pwc-archive/papers-with-abstracts huggingface dataset:
PhishGAN: Data Augmentation and Identification of Homoglpyh Attacks
Authors: Joon Sern Lee, Gui Peng David Yam, Jin Hao Chan
Date: 2020-06-24 00:00:00
Tasks: Data Augmentation, Generative Adversarial Network

Homoglyph attacks are a common technique used by hackers to conduct phishing. Domain names or links that are visually similar to actual ones are created via punycode to obfuscate the attack, making the victim more susceptible to phishing. For example, victims may mistake "|inkedin.com" for "linkedin.com" and in the process, divulge personal details to the fake website. Current State of The Art (SOTA) typically make use of string comparison algorithms (e.g. Levenshtein Distance), which are computationally heavy. One reason for this is the lack of publicly available datasets thus hindering the training of more advanced Machine Learning (ML) models. Furthermore, no one font is able to render all types of punycode correctly, posing a significant challenge to the creation of a dataset that is unbiased toward any particular font. This coupled with the vast number of internet domains pose a challenge in creating a dataset that can capture all possible variations. Here, we show how a conditional Generative Adversarial Network (GAN), PhishGAN, can be used to generate images of hieroglyphs, conditioned on non-homoglpyh input text images. Practical changes to current SOTA were required to facilitate the generation of more varied homoglyph text-based images. We also demonstrate a workflow of how PhishGAN together with a Homoglyph Identifier (HI) model can be used to identify the domain the homoglyph was trying to imitate. Furthermore, we demonstrate how PhishGAN's ability to generate datasets on the fly facilitate the quick adaptation of cybersecurity systems to detect new threats as they emerge.
A Parameterized Family of Meta-Submodular Functions
Authors: Mehrdad Ghadiri, Richard Santiago, Bruce Shepherd
Date: 2020-06-23 00:00:00
Tasks: Diversity

Submodular function maximization has found a wealth of new applications in machine learning models during the past years. The related supermodular maximization models (submodular minimization) also offer an abundance of applications, but they appeared to be highly intractable even under simple cardinality constraints. Hence, while there are well-developed tools for maximizing a submodular function subject to a matroid constraint, there is much less work on the corresponding supermodular maximization problems. We give a broad parameterized family of monotone functions which includes submodular functions and a class of supermodular functions containing diversity functions. Functions in this parameterized family are called \emph{$\gamma$-meta-submodular}. We develop local search algorithms with approximation factors that depend only on the parameter $\gamma$. We show that the $\gamma$-meta-submodular families include well-known classes of functions such as meta-submodular functions ($\gamma=0$), metric diversity functions and proportionally submodular functions (both with $\gamma=1$), diversity functions based on negative-type distances or Jensen-Shannon divergence (both with $\gamma=2$), and $\sigma$-semi metric diversity functions ($\gamma = \sigma$).
The Boomerang Sampler
Authors: Joris Bierkens, Sebastiano Grazzi, Kengo Kamatani, Gareth Roberts
Date: 2020-06-24 00:00:00
Proceeding: ICML 2020 1

This paper introduces the Boomerang Sampler as a novel class of continuous-time non-reversible Markov chain Monte Carlo algorithms. The methodology begins by representing the target density as a density, $e^{-U}$, with respect to a prescribed (usually) Gaussian measure and constructs a continuous trajectory consisting of a piecewise elliptical path. The method moves from one elliptical orbit to another according to a rate function which can be written in terms of $U$. We demonstrate that the method is easy to implement and demonstrate empirically that it can out-perform existing benchmark piecewise deterministic Markov processes such as the bouncy particle sampler and the Zig-Zag. In the Bayesian statistics context, these competitor algorithms are of substantial interest in the large data context due to the fact that they can adopt data subsampling techniques which are exact (ie induce no error in the stationary distribution). We demonstrate theoretically and empirically that we can also construct a control-variate subsampling boomerang sampler which is also exact, and which possesses remarkable scaling properties in the large data limit. We furthermore illustrate a factorised version on the simulation of diffusion bridges.
Post-DAE: Anatomically Plausible Segmentation via Post-Processing with Denoising Autoencoders
Authors: Agostina J. Larrazabal, César Martínez, Ben Glocker, Enzo Ferrante
Date: 2020-06-24 00:00:00
Tasks: Denoising, Image Segmentation, Segmentation, Semantic Segmentation, valid

We introduce Post-DAE, a post-processing method based on denoising autoencoders (DAE) to improve the anatomical plausibility of arbitrary biomedical image segmentation algorithms. Some of the most popular segmentation methods (e.g. based on convolutional neural networks or random forest classifiers) incorporate additional post-processing steps to ensure that the resulting masks fulfill expected connectivity constraints. These methods operate under the hypothesis that contiguous pixels with similar aspect should belong to the same class. Even if valid in general, this assumption does not consider more complex priors like topological restrictions or convexity, which cannot be easily incorporated into these methods. Post-DAE leverages the latest developments in manifold learning via denoising autoencoders. First, we learn a compact and non-linear embedding that represents the space of anatomically plausible segmentations. Then, given a segmentation mask obtained with an arbitrary method, we reconstruct its anatomically plausible version by projecting it onto the learnt manifold. The proposed method is trained using unpaired segmentation mask, what makes it independent of intensity information and image modality. We performed experiments in binary and multi-label segmentation of chest X-ray and cardiac magnetic resonance images. We show how erroneous and noisy segmentation masks can be improved using Post-DAE. With almost no additional computation cost, our method brings erroneous segmentations back to a feasible space.
COVID-CXNet: Detecting COVID-19 in Frontal Chest X-ray Images using Deep Learning
Authors: Arman Haghanifar, Mahdiyar Molahasani Majdabadi, Younhee Choi, S. Deivalakshmi, Seokbum Ko
Date: 2020-06-16 00:00:00
Tasks: Decision Making, Image Classification, Multi-class Classification, Pneumonia Detection, Transfer Learning

One of the primary clinical observations for screening the infectious by the novel coronavirus is capturing a chest x-ray image. In most of the patients, a chest x-ray contains abnormalities, such as consolidation, which are the results of COVID-19 viral pneumonia. In this study, research is conducted on efficiently detecting imaging features of this type of pneumonia using deep convolutional neural networks in a large dataset. It is demonstrated that simple models, alongside the majority of pretrained networks in the literature, focus on irrelevant features for decision-making. In this paper, numerous chest x-ray images from various sources are collected, and the largest publicly accessible dataset is prepared. Finally, using the transfer learning paradigm, the well-known CheXNet model is utilized for developing COVID-CXNet. This powerful model is capable of detecting the novel coronavirus pneumonia based on relevant and meaningful features with precise localization. COVID-CXNet is a step towards a fully automated and robust COVID-19 detection system.
Role of Edge Device and Cloud Machine Learning in Point-of-Care Solutions Using Imaging Diagnostics for Population Screening
Authors: Amit Kharat, Vinay Duddalwar, Krishna Saoji, Ashrika Gaikwad, Viraj Kulkarni, Gunjan Naik, Rohit Lokwani, Swaraj Kasliwal, Sudeep Kondal, Tanveer Gupte, Aniruddha Pant
Date: 2020-06-18 00:00:00

Edge devices are revolutionizing diagnostics. Edge devices can reside within or adjacent to imaging tools such as digital Xray, CT, MRI, or ultrasound equipment. These devices are either CPUs or GPUs with advanced processing deep and machine learning (artificial intelligence) algorithms that assist in classification and triage solutions to flag studies as either normal or abnormal, TB or healthy (in case of TB screening), suspected COVID-19/other pneumonia or unremarkable (in hospital or hotspot settings). These can be deployed as screening point-of-care (PoC) solutions; this is particularly true for digital and portable X-ray devices. Edge device learning can also be used for mammography and CT studies where it can identify microcalcification and stroke, respectively. These solutions can be considered the first line of pre-screening before the imaging specialist actually reviews scans and makes a final diagnosis. The key advantage of these tools is that they are instant, can be deployed remotely where experts are not available to perform pre-screening before the experts actually review, and are not limited by internet bandwidth as the nano learning data centers are placed next to the device.
Interpretable Deep Models for Cardiac Resynchronisation Therapy Response Prediction
Authors: Esther Puyol-Antón, Chen Chen, James R. Clough, Bram Ruijsink, Baldeep S. Sidhu, Justin Gould, Bradley Porter, Mark Elliott, Vishal Mehta, Daniel Rueckert, Christopher A. Rinaldi, Andrew P. King
Date: 2020-06-24 00:00:00
Tasks: Clinical Knowledge, image-classification, Image Classification, Medical Image Classification, Prediction, Specificity, Transfer Learning

Advances in deep learning (DL) have resulted in impressive accuracy in some medical image classification tasks, but often deep models lack interpretability. The ability of these models to explain their decisions is important for fostering clinical trust and facilitating clinical translation. Furthermore, for many problems in medicine there is a wealth of existing clinical knowledge to draw upon, which may be useful in generating explanations, but it is not obvious how this knowledge can be encoded into DL models - most models are learnt either from scratch or using transfer learning from a different domain. In this paper we address both of these issues. We propose a novel DL framework for image-based classification based on a variational autoencoder (VAE). The framework allows prediction of the output of interest from the latent space of the autoencoder, as well as visualisation (in the image domain) of the effects of crossing the decision boundary, thus enhancing the interpretability of the classifier. Our key contribution is that the VAE disentangles the latent space based on `explanations' drawn from existing clinical knowledge. The framework can predict outputs as well as explanations for these outputs, and also raises the possibility of discovering new biomarkers that are separate (or disentangled) from the existing knowledge. We demonstrate our framework on the problem of predicting response of patients with cardiomyopathy to cardiac resynchronization therapy (CRT) from cine cardiac magnetic resonance images. The sensitivity and specificity of the proposed model on the task of CRT response prediction are 88.43% and 84.39% respectively, and we showcase the potential of our model in enhancing understanding of the factors contributing to CRT response.
Stacked Convolutional Neural Network for Diagnosis of COVID-19 Disease from X-ray Images
Authors: Mahesh Gour, Sweta Jain
Date: 2020-06-22 00:00:00

Automatic and rapid screening of COVID-19 from the chest X-ray images has become an urgent need in this pandemic situation of SARS-CoV-2 worldwide in 2020. However, accurate and reliable screening of patients is a massive challenge due to the discrepancy between COVID-19 and other viral pneumonia in X-ray images. In this paper, we design a new stacked convolutional neural network model for the automatic diagnosis of COVID-19 disease from the chest X-ray images. We obtain different sub-models from the VGG19 and developed a 30-layered CNN model (named as CovNet30) during the training, and obtained sub-models are stacked together using logistic regression. The proposed CNN model combines the discriminating power of the different CNN`s sub-models and classifies chest X-ray images into COVID-19, Normal, and Pneumonia classes. In addition, we generate X-ray images dataset referred to as COVID19CXr, which includes 2764 chest x-ray images of 1768 patients from the three publicly available data repositories. The proposed stacked CNN achieves an accuracy of 92.74%, the sensitivity of 93.33%, PPV of 92.13%, and F1-score of 0.93 for the classification of X-ray images. Our proposed approach shows its superiority over the existing methods for the diagnosis of the COVID-19 from the X-ray images.
MRI Image Reconstruction via Learning Optimization Using Neural ODEs
Authors: Eric Z. Chen, Terrence Chen, Shanhui Sun
Date: 2020-06-24 00:00:00
Tasks: Image Reconstruction, MRI Reconstruction

We propose to formulate MRI image reconstruction as an optimization problem and model the optimization trajectory as a dynamic process using ordinary differential equations (ODEs). We model the dynamics in ODE with a neural network and solve the desired ODE with the off-the-shelf (fixed) solver to obtain reconstructed images. We extend this model and incorporate the knowledge of off-the-shelf ODE solvers into the network design (learned solvers). We investigate several models based on three ODE solvers and compare models with fixed solvers and learned solvers. Our models achieve better reconstruction results and are more parameter efficient than other popular methods such as UNet and cascaded CNN. We introduce a new way of tackling the MRI reconstruction problem by modeling the continuous optimization dynamics using neural ODEs.
Caffe Barista: Brewing Caffe with FPGAs in the Training Loop
Authors: Diederik Adriaan Vink, Aditya Rajagopal, Stylianos I. Venieris, Christos-Savvas Bouganis
Date: 2020-06-18 00:00:00

As the complexity of deep learning (DL) models increases, their compute requirements increase accordingly. Deploying a Convolutional Neural Network (CNN) involves two phases: training and inference. With the inference task typically taking place on resource-constrained devices, a lot of research has explored the field of low-power inference on custom hardware accelerators. On the other hand, training is both more compute- and memory-intensive and is primarily performed on power-hungry GPUs in large-scale data centres. CNN training on FPGAs is a nascent field of research. This is primarily due to the lack of tools to easily prototype and deploy various hardware and/or algorithmic techniques for power-efficient CNN training. This work presents Barista, an automated toolflow that provides seamless integration of FPGAs into the training of CNNs within the popular deep learning framework Caffe. To the best of our knowledge, this is the only tool that allows for such versatile and rapid deployment of hardware and algorithms for the FPGA-based training of CNNs, providing the necessary infrastructure for further research and development.
Movement Tracking by Optical Flow Assisted Inertial Navigation
Authors: Lassi Meronen, William J. Wilkinson, Arno Solin
Date: 2020-06-24 00:00:00
Tasks: Optical Flow Estimation, Probabilistic Deep Learning

Robust and accurate six degree-of-freedom tracking on portable devices remains a challenging problem, especially on small hand-held devices such as smartphones. For improved robustness and accuracy, complementary movement information from an IMU and a camera is often fused. Conventional visual-inertial methods fuse information from IMUs with a sparse cloud of feature points tracked by the device camera. We consider a visually dense approach, where the IMU data is fused with the dense optical flow field estimated from the camera data. Learning-based methods applied to the full image frames can leverage visual cues and global consistency of the flow field to improve the flow estimates. We show how a learning-based optical flow model can be combined with conventional inertial navigation, and how ideas from probabilistic deep learning can aid the robustness of the measurement updates. The practical applicability is demonstrated on real-world data acquired by an iPad in a challenging low-texture environment.
Feedback Graph Attention Convolutional Network for Medical Image Enhancement
Authors: Xiaobin Hu, Yanyang Yan, Wenqi Ren, Hongwei Li, Yu Zhao, Amirhossein Bayat, Bjoern Menze
Date: 2020-06-24 00:00:00
Tasks: Diffusion  MRI, Graph Attention, Graph Similarity, Image Enhancement, Medical Image Enhancement, Super-Resolution

Artifacts, blur and noise are the common distortions degrading MRI images during the acquisition process, and deep neural networks have been demonstrated to help in improving image quality. To well exploit global structural information and texture details, we propose a novel biomedical image enhancement network, named Feedback Graph Attention Convolutional Network (FB-GACN). As a key innovation, we consider the global structure of an image by building a graph network from image sub-regions that we consider to be node features, linking them non-locally according to their similarity. The proposed model consists of three main parts: 1) The parallel graph similarity branch and content branch, where the graph similarity branch aims at exploiting the similarity and symmetry across different image sub-regions in low-resolution feature space and provides additional priors for the content branch to enhance texture details. 2) A feedback mechanism with a recurrent structure to refine low-level representations with high-level information and generate powerful high-level texture details by handling the feedback connections. 3) A reconstruction to remove the artifacts and recover super-resolution images by using the estimated sub-region correlation priors obtained from the graph similarity branch. We evaluate our method on two image enhancement tasks: i) cross-protocol super resolution of diffusion MRI; ii) artifact removal of FLAIR MR images. Experimental results demonstrate that the proposed algorithm outperforms the state-of-the-art methods.
COVIDLite: A depth-wise separable deep neural network with white balance and CLAHE for detection of COVID-19
Authors: Manu Siddhartha, Avik Santra
Date: 2020-06-19 00:00:00
Tasks: Binary Classification, Diagnostic, General Classification, image-classification, Image Classification, Quantization

Background and Objective:Currently, the whole world is facing a pandemic disease, novel Coronavirus also known as COVID-19, which spread in more than 200 countries with around 3.3 million active cases and 4.4 lakh deaths approximately. Due to rapid increase in number of cases and limited supply of testing kits, availability of alternative diagnostic method is necessary for containing the spread of COVID-19 cases at an early stage and reducing the death count. For making available an alternative diagnostic method, we proposed a deep neural network based diagnostic method which can be easily integrated with mobile devices for detection of COVID-19 and viral pneumonia using Chest X-rays (CXR) images. Methods:In this study, we have proposed a method named COVIDLite, which is a combination of white balance followed by Contrast Limited Adaptive Histogram Equalization (CLAHE) and depth-wise separable convolutional neural network (DSCNN). In this method, white balance followed by CLAHE is used as an image preprocessing step for enhancing the visibility of CXR images and DSCNN trained using sparse cross entropy is used for image classification with lesser parameters and significantly lighter in size, i.e., 8.4 MB without quantization. Results:The proposed COVIDLite method resulted in improved performance in comparison to vanilla DSCNN with no pre-processing. The proposed method achieved higher accuracy of 99.58% for binary classification, whereas 96.43% for multiclass classification and out-performed various state-of-the-art methods. Conclusion:Our proposed method, COVIDLite achieved exceptional results on various performance metrics. With detailed model interpretations, COVIDLite can assist radiologists in detecting COVID-19 patients from CXR images and can reduce the diagnosis time significantly.
Effective Elastic Scaling of Deep Learning Workloads
Authors: Vaibhav Saxena, K. R. Jayaram, Saurav Basu, Yogish Sabharwal, Ashish Verma
Date: 2020-06-24 00:00:00
Tasks: Deep Learning

The increased use of deep learning (DL) in academia, government and industry has, in turn, led to the popularity of on-premise and cloud-hosted deep learning platforms, whose goals are to enable organizations utilize expensive resources effectively, and to share said resources among multiple teams in a fair and effective manner. In this paper, we examine the elastic scaling of Deep Learning (DL) jobs over large-scale training platforms and propose a novel resource allocation strategy for DL training jobs, resulting in improved job run time performance as well as increased cluster utilization. We begin by analyzing DL workloads and exploit the fact that DL jobs can be run with a range of batch sizes without affecting their final accuracy. We formulate an optimization problem that explores a dynamic batch size allocation to individual DL jobs based on their scaling efficiency, when running on multiple nodes. We design a fast dynamic programming based optimizer to solve this problem in real-time to determine jobs that can be scaled up/down, and use this optimizer in an autoscaler to dynamically change the allocated resources and batch sizes of individual DL jobs. We demonstrate empirically that our elastic scaling algorithm can complete up to $\approx 2 \times$ as many jobs as compared to a strong baseline algorithm that also scales the number of GPUs but does not change the batch size. We also demonstrate that the average completion time with our algorithm is up to $\approx 10 \times$ faster than that of the baseline.
Learning Tumor Growth via Follow-Up Volume Prediction for Lung Nodules
Authors: Yamin Li, Jiancheng Yang, Yi Xu, Jingwei Xu, Xiaodan Ye, Guangyu Tao, Xueqian Xie, Guixue Liu
Date: 2020-06-24 00:00:00
Tasks: Diagnostic, Management, Representation Learning

Follow-up serves an important role in the management of pulmonary nodules for lung cancer. Imaging diagnostic guidelines with expert consensus have been made to help radiologists make clinical decision for each patient. However, tumor growth is such a complicated process that it is difficult to stratify high-risk nodules from low-risk ones based on morphologic characteristics. On the other hand, recent deep learning studies using convolutional neural networks (CNNs) to predict the malignancy score of nodules, only provides clinicians with black-box predictions. To this end, we propose a unified framework, named Nodule Follow-Up Prediction Network (NoFoNet), which predicts the growth of pulmonary nodules with high-quality visual appearances and accurate quantitative results, given any time interval from baseline observations. It is achieved by predicting future displacement field of each voxel with a WarpNet. A TextureNet is further developed to refine textural details of WarpNet outputs. We also introduce techniques including Temporal Encoding Module and Warp Segmentation Loss to encourage time-aware and shape-aware representation learning. We build an in-house follow-up dataset from two medical centers to validate the effectiveness of the proposed method. NoFoNet significantly outperforms direct prediction by a U-Net in terms of visual quality; more importantly, it demonstrates accurate differentiating performance between high- and low-risk nodules. Our promising results suggest the potentials in computer aided intervention for lung nodule management.