learning Non-Rigid Surface Reconstruction from Spatio-Temporal Image Patches

Matteo Pedone, Abdelrahman Mostafa, Janne Heikkilä

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Auto-TLDR; Dense Spatio-Temporal Depth Maps of Deformable Objects from Video Sequences

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We present a method to reconstruct a dense spatio-temporal depth map of a non-rigidly deformable object directly from a video sequence. The estimation of depth is performed locally on spatio-temporal patches of the video, and then the full depth video of the entire shape is recovered by combining them together. Since the geometric complexity of a local spatio-temporal patch of a deforming non-rigid object is often simple enough to be faithfully represented with a parametric model, we artificially generate a database of small deforming rectangular meshes rendered with different material properties and light conditions, along with their corresponding depth videos, and use such data to train a convolutional neural network. We tested our method on both synthetic and Kinect data and experimentally observed that the reconstruction error is significantly lower than the one obtained using other approaches like conventional non-rigid structure from motion.

Deep Iterative Residual Convolutional Network for Single Image Super-Resolution

Rao Muhammad Umer, Gian Luca Foresti, Christian Micheloni

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Auto-TLDR; ISRResCNet: Deep Iterative Super-Resolution Residual Convolutional Network for Single Image Super-resolution

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Deep convolutional neural networks (CNNs) have recently achieved great success for single image super-resolution (SISR) task due to their powerful feature representation capabilities. Most recent deep learning based SISR methods focus on designing deeper / wider models to learn the non-linear mapping between low-resolution (LR) inputs and the high-resolution (HR) outputs. These existing SR methods do not take into account the image observation (physical) model and thus require a large number of network's trainable parameters with a huge volume of training data. To address these issues, we propose a deep Iterative Super-Resolution Residual Convolutional Network (ISRResCNet) that exploits the powerful image regularization and large-scale optimization techniques by training the deep network in an iterative manner with a residual learning approach. Extensive experimental results on various super-resolution benchmarks demonstrate that our method with a few trainable parameters improves results for different scaling factors in comparison with the state-of-art methods.

Edge-Guided CNN for Denoising Images from Portable Ultrasound Devices

Yingnan Ma, Fei Yang, Anup Basu

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Auto-TLDR; Edge-Guided Convolutional Neural Network for Portable Ultrasound Images

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Ultrasound is a non-invasive tool that is useful for medical diagnosis and treatment. To reduce long wait times and add convenience to patients, portable ultrasound scanning devices are becoming increasingly popular. These devices can be held in one palm, and are compatible with modern cell phones. However, the quality of ultrasound images captured from the portable scanners is relatively poor compared to standard ultrasound scanning systems in hospitals. To improve the quality of the ultrasound images obtained from portable ultrasound devices, we propose a new neural network architecture called Edge-Guided Convolutional Neural Network (EGCNN), which can preserve significant edge information in ultrasound images when removing noise. We also study and compare the effectiveness of classical filtering approaches in removing speckle noise in these images. Experimental results show that after applying the proposed EGCNN, various organs can be better recognized from ultrasound images. This approach is expected to lead to better accuracy in diagnostics in the future.

Space-Time Domain Tensor Neural Networks: An Application on Human Pose Classification

Konstantinos Makantasis, Athanasios Voulodimos, Anastasios Doulamis, Nikolaos Doulamis, Nikolaos Bakalos

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Auto-TLDR; Tensor-Based Neural Network for Spatiotemporal Pose Classifiaction using Three-Dimensional Skeleton Data

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Recent advances in sensing technologies require the design and development of pattern recognition models capable of processing spatiotemporal data efficiently. In this study, we propose a spatially and temporally aware tensor-based neural network for human pose classifiaction using three-dimensional skeleton data. Our model employs three novel components. First, an input layer capable of constructing highly discriminative spatiotemporal features. Second, a tensor fusion operation that produces compact yet rich representations of the data, and third, a tensor-based neural network that processes data representations in their original tensor form. Our model is end-to-end trainable and characterized by a small number of trainable parameters making it suitable for problems where the annotated data is limited. Experimental evaluation of the proposed model indicates that it can achieve state-of-the-art performance.

EEG-Based Cognitive State Assessment Using Deep Ensemble Model and Filter Bank Common Spatial Pattern

Debashis Das Chakladar, Shubhashis Dey, Partha Pratim Roy, Masakazu Iwamura

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Auto-TLDR; A Deep Ensemble Model for Cognitive State Assessment using EEG-based Cognitive State Analysis

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Electroencephalography (EEG) is the most used physiological measure to evaluate the cognitive state of a user efficiently. As EEG inherently suffers from a poor spatial resolution, features extracted from each EEG channel may not efficiently used for cognitive state assessment. In this paper, the EEG-based cognitive state assessment has been performed during the mental arithmetic experiment, which includes two cognitive states (task and rest) of a user. To obtain the temporal as well as spatial resolution of the EEG signal, we combined the Filter Bank Common Spatial Pattern (FBCSP) method and Long Short-Term Memory (LSTM)-based deep ensemble model for classifying the cognitive state of a user. Subject-wise data distribution has been performed due to the execution of a large volume of data in a low computing environment. In the FBCSP method, the input EEG is decomposed into multiple equal-sized frequency bands, and spatial features of each frequency bands are extracted using the Common Spatial Pattern (CSP) algorithm. Next, a feature selection algorithm has been applied to identify the most informative features for classification. The proposed deep ensemble model consists of multiple similar structured LSTM networks that work in parallel. The output of the ensemble model (i.e., the cognitive state of a user) is computed using the average weighted combination of individual model prediction. This proposed model achieves 87\% classification accuracy, and it can also effectively estimate the cognitive state of a user in a low computing environment.

Digit Recognition Applied to Reconstructed Audio Signals Using Deep Learning

Anastasia-Sotiria Toufa, Constantine Kotropoulos

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Auto-TLDR; Compressed Sensing for Digit Recognition in Audio Reconstruction

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Compressed sensing allows signal reconstruction from a few measurements. This work proposes a complete pipeline for digit recognition applied to audio reconstructed signals. The reconstruction procedure exploits the assumption that the original signal lies in the range of a generator. A pretrained generator of a Generative Adversarial Network generates audio digits. A new method for reconstruction is proposed, using only the most active segment of the signal, i.e., the segment with the highest energy. The underlying assumption is that such segment offers a more compact representation, preserving the meaningful content of signal. Cases when the reconstruction produces noise, instead of digit, are treated as outliers. In order to detect and reject them, three unsupervised indicators are used, namely, the total energy of reconstructed signal, the predictions of an one-class Support Vector Machine, and the confidence of a pretrained classifier used for recognition. This classifier is based on neural networks architectures and is pretrained on original audio recordings, employing three input representations, i.e., raw audio, spectrogram, and gammatonegram. Experiments are conducted, analyzing both the quality of reconstruction and the performance of classifiers in digit recognition, demonstrating that the proposed method yields higher performance in both the quality of reconstruction and digit recognition accuracy.

Video Reconstruction by Spatio-Temporal Fusion of Blurred-Coded Image Pair

Anupama S, Prasan Shedligeri, Abhishek Pal, Kaushik Mitr

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Auto-TLDR; Recovering Video from Motion-Blurred and Coded Exposure Images Using Deep Learning

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Learning-based methods have enabled the recovery of a video sequence from a single motion-blurred image or a single coded exposure image. Recovering video from a single motion-blurred image is a very ill-posed problem and the recovered video usually has many artifacts. In addition to this, the direction of motion is lost and it results in motion ambiguity. However, it has the advantage of fully preserving the information in the static parts of the scene. The traditional coded exposure framework is better-posed but it only samples a fraction of the space-time volume, which is at best $50\%$ of the space-time volume. Here, we propose to use the complementary information present in the fully-exposed (blurred) image along with the coded exposure image to recover a high fidelity video without any motion ambiguity. Our framework consists of a shared encoder followed by an attention module to selectively combine the spatial information from the fully-exposed image with the temporal information from the coded image, which is then super-resolved to recover a non-ambiguous high-quality video. The input to our algorithm is a fully-exposed and coded image pair. Such an acquisition system already exists in the form of a Coded-two-bucket (C2B) camera. We demonstrate that our proposed deep learning approach using blurred-coded image pair produces much better results than those from just a blurred image or just a coded image.

Automatic Semantic Segmentation of Structural Elements related to the Spinal Cord in the Lumbar Region by Using Convolutional Neural Networks

Jhon Jairo Sáenz Gamboa, Maria De La Iglesia-Vaya, Jon Ander Gómez

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Auto-TLDR; Semantic Segmentation of Lumbar Spine Using Convolutional Neural Networks

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This work addresses the problem of automatically segmenting the MR images corresponding to the lumbar spine. The purpose is to detect and delimit the different structural elements like vertebrae, intervertebral discs, nerves, blood vessels, etc. This task is known as semantic segmentation. The approach proposed in this work is based on convolutional neural networks whose output is a mask where each pixel from the input image is classified into one of the possible classes. Classes were defined by radiologists and correspond to structural elements and tissues. The proposed network architectures are variants of the U-Net. Several complementary blocks were used to define the variants: spatial attention models, deep supervision and multi-kernels at input, this last block type is based on the idea of inception. Those architectures which got the best results are described in this paper, and their results are discussed. Two of the proposed architectures outperform the standard U-Net used as baseline.

Deep Residual Attention Network for Hyperspectral Image Reconstruction

Kohei Yorimoto, Xian-Hua Han

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Auto-TLDR; Deep Convolutional Neural Network for Hyperspectral Image Reconstruction from a Snapshot

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Coded aperture snapshot spectral imaging (CASSI) captures a full frame spectral image as a single compressive image and is mandatory to reconstruct the underlying hyperspectral image (HSI) from the snapshot as the post-processing, which is challenge inverse problem due to its ill-posed nature. Existing methods for HSI reconstruction from a snapshot usually employs optimization for solving the formulated image degradation model regularized with the empirically designed priors, and still cannot achieve enough reconstruction accuracy for real HS image analysis systems. Motivated by the recent advances of deep learning for different inverse problems, deep learning based HSI reconstruction method has attracted a lot of attention, and can boost the reconstruction performance. This study proposes a novel deep convolutional neural network (DCNN) based framework for effectively learning the spatial structure and spectral attribute in the underlying HSI with the reciprocal spatial and spectral modules. Further, to adaptively leverage the useful learned feature for better HSI image reconstruction, we integrate residual attention modules into our DCNN via exploring both spatial and spectral attention maps. Experimental results on two benchmark HSI datasets show that our method outperforms state-of-the-art methods in both quantitative values and visual effect.

MBD-GAN: Model-Based Image Deblurring with a Generative Adversarial Network

Li Song, Edmund Y. Lam

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Auto-TLDR; Model-Based Deblurring GAN for Inverse Imaging

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This paper presents a methodology to tackle inverse imaging problems by leveraging the synergistic power of imaging model and deep learning. The premise is that while learning-based techniques have quickly become the methods of choice in various applications, they often ignore the prior knowledge embedded in imaging models. Incorporating the latter has the potential to improve the image estimation. Specifically, we first provide a mathematical basis of using generative adversarial network (GAN) in inverse imaging through considering an optimization framework. Then, we develop the specific architecture that connects the generator and discriminator networks with the imaging model. While this technique can be applied to a variety of problems, from image reconstruction to super-resolution, we take image deblurring as the example here, where we show in detail the implementation and experimental results of what we call the model-based deblurring GAN (MBD-GAN).

Ultrasound Image Restoration Using Weighted Nuclear Norm Minimization

Hanmei Yang, Ye Luo, Jianwei Lu, Jian Lu

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Auto-TLDR; A Nonconvex Low-Rank Matrix Approximation Model for Ultrasound Images Restoration

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Ultrasound images are often contaminated by speckle noise during the acquisition process, which influences the performance of subsequent application. The paper introduces a nonconvex low-rank matrix approximation model for ultrasound images restoration, which integrates the weighted unclear norm minimization (WNNM) and data fidelity term. WNNM can adaptively assign weights on differnt singular values to preserve more details in restored images. The fidelity term about ultrasound images do not be utilized in existing low-rank ultrasound denoising methods. This optimization question can effectively solved by alternating direction method of multipliers (ADMM). The experimental results on simulated images and real medical ultrasound images demonstrate the excellent performance of the proposed method compared with other four state-of-the-art methods.

Variational Capsule Encoder

Harish Raviprakash, Syed Anwar, Ulas Bagci

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Auto-TLDR; Bayesian Capsule Networks for Representation Learning in latent space

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We propose a novel capsule network based variational encoder architecture, called Bayesian capsules (B-Caps), to modulate the mean and standard deviation of the sampling distribution in the latent space. We hypothesize that this approach can learn a better representation of features in the latent space than traditional approaches. Our hypothesis was tested by using the learned latent variables for image reconstruction task, where for MNIST and Fashion-MNIST datasets, different classes were separated successfully in the latent space using our proposed model. Our experimental results have shown improved reconstruction and classification performances for both datasets adding credence to our hypothesis. We also showed that by increasing the latent space dimension, the proposed B-Caps was able to learn a better representation when compared to the traditional variational auto-encoders (VAE). Hence our results indicate the strength of capsule networks in representation learning which has never been examined under the VAE settings before.

Weakly Supervised Geodesic Segmentation of Egyptian Mummy CT Scans

Avik Hati, Matteo Bustreo, Diego Sona, Vittorio Murino, Alessio Del Bue

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Auto-TLDR; A Weakly Supervised and Efficient Interactive Segmentation of Ancient Egyptian Mummies CT Scans Using Geodesic Distance Measure and GrabCut

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In this paper, we tackle the task of automatically analyzing 3D volumetric scans obtained from computed tomography (CT) devices. In particular, we address a particular task for which data is very limited: the segmentation of ancient Egyptian mummies CT scans. We aim at digitally unwrapping the mummy and identify different segments such as body, bandages and jewelry. The problem is complex because of the lack of annotated data for the different semantic regions to segment, thus discouraging the use of strongly supervised approaches. We, therefore, propose a weakly supervised and efficient interactive segmentation method to solve this challenging problem. After segmenting the wrapped mummy from its exterior region using histogram analysis and template matching, we first design a voxel distance measure to find an approximate solution for the body and bandage segments. Here, we use geodesic distances since voxel features as well as spatial relationship among voxels is incorporated in this measure. Next, we refine the solution using a GrabCut based segmentation together with a tracking method on the slices of the scan that assigns labels to different regions in the volume, using limited supervision in the form of scribbles drawn by the user. The efficiency of the proposed method is demonstrated using visualizations and validated through quantitative measures and qualitative unwrapping of the mummy.

End-To-End Multi-Task Learning of Missing Value Imputation and Forecasting in Time-Series Data

Jinhee Kim, Taesung Kim, Jang-Ho Choi, Jaegul Choo

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Auto-TLDR; Time-Series Prediction with Denoising and Imputation of Missing Data

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Multivariate time-series prediction is a common task, but it often becomes challenging due to missing values involved in data caused by unreliable sensors and other issues. In fact, inaccurate imputation of missing values can degrade the downstream prediction performance, so it may be better not to rely on the estimated values of missing data. Furthermore, observed data may contain noise, so denoising them can be helpful for the main task at hand. In response, we propose a novel approach that can automatically utilize the optimal combination of the observed and the estimated values to generate not only complete, but also noise-reduced data by our own gating mechanism. We evaluate our model on real-world time-series datasets and achieved state-of-the-art performance, demonstrating that our method successfully handle the incomplete datasets. Moreover, we present in-depth studies using a carefully designed, synthetic multivariate time-series dataset to verify the effectiveness of the proposed model. The ablation studies and the experimental analysis of the proposed gating mechanism show that the proposed method works as an effective denoising as well as imputation method for time-series classification tasks.

A New Geodesic-Based Feature for Characterization of 3D Shapes: Application to Soft Tissue Organ Temporal Deformations

Karim Makki, Amine Bohi, Augustin Ogier, Marc-Emmanuel Bellemare

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Auto-TLDR; Spatio-Temporal Feature Descriptors for 3D Shape Characterization from Point Clouds

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Spatio-temporal feature descriptors are of great importance for characterizing the local changes of 3D deformable shapes. In this study, we propose a method for characterizing 3D shapes from point clouds and we show a direct application on a study of organ temporal deformations. As an example, we characterize the behavior of the bladder during forced respiratory motion with a reduced number of 3D surface points: first, a set of equidistant points representing the vertices of quadrilateral mesh for the organ surface are tracked throughout a long dynamic MRI sequence using a large deformation diffeomorphic metric mapping (LDDMM) framework. Second, a novel 3D shape descriptor invariant to translation, scale and rotation is proposed for characterizing the temporal organ deformations by employing an Eulerian Partial Differential Equations (PDEs) methodology. We demonstrate the robustness of our feature on both synthetic 3D shapes and realistic dynamic Magnetic Resonance Imaging (MRI) data sequences portraying the bladder deformation during a forced breathing exercise. Promising results are obtained, showing that the proposed feature may be useful for several computer vision applications such as medical imaging, aerodynamics and robotics.

Extended Depth of Field Preserving Color Fidelity for Automated Digital Cytology

Alexandre Bouyssoux, Riadh Fezzani, Jean-Christophe Olivo-Marin

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Auto-TLDR; Multi-Channel Extended Depth of Field for Digital cytology based on the stationary wavelet transform

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This paper presents a multi-channel Extended Depth of Field (EDF) method for digital cytology based on the stationary wavelet transform. With a coefficient selection rule adapted to a precise color recovery, a sharp image can be reconstructed even on images with transparent overlapping cells. The precision and the color fidelity of the proposed method is analyzed. Moreover, an experiment demonstrating the necessity of volume analysis in cytology to achieve precise segmentation on cell clumps is conducted, and the importance of color fidelity in this context is asserted. The proposed method was tested on pap-stained urothelial cells and gray-scale cervical cells with important overlapping.

DSPNet: Deep Learning-Enabled Blind Reduction of Speckle Noise

Yuxu Lu, Meifang Yang, Liu Wen

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Auto-TLDR; Deep Blind DeSPeckling Network for Imaging Applications

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Blind reduction of speckle noise has become a long-standing unsolved problem in several imaging applications, such as medical ultrasound imaging, synthetic aperture radar (SAR) imaging, and underwater sonar imaging, etc. The unwanted noise could lead to negative effects on the reliable detection and recognition of objects of interest. From a statistical point of view, speckle noise could be assumed to be multiplicative, significantly different from the common additive Gaussian noise. The purpose of this study is to blindly reduce the speckle noise under non-ideal imaging conditions. The multiplicative relationship between latent sharp image and random noise will be first converted into an additive version through a logarithmic transformation. To promote imaging performance, we introduced the feature pyramid network (FPN) and atrous spatial pyramid pooling (ASPP), contributing to a more powerful deep blind DeSPeckling Network (named as DSPNet). In particular, DSPNet is mainly composed of two subnetworks, i.e., Log-NENet (i.e., noise estimation network in logarithmic domain) and Log-DNNet (i.e., denoising network in logarithmic domain). Log-NENet and Log-DNNet are, respectively, proposed to estimate noise level map and reduce random noise in logarithmic domain. The multi-scale mixed loss function is further proposed to improve the robust generalization of DSPNet. The proposed deep blind despeckling network is capable of reducing random noise and preserving salient image details. Both synthetic and realistic experiments have demonstrated the superior performance of our DSPNet in terms of quantitative evaluations and visual image qualities.

JUMPS: Joints Upsampling Method for Pose Sequences

Lucas Mourot, Francois Le Clerc, Cédric Thébault, Pierre Hellier

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Auto-TLDR; JUMPS: Increasing the Number of Joints in 2D Pose Estimation and Recovering Occluded or Missing Joints

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Human Pose Estimation is a low-level task useful for surveillance, human action recognition, and scene understanding at large. It also offers promising perspectives for the animation of synthetic characters. For all these applications, and especially the latter, estimating the positions of many joints is desirable for improved performance and realism. To this purpose, we propose a novel method called JUMPS for increasing the number of joints in 2D pose estimates and recovering occluded or missing joints. We believe this is the first attempt to address the issue. We build on a deep generative model that combines a GAN and an encoder. The GAN learns the distribution of high-resolution human pose sequences, the encoder maps the input low-resolution sequences to its latent space. Inpainting is obtained by computing the latent representation whose decoding by the GAN generator optimally matches the joints locations at the input. Post-processing a 2D pose sequence using our method provides a richer representation of the character motion. We show experimentally that the localization accuracy of the additional joints is on average on par with the original pose estimates.

Segmentation of Axillary and Supraclavicular Tumoral Lymph Nodes in PET/CT: A Hybrid CNN/Component-Tree Approach

Diana Lucia Farfan Cabrera, Nicolas Gogin, David Morland, Benoît Naegel, Dimitri Papathanassiou, Nicolas Passat

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Auto-TLDR; Coupling Convolutional Neural Networks and Component-Trees for Lymph node Segmentation from PET/CT Images

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The analysis of axillary and supraclavicular lymph nodes is a primary prognostic factor for the staging of breast cancer. However, due to the size of lymph nodes and the low resolution of PET data, their segmentation is challenging. We investigate the relevance of considering axillary and supraclavicular lymph node segmentation from PET/CT images by coupling Convolutional Neural Networks (CNNs) and Component-Trees (C-Trees). Building upon the U-Net architecture, we propose a framework that couples a multi-modal U-Net fed with PET and CT, coupled with a hierarchical model obtained from the PET that provides additional high-level region-based features as input channels. Our working hypotheses are twofold. First, we take advantage of both anatomical information from CT for detecting the nodes, and from functional information from PET for detecting the pathological ones. Second, we consider region-based attributes extracted from C-Tree analysis of 3D PET/CT images to improve the CNN segmentation. We carried out experiments on a dataset of 240 pathological lymph nodes from 52 patients scans, and compared our outputs with human expert-defined ground-truth, leading to promising results.

Galaxy Image Translation with Semi-Supervised Noise-Reconstructed Generative Adversarial Networks

Qiufan Lin, Dominique Fouchez, Jérôme Pasquet

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Auto-TLDR; Semi-supervised Image Translation with Generative Adversarial Networks Using Paired and Unpaired Images

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Image-to-image translation with Deep Learning neural networks, particularly with Generative Adversarial Networks (GANs), is one of the most powerful methods for simulating astronomical images. However, current work is limited to utilizing paired images with supervised translation, and there has been rare discussion on reconstructing noise background that encodes instrumental and observational effects. These limitations might be harmful for subsequent scientific applications in astrophysics. Therefore, we aim to develop methods for using unpaired images and preserving noise characteristics in image translation. In this work, we propose a two-way image translation model using GANs that exploits both paired and unpaired images in a semi-supervised manner, and introduce a noise emulating module that is able to learn and reconstruct noise characterized by high-frequency features. By experimenting on multi-band galaxy images from the Sloan Digital Sky Survey (SDSS) and the Canada France Hawaii Telescope Legacy Survey (CFHT), we show that our method recovers global and local properties effectively and outperforms benchmark image translation models. To our best knowledge, this work is the first attempt to apply semi-supervised methods and noise reconstruction techniques in astrophysical studies.

FOANet: A Focus of Attention Network with Application to Myocardium Segmentation

Zhou Zhao, Elodie Puybareau, Nicolas Boutry, Thierry Geraud

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Auto-TLDR; FOANet: A Hybrid Loss Function for Myocardium Segmentation of Cardiac Magnetic Resonance Images

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In myocardium segmentation of cardiac magnetic resonance images, ambiguities often appear near the boundaries of the target domains due to tissue similarities. To address this issue, we propose a new architecture, called FOANet, which can be decomposed in three main steps: a localization step, a Gaussian-based contrast enhancement step, and a segmentation step. This architecture is supplied with a hybrid loss function that guides the FOANet to study the transformation relationship between the input image and the corresponding label in a threelevel hierarchy (pixel-, patch- and map-level), which is helpful to improve segmentation and recovery of the boundaries. We demonstrate the efficiency of our approach on two public datasets in terms of regional and boundary segmentations.

Wireless Localisation in WiFi Using Novel Deep Architectures

Peizheng Li, Han Cui, Aftab Khan, Usman Raza, Robert Piechocki, Angela Doufexi, Tim Farnham

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Auto-TLDR; Deep Neural Network for Indoor Localisation of WiFi Devices in Indoor Environments

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This paper studies the indoor localisation of WiFi devices based on a commodity chipset and standard channel sounding. First, we present a novel shallow neural network (SNN) in which features are extracted from the channel state information (CSI) corresponding to WiFi subcarriers received on different antennas and used to train the model. The single layer architecture of this localisation neural network makes it lightweight and easy-to-deploy on devices with stringent constraints on computational resources. We further investigate for localisation the use of deep learning models and design novel architectures for convolutional neural network (CNN) and long-short term memory (LSTM). We extensively evaluate these localisation algorithms for continuous tracking in indoor environments. Experimental results prove that even an SNN model, after a careful handcrafted feature extraction, can achieve accurate localisation. Meanwhile, using a well-organised architecture, the neural network models can be trained directly with raw data from the CSI and localisation features can be automatically extracted to achieve accurate position estimates. We also found that the performance of neural network-based methods are directly affected by the number of anchor access points (APs) regardless of their structure. With three APs, all neural network models proposed in this paper can obtain localisation accuracy of around 0.5 metres. In addition the proposed deep NN architecture reduces the data pre-processing time by 6.5 hours compared with a shallow NN using the data collected in our testbed. In the deployment phase, the inference time is also significantly reduced to 0.1 ms per sample. We also demonstrate the generalisation capability of the proposed method by evaluating models using different target movement characteristics to the ones in which they were trained.

Deep Multi-Stage Model for Automated Landmarking of Craniomaxillofacial CT Scans

Simone Palazzo, Giovanni Bellitto, Luca Prezzavento, Francesco Rundo, Ulas Bagci, Daniela Giordano, Rosalia Leonardi, Concetto Spampinato

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Auto-TLDR; Automated Landmarking of Craniomaxillofacial CT Images Using Deep Multi-Stage Architecture

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In this paper we define a deep multi-stage architecture for automated landmarking of craniomaxillofacial (CMF) CT images. Our model is composed of three subnetworks that first localize, on reduced-resolution images, areas where land-marks may be found and then refine the search, at full-resolution scale, through a hierarchical structure aiming at increasing the granularity of the investigated region. The multi-stage pipeline is designed to deal with full resolution data and does not require any additional pre-processing step to reduce search space, as opposed to existing methods that can be only adopted for searching landmarks located in well-defined anatomical structures (e.g.,mandibles). The automated landmarking system is tested on identifying landmarks located in several CMF regions, achieving an average error of 0.8 mm, significantly lower than expert readings. The proposed model also outperforms baselines and is on par with existing models that employ additional upstream segmentation, on state-of-the-art benchmarks.

FMRI Brain Networks As Statistical Mechanical Ensembles

Jianjia Wang, Hui Wu, Edwin Hancock

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Auto-TLDR; Microcanonical Ensemble Methods for FMRI Brain Networks for Alzheimer's Disease

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In this paper, we apply ensemble methods from statistical physics to analyse fMRI brain networks for Alzheimer's patients. By mapping the nodes in a network to virtual particles in a thermal system, the microcanonical ensemble and the canonical ensemble are analogous to two different fMRI network representations. These representations are obtained by selecting a threshold on the BOLD time series correlations between nodes in different ways. The microcanonical ensemble corresponds to a set of networks with a fixed fraction of edges, while the canonical ensemble corresponds to the set networks with edges obtained with a fixed value of the threshold. In the former case, there is zero variance in the number of edges in each network, while in the latter case the set of networks have a variance in the number of edges. Ensemble methods describe the macroscopic properties of a network by considering the underlying microscopic characterisations which are in turn closely related to the degree configuration and network entropy. Our treatment allows us to specify new partition functions for fMRI brain networks, and to explore a phase transition in the degree distribution. The resulting method turns out to be an effective tool to identify the most salient anatomical brain regions in Alzheimer's disease and provides a tool to distinguish groups of patients in different stages of the disease.

Modulation Pattern Detection Using Complex Convolutions in Deep Learning

Jakob Krzyston, Rajib Bhattacharjea, Andrew Stark

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Auto-TLDR; Complex Convolutional Neural Networks for Modulation Pattern Classification

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Telecommunications relies on transmitting and receiving signals containing specific modulation patterns in both the real and complex domains. Classifying modulation patterns is difficult because noise and poor signal to noise ratio (SNR) obfuscate the `input' signal. Although deep learning approaches have shown great promise over statistical methods in this problem space, deep learning frameworks have been developed to deal with exclusively real-valued data and are unable to compute convolutions for complex-valued data. In previous work, we have shown that CNNs using complex convolutions are able to classify modulation patterns by up to 35\% more accurately than comparable CNN architectures. In this paper, we demonstrate that enabling complex convolutions in CNNs are (1) up to 50\% better at recognizing modulation patterns in complex signals with high SNR when trained on low SNR data, and (2) up to 12\% better at recognizing modulation patterns in complex signals with low SNR when trained on high SNR data. Additionally, we compare the features learned in each experiment by visualizing the inputs that results in one-hot modulation pattern classification for each network.

Boosting High-Level Vision with Joint Compression Artifacts Reduction and Super-Resolution

Xiaoyu Xiang, Qian Lin, Jan Allebach

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Auto-TLDR; A Context-Aware Joint CAR and SR Neural Network for High-Resolution Text Recognition and Face Detection

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Due to the limits of bandwidth and storage space, digital images are usually down-scaled and compressed when transmitted over networks, resulting in loss of details and jarring artifacts that can lower the performance of high-level visual tasks. In this paper, we aim to generate an artifact-free high-resolution image from a low-resolution one compressed with an arbitrary quality factor by exploring joint compression artifacts reduction (CAR) and super-resolution (SR) tasks. First, we propose a context-aware joint CAR and SR neural network (CAJNN) that integrates both local and non-local features to solve CAR and SR in one-stage. Finally, a deep reconstruction network is adopted to predict high quality and high-resolution images. Evaluation on CAR and SR benchmark datasets shows that our CAJNN model outperforms previous methods and also takes 26.2% less runtime. Based on this model, we explore addressing two critical challenges in high-level computer vision: optical character recognition of low-resolution texts, and extremely tiny face detection. We demonstrate that CAJNN can serve as an effective image preprocessing method and improve the accuracy for real-scene text recognition (from 85.30% to 85.75%) and the average precision for tiny face detection (from 0.317 to 0.611).

Leveraging Synthetic Subject Invariant EEG Signals for Zero Calibration BCI

Nik Khadijah Nik Aznan, Amir Atapour-Abarghouei, Stephen Bonner, Jason Connolly, Toby Breckon

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Auto-TLDR; SIS-GAN: Subject Invariant SSVEP Generative Adversarial Network for Brain-Computer Interface

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Recently, substantial progress has been made in the area of Brain-Computer Interface (BCI) using modern machine learning techniques to decode and interpret brain signals. While Electroencephalography (EEG) has provided a non-invasive method of interfacing with a human brain, the acquired data is often heavily subject and session dependent. This makes seamless incorporation of such data into real-world applications intractable as the subject and session data variance can lead to long and tedious calibration requirements and cross-subject generalisation issues. Focusing on a Steady State Visual Evoked Potential (SSVEP) classification systems, we propose a novel means of generating highly-realistic synthetic EEG data invariant to any subject, session or other environmental conditions. Our approach, entitled the Subject Invariant SSVEP Generative Adversarial Network (SIS-GAN), produces synthetic EEG data from multiple SSVEP classes using a single network. Additionally, by taking advantage of a fixed-weight pre-trained subject classification network, we ensure that our generative model remains agnostic to subject-specific features and thus produces subject-invariant data that can be applied to new previously unseen subjects. Our extensive experimental evaluation demonstrates the efficacy of our synthetic data, leading to superior performance, with improvements of up to 16% in zero-calibration classification tasks when trained using our subject-invariant synthetic EEG signals.

Radar Image Reconstruction from Raw ADC Data Using Parametric Variational Autoencoder with Domain Adaptation

Michael Stephan, Thomas Stadelmayer, Avik Santra, Georg Fischer, Robert Weigel, Fabian Lurz

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Auto-TLDR; Parametric Variational Autoencoder-based Human Target Detection and Localization for Frequency Modulated Continuous Wave Radar

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This paper presents a parametric variational autoencoder-based human target detection and localization framework working directly with the raw analog-to-digital converter data from the frequency modulated continuous wave radar. We propose a parametrically constrained variational autoencoder, with residual and skip connections, capable of generating the clustered and localized target detections on the range-angle image. Furthermore, to circumvent the problem of training the proposed neural network on all possible scenarios using real radar data, we propose domain adaptation strategies whereby we first train the neural network using ray tracing based model data and then adapt the network to work on real sensor data. This strategy ensures better generalization and scalability of the proposed neural network even though it is trained with limited radar data. We demonstrate the superior detection and localization performance of our proposed solution compared to the conventional signal processing pipeline and earlier state-of-art deep U-Net architecture with range-doppler images as inputs.