pwc-archive/papers-with-abstracts huggingface dataset:
Deep Mining Generation of Lung Cancer Malignancy Models from Chest X-ray Images
Authors: Michael J. Horry, Subrata Chakraborty, Biswajeet Pradhan, Manoranjan Paul, Douglas P. S. Gomes, Anwaar Ul-Haq
Date: 2020-12-10 00:00:00
Tasks: Deep Learning, Lung Nodule Detection, Specificity

Lung cancer is the leading cause of cancer death and morbidity worldwide. Many studies have shown machine learning models to be effective at detecting lung nodules from chest X-ray images. However, these techniques have yet to be embraced by the medical community due to several practical, ethical, and regulatory constraints stemming from the black-box nature of deep learning models. Additionally, most lung nodules visible on chest X-ray are benign; therefore, the narrow task of computer vision-based lung nodule detection cannot be equated to automated lung cancer detection. Addressing both concerns, this study introduces a novel hybrid deep learning and decision tree-based computer vision model which presents lung cancer malignancy predictions as interpretable decision trees. The deep learning component of this process is trained using a large publicly available dataset on pathological biomarkers associated with lung cancer. These models are then used to inference biomarker scores for chest X-ray images from two, independent data sets for which malignancy metadata is available. We mine multi-variate predictive models by fitting shallow decision trees to the malignancy stratified datasets and interrogate a range of metrics to determine the best model. Our best decision tree model achieves sensitivity and specificity of 86.7% and 80.0% respectively with a positive predictive value of 92.9%. Decision trees mined using this method may be considered as a starting point for refinement into clinically useful multi-variate lung cancer malignancy models for implementation as a workflow augmentation tool to improve the efficiency of human radiologists.
Deep Learning Methods For Synthetic Aperture Radar Image Despeckling: An Overview Of Trends And Perspectives
Authors: Giulia Fracastoro, Enrico Magli, Giovanni Poggi, Giuseppe Scarpa, Diego Valsesia, Luisa Verdoliva
Date: 2020-12-10 00:00:00
Tasks: Deep Learning, Sar Image Despeckling

Synthetic aperture radar (SAR) images are affected by a spatially-correlated and signal-dependent noise called speckle, which is very severe and may hinder image exploitation. Despeckling is an important task that aims at removing such noise, so as to improve the accuracy of all downstream image processing tasks. The first despeckling methods date back to the 1970's, and several model-based algorithms have been developed in the subsequent years. The field has received growing attention, sparkled by the availability of powerful deep learning models that have yielded excellent performance for inverse problems in image processing. This paper surveys the literature on deep learning methods applied to SAR despeckling, covering both the supervised and the more recent self-supervised approaches. We provide a critical analysis of existing methods with the objective to recognize the most promising research lines, to identify the factors that have limited the success of deep models, and to propose ways forward in an attempt to fully exploit the potential of deep learning for SAR despeckling.
COVID-MTL: Multitask Learning with Shift3D and Random-weighted Loss for Automated Diagnosis and Severity Assessment of COVID-19
Authors: Guoqing Bao, Huai Chen, Tongliang Liu, Guanzhong Gong, Yong Yin, Lisheng Wang, Xiuying Wang
Date: 2020-12-10 00:00:00
Tasks: COVID-19 Diagnosis, Transfer Learning

There is an urgent need for automated methods to assist accurate and effective assessment of COVID-19. Radiology and nucleic acid test (NAT) are complementary COVID-19 diagnosis methods. In this paper, we present an end-to-end multitask learning (MTL) framework (COVID-MTL) that is capable of automated and simultaneous detection (against both radiology and NAT) and severity assessment of COVID-19. COVID-MTL learns different COVID-19 tasks in parallel through our novel random-weighted loss function, which assigns learning weights under Dirichlet distribution to prevent task dominance; our new 3D real-time augmentation algorithm (Shift3D) introduces space variances for 3D CNN components by shifting low-level feature representations of volumetric inputs in three dimensions; thereby, the MTL framework is able to accelerate convergence and improve joint learning performance compared to single-task models. By only using chest CT scans, COVID-MTL was trained on 930 CT scans and tested on separate 399 cases. COVID-MTL achieved AUCs of 0.939 and 0.846, and accuracies of 90.23% and 79.20% for detection of COVID-19 against radiology and NAT, respectively, which outperformed the state-of-the-art models. Meanwhile, COVID-MTL yielded AUC of 0.800 $\pm$ 0.020 and 0.813 $\pm$ 0.021 (with transfer learning) for classifying control/suspected, mild/regular, and severe/critically-ill cases. To decipher the recognition mechanism, we also identified high-throughput lung features that were significantly related (P < 0.001) to the positivity and severity of COVID-19.
Detection of Covid-19 Patients with Convolutional Neural Network Based Features on Multi-class X-ray Chest Images
Authors: Ali Narin
Date: 2020-12-10 00:00:00

Covid-19 is a very serious deadly disease that has been announced as a pandemic by the world health organization (WHO). The whole world is working with all its might to end Covid-19 pandemic, which puts countries in serious health and economic problems, as soon as possible. The most important of these is to correctly identify those who get the Covid-19. Methods and approaches to support the reverse transcription polymerase chain reaction (RT-PCR) test have begun to take place in the literature. In this study, chest X-ray images, which can be accessed easily and quickly, were used because the covid-19 attacked the respiratory systems. Classification performances with support vector machines have been obtained by using the features extracted with residual networks (ResNet-50), one of the convolutional neural network models, from these images. While Covid-19 detection is obtained with support vector machines (SVM)-quadratic with the highest sensitivity value of 96.35% with the 5-fold cross-validation method, the highest overall performance value has been detected with both SVM-quadratic and SVM-cubic above 99%. According to these high results, it is thought that this method, which has been studied, will help radiology specialists and reduce the rate of false detection.
Effect of Different Batch Size Parameters on Predicting of COVID19 Cases
Authors: Ali Narin, Ziynet Pamuk
Date: 2020-12-10 00:00:00
Tasks: Diagnostic

The new coronavirus 2019, also known as COVID19, is a very serious epidemic that has killed thousands or even millions of people since December 2019. It was defined as a pandemic by the world health organization in March 2020. It is stated that this virus is usually transmitted by droplets caused by sneezing or coughing, or by touching infected surfaces. The presence of the virus is detected by real-time reverse transcriptase polymerase chain reaction (rRT-PCR) tests with the help of a swab taken from the nose or throat. In addition, X-ray and CT imaging methods are also used to support this method. Since it is known that the accuracy sensitivity in rRT-PCR test is low, auxiliary diagnostic methods have a very important place. Computer-aided diagnosis and detection systems are developed especially with the help of X-ray and CT images. Studies on the detection of COVID19 in the literature are increasing day by day. In this study, the effect of different batch size (BH=3, 10, 20, 30, 40, and 50) parameter values on their performance in detecting COVID19 and other classes was investigated using data belonging to 4 different (Viral Pneumonia, COVID19, Normal, Bacterial Pneumonia) classes. The study was carried out using a pre-trained ResNet50 convolutional neural network. According to the obtained results, they performed closely on the training and test data. However, it was observed that the steady state in the test data was delayed as the batch size value increased. The highest COVID19 detection was 95.17% for BH = 3, while the overall accuracy value was 97.97% with BH = 20. According to the findings, it can be said that the batch size value does not affect the overall performance significantly, but the increase in the batch size value delays obtaining stable results.
Large-Scale Generative Data-Free Distillation
Authors: Liangchen Luo, Mark Sandler, Zi Lin, Andrey Zhmoginov, Andrew Howard
Date: 2020-12-10 00:00:00
Tasks: Knowledge Distillation, Model Compression, Transfer Learning

Knowledge distillation is one of the most popular and effective techniques for knowledge transfer, model compression and semi-supervised learning. Most existing distillation approaches require the access to original or augmented training samples. But this can be problematic in practice due to privacy, proprietary and availability concerns. Recent work has put forward some methods to tackle this problem, but they are either highly time-consuming or unable to scale to large datasets. To this end, we propose a new method to train a generative image model by leveraging the intrinsic normalization layers' statistics of the trained teacher network. This enables us to build an ensemble of generators without training data that can efficiently produce substitute inputs for subsequent distillation. The proposed method pushes forward the data-free distillation performance on CIFAR-10 and CIFAR-100 to 95.02% and 77.02% respectively. Furthermore, we are able to scale it to ImageNet dataset, which to the best of our knowledge, has never been done using generative models in a data-free setting.
Performance Comparison of Balanced and Unbalanced Cancer Datasets using Pre-Trained Convolutional Neural Network
Authors: Ali Narin
Date: 2020-12-10 00:00:00
Tasks: Specificity

Cancer disease is one of the leading causes of death all over the world. Breast cancer, which is a common cancer disease especially in women, is quite common. The most important tool used for early detection of this cancer type, which requires a long process to establish a definitive diagnosis, is histopathological images taken by biopsy. These obtained images are examined by pathologists and a definitive diagnosis is made. It is quite common to detect this process with the help of a computer. Detection of benign or malignant tumors, especially by using data with different magnification rates, takes place in the literature. In this study, two different balanced and unbalanced study groups have been formed by using the histopathological data in the BreakHis data set. We have examined how the performances of balanced and unbalanced data sets change in detecting tumor type. In conclusion, in the study performed using the InceptionV3 convolution neural network model, 93.55% accuracy, 99.19% recall and 87.10% specificity values have been obtained for balanced data, while 89.75% accuracy, 82.89% recall and 91.51% specificity values have been obtained for unbalanced data. According to the results obtained in two different studies, the balance of the data increases the overall performance as well as the detection performance of both benign and malignant tumors. It can be said that the model trained with the help of data sets created in a balanced way will give pathology specialists higher and accurate results.
Effect of the regularization hyperparameter on deep learning-based segmentation in LGE-MRI
Authors: Olivier Rukundo
Date: 2020-12-10 00:00:00
Tasks: Deep Learning, L2 Regularization, Segmentation, Semantic Segmentation

The extent to which the arbitrarily selected L2 regularization hyperparameter value affects the outcome of semantic segmentation with deep learning is demonstrated. Demonstrations rely on training U-net on small LGE-MRI datasets using the arbitrarily selected L2 regularization values. The remaining hyperparameters are to be manually adjusted or tuned only when 10 % of all epochs are reached before the training validation accuracy reaches 90%. Semantic segmentation with deep learning outcomes are objectively and subjectively evaluated against the manual ground truth segmentation.
3D Bounding Box Detection in Volumetric Medical Image Data: A Systematic Literature Review
Authors: Daria Kern, Andre Mastmeyer
Date: 2020-12-10 00:00:00
Tasks: Feature Engineering, regression, Systematic Literature Review

This paper discusses current methods and trends for 3D bounding box detection in volumetric medical image data. For this purpose, an overview of relevant papers from recent years is given. 2D and 3D implementations are discussed and compared. Multiple identified approaches for localizing anatomical structures are presented. The results show that most research recently focuses on Deep Learning methods, such as Convolutional Neural Networks vs. methods with manual feature engineering, e.g. Random-Regression-Forests. An overview of bounding box detection options is presented and helps researchers to select the most promising approach for their target objects.
Learning Tubule-Sensitive CNNs for Pulmonary Airway and Artery-Vein Segmentation in CT
Authors: Yulei Qin, Hao Zheng, Yun Gu, Xiaolin Huang, Jie Yang, Lihui Wang, Feng Yao, Yue-Min Zhu, Guang-Zhong Yang
Date: 2020-12-10 00:00:00
Tasks: Anatomy, Representation Learning, Segmentation

Training convolutional neural networks (CNNs) for segmentation of pulmonary airway, artery, and vein is challenging due to sparse supervisory signals caused by the severe class imbalance between tubular targets and background. We present a CNNs-based method for accurate airway and artery-vein segmentation in non-contrast computed tomography. It enjoys superior sensitivity to tenuous peripheral bronchioles, arterioles, and venules. The method first uses a feature recalibration module to make the best use of features learned from the neural networks. Spatial information of features is properly integrated to retain relative priority of activated regions, which benefits the subsequent channel-wise recalibration. Then, attention distillation module is introduced to reinforce representation learning of tubular objects. Fine-grained details in high-resolution attention maps are passing down from one layer to its previous layer recursively to enrich context. Anatomy prior of lung context map and distance transform map is designed and incorporated for better artery-vein differentiation capacity. Extensive experiments demonstrated considerable performance gains brought by these components. Compared with state-of-the-art methods, our method extracted much more branches while maintaining competitive overall segmentation performance. Codes and models are available at http://www.pami.sjtu.edu.cn/News/56
MLComp: A Methodology for Machine Learning-based Performance Estimation and Adaptive Selection of Pareto-Optimal Compiler Optimization Sequences
Authors: Alessio Colucci, Dávid Juhász, Martin Mosbeck, Alberto Marchisio, Semeen Rehman, Manfred Kreutzer, Guenther Nadbath, Axel Jantsch, Muhammad Shafique
Date: 2020-12-09 00:00:00
Tasks: Compiler Optimization, reinforcement-learning, Reinforcement Learning (RL)

Embedded systems have proliferated in various consumer and industrial applications with the evolution of Cyber-Physical Systems and the Internet of Things. These systems are subjected to stringent constraints so that embedded software must be optimized for multiple objectives simultaneously, namely reduced energy consumption, execution time, and code size. Compilers offer optimization phases to improve these metrics. However, proper selection and ordering of them depends on multiple factors and typically requires expert knowledge. State-of-the-art optimizers facilitate different platforms and applications case by case, and they are limited by optimizing one metric at a time, as well as requiring a time-consuming adaptation for different targets through dynamic profiling. To address these problems, we propose the novel MLComp methodology, in which optimization phases are sequenced by a Reinforcement Learning-based policy. Training of the policy is supported by Machine Learning-based analytical models for quick performance estimation, thereby drastically reducing the time spent for dynamic profiling. In our framework, different Machine Learning models are automatically tested to choose the best-fitting one. The trained Performance Estimator model is leveraged to efficiently devise Reinforcement Learning-based multi-objective policies for creating quasi-optimal phase sequences. Compared to state-of-the-art estimation models, our Performance Estimator model achieves lower relative error (<2%) with up to 50x faster training time over multiple platforms and application domains. Our Phase Selection Policy improves execution time and energy consumption of a given code by up to 12% and 6%, respectively. The Performance Estimator and the Phase Selection Policy can be trained efficiently for any target platform and application domain.
Securing Deep Spiking Neural Networks against Adversarial Attacks through Inherent Structural Parameters
Authors: Rida El-Allami, Alberto Marchisio, Muhammad Shafique, Ihsen Alouani
Date: 2020-12-09 00:00:00

Deep Learning (DL) algorithms have gained popularity owing to their practical problem-solving capacity. However, they suffer from a serious integrity threat, i.e., their vulnerability to adversarial attacks. In the quest for DL trustworthiness, recent works claimed the inherent robustness of Spiking Neural Networks (SNNs) to these attacks, without considering the variability in their structural spiking parameters. This paper explores the security enhancement of SNNs through internal structural parameters. Specifically, we investigate the SNNs robustness to adversarial attacks with different values of the neuron's firing voltage thresholds and time window boundaries. We thoroughly study SNNs security under different adversarial attacks in the strong white-box setting, with different noise budgets and under variable spiking parameters. Our results show a significant impact of the structural parameters on the SNNs' security, and promising sweet spots can be reached to design trustworthy SNNs with 85% higher robustness than a traditional non-spiking DL system. To the best of our knowledge, this is the first work that investigates the impact of structural parameters on SNNs robustness to adversarial attacks. The proposed contributions and the experimental framework is available online to the community for reproducible research.
Modeling Disease Progression Trajectories from Longitudinal Observational Data
Authors: Bum Chul Kwon, Peter Achenbach, Jessica L. Dunne, William Hagopian, Markus Lundgren, Kenney Ng, Riitta Veijola, Brigitte I. Frohnert, Vibha Anand, the T1DI Study Group
Date: 2020-12-09 00:00:00

Analyzing disease progression patterns can provide useful insights into the disease processes of many chronic conditions. These analyses may help inform recruitment for prevention trials or the development and personalization of treatments for those affected. We learn disease progression patterns using Hidden Markov Models (HMM) and distill them into distinct trajectories using visualization methods. We apply it to the domain of Type 1 Diabetes (T1D) using large longitudinal observational data from the T1DI study group. Our method discovers distinct disease progression trajectories that corroborate with recently published findings. In this paper, we describe the iterative process of developing the model. These methods may also be applied to other chronic conditions that evolve over time.
Know Your Limits: Uncertainty Estimation with ReLU Classifiers Fails at Reliable OOD Detection
Authors: Dennis Ulmer, Giovanni Cinà
Date: 2020-12-09 00:00:00
Tasks: General Classification, Out of Distribution (OOD) Detection

A crucial requirement for reliable deployment of deep learning models for safety-critical applications is the ability to identify out-of-distribution (OOD) data points, samples which differ from the training data and on which a model might underperform. Previous work has attempted to tackle this problem using uncertainty estimation techniques. However, there is empirical evidence that a large family of these techniques do not detect OOD reliably in classification tasks. This paper gives a theoretical explanation for said experimental findings and illustrates it on synthetic data. We prove that such techniques are not able to reliably identify OOD samples in a classification setting, since their level of confidence is generalized to unseen areas of the feature space. This result stems from the interplay between the representation of ReLU networks as piece-wise affine transformations, the saturating nature of activation functions like softmax, and the most widely-used uncertainty metrics.
Contrastive Predictive Coding for Human Activity Recognition
Authors: Harish Haresamudram, Irfan Essa, Thomas Ploetz
Date: 2020-12-09 00:00:00
Tasks: Activity Recognition, Human Activity Recognition

Feature extraction is crucial for human activity recognition (HAR) using body-worn movement sensors. Recently, learned representations have been used successfully, offering promising alternatives to manually engineered features. Our work focuses on effective use of small amounts of labeled data and the opportunistic exploitation of unlabeled data that are straightforward to collect in mobile and ubiquitous computing scenarios. We hypothesize and demonstrate that explicitly considering the temporality of sensor data at representation level plays an important role for effective HAR in challenging scenarios. We introduce the Contrastive Predictive Coding (CPC) framework to human activity recognition, which captures the long-term temporal structure of sensor data streams. Through a range of experimental evaluations on real-life recognition tasks, we demonstrate its effectiveness for improved HAR. CPC-based pre-training is self-supervised, and the resulting learned representations can be integrated into standard activity chains. It leads to significantly improved recognition performance when only small amounts of labeled training data are available, thereby demonstrating the practical value of our approach.
Transfer Learning for Efficient Iterative Safety Validation
Authors: Anthony Corso, Mykel J. Kochenderfer
Date: 2020-12-09 00:00:00
Tasks: Autonomous Driving, reinforcement-learning, Reinforcement Learning (RL), Transfer Learning

Safety validation is important during the development of safety-critical autonomous systems but can require significant computational effort. Existing algorithms often start from scratch each time the system under test changes. We apply transfer learning to improve the efficiency of reinforcement learning based safety validation algorithms when applied to related systems. Knowledge from previous safety validation tasks is encoded through the action value function and transferred to future tasks with a learned set of attention weights. Including a learned state and action value transformation for each source task can improve performance even when systems have substantially different failure modes. We conduct experiments on safety validation tasks in gridworld and autonomous driving scenarios. We show that transfer learning can improve the initial and final performance of validation algorithms and reduce the number of training steps.