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Unsupervised Detection of Pulmonary Opacities for Computer-Aided Diagnosis of COVID-19 on CT Images

Rui Xu, Xiao Cao, Yufeng Wang, Yen-Wei Chen, Xinchen Ye, Lin Lin, Wenchao Zhu, Chao Chen, Fangyi Xu, Yong Zhou, Hongjie Hu, Shoji Kido, Noriyuki Tomiyama

Auto-TLDR; A computer-aided diagnosis of COVID-19 from CT images using unsupervised pulmonary opacity detection

Abstract Slides Poster

COVID-19 emerged towards the end of 2019 which was identified as a global pandemic by the world heath organization (WHO). With the rapid spread of COVID-19, the number of infected and suspected patients has increased dramatically. Chest computed tomography (CT) has been recognized as an efficient tool for the diagnosis of COVID-19. However, the huge CT data make it difficult for radiologist to fully exploit them on the diagnosis. In this paper, we propose a computer-aided diagnosis system that can automatically analyze CT images to distinguish the COVID-19 against to community-acquired pneumonia (CAP). The proposed system is based on an unsupervised pulmonary opacity detection method that locates opacity regions by a detector unsupervisedly trained from CT images with normal lung tissues. Radiomics based features are extracted insides the opacity regions, and fed into classifiers for classification. We evaluate the proposed CAD system by using 200 CT images collected from different patients in several hospitals. The accuracy, precision, recall, f1-score and AUC achieved are 95.5%, 100%, 91%, 95.1% and 95.9% respectively, exhibiting the promising capacity on the differential diagnosis of COVID-19 from CT images.

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BG-Net: Boundary-Guided Network for Lung Segmentation on Clinical CT Images

Rui Xu, Yi Wang, Tiantian Liu, Xinchen Ye, Lin Lin, Yen-Wei Chen, Shoji Kido, Noriyuki Tomiyama

Auto-TLDR; Boundary-Guided Network for Lung Segmentation on CT Images

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Lung segmentation on CT images is a crucial step for a computer-aided diagnosis system of lung diseases. The existing deep learning based lung segmentation methods are less efficient to segment lungs on clinical CT images, especially that the segmentation on lung boundaries is not accurate enough due to complex pulmonary opacities in practical clinics. In this paper, we propose a boundary-guided network (BG-Net) to address this problem. It contains two auxiliary branches that separately segment lungs and extract the lung boundaries, and an aggregation branch that efficiently exploits lung boundary cues to guide the network for more accurate lung segmentation on clinical CT images. We evaluate the proposed method on a private dataset collected from the Osaka university hospital and four public datasets including StructSeg, HUG, VESSEL12, and a Novel Coronavirus 2019 (COVID-19) dataset. Experimental results show that the proposed method can segment lungs more accurately and outperform several other deep learning based methods.

MTGAN: Mask and Texture-Driven Generative Adversarial Network for Lung Nodule Segmentation

Wei Chen, Qiuli Wang, Kun Wang, Dan Yang, Xiaohong Zhang, Chen Liu, Yucong Li

Auto-TLDR; Mask and Texture-driven Generative Adversarial Network for Lung Nodule Segmentation

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Accurate segmentation for lung nodules in lung computed tomography (CT) scans plays a key role in the early diagnosis of lung cancer. Many existing methods, especially UNet, have made significant progress in lung nodule segmentation. However, due to the complex shapes of lung nodules and the similarity of visual characteristics between nodules and lung tissues, an accurate segmentation with few false positives of lung nodules is still a challenging problem. Considering the fact that both boundary and texture information of lung nodules are important for obtaining an accurate segmentation result, we propose a novel Mask and Texture-driven Generative Adversarial Network (MTGAN) with a joint multi-scale L1 loss for lung nodule segmentation, which takes full advantages of U-Net and adversarial training. The proposed MTGAN leverages adversarial learning strategy guided by the boundary and texture information of lung nodules to generate more accurate segmentation results with lesser false positives. We validate our model with the LIDC–IDRI dataset, and experimental results show that our method achieves excellent segmentation results for a variety of lung nodules, especially for juxtapleural nodules and low-dense nodules. Without any bells and whistles, the proposed MTGAN achieves significant segmentation performance with the Dice similarity coefficient (DSC) of 85.24% on the LIDC–IDRI dataset.

End-To-End Multi-Task Learning for Lung Nodule Segmentation and Diagnosis

Wei Chen, Qiuli Wang, Dan Yang, Xiaohong Zhang, Chen Liu, Yucong Li

Auto-TLDR; A novel multi-task framework for lung nodule diagnosis based on deep learning and medical features

Abstract Slides Similar

Computer-Aided Diagnosis (CAD) systems for lung nodule diagnosis based on deep learning have attracted much attention in recent years. However, most existing methods ignore the relationships between the segmentation and classification tasks, which leads to unstable performances. To address this problem, we propose a novel multi-task framework, which can provide lung nodule segmentation mask, malignancy prediction, and medical features for interpretable diagnosis at the same time. Our framework mainly contains two sub-network: (1) Multi-Channel Segmentation Sub-network (MSN) for lung nodule segmentation, and (2) Joint Classification Sub-network (JCN) for interpretable lung nodule diagnosis. In the proposed framework, we use U-Net down-sampling processes for extracting low-level deep learning features, which are shared by two sub-networks. The JCN forces the down-sampling processes to learn better lowlevel deep features, which lead to a better construct of segmentation masks. Meanwhile, two additional channels constructed by OTSU and super-pixel (SLIC) methods, are utilized as the guideline of the feature extraction. The proposed framework takes advantages of deep learning methods and classical methods, which can significantly improve the performances of all tasks. We evaluate the proposed framework on public dataset LIDCIDRI. Our framework achieves a promising Dice score of 86.43% in segmentation, 87.07% in malignancy level prediction, and convincing results in interpretable medical feature predictions.

Dealing with Scarce Labelled Data: Semi-Supervised Deep Learning with Mix Match for Covid-19 Detection Using Chest X-Ray Images

Saúl Calderón Ramirez, Raghvendra Giri, Shengxiang Yang, Armaghan Moemeni, Mario Umaña, David Elizondo, Jordina Torrents-Barrena, Miguel A. Molina-Cabello

Auto-TLDR; Semi-supervised Deep Learning for Covid-19 Detection using Chest X-rays

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Coronavirus (Covid-19) is spreading fast, infecting people through contact in various forms including droplets from sneezing and coughing. Therefore, the detection of infected subjects in an early, quick and cheap manner is urgent. Currently available tests are scarce and limited to people in danger of serious illness. The application of deep learning to chest X-ray images for Covid-19 detection is an attractive approach. However, this technology usually relies on the availability of large labelled datasets, a requirement hard to meet in the context of a virus outbreak. To overcome this challenge, a semi-supervised deep learning model using both labelled and unlabelled data is proposed. We developed and tested a semi-supervised deep learning framework based on the Mix Match architecture to classify chest X-rays into Covid-19, pneumonia and healthy cases. The presented approach was calibrated using two publicly available datasets. The results show an accuracy increase of around $15\%$ under low labelled / unlabelled data ratio. This indicates that our semi-supervised framework can help improve performance levels towards Covid-19 detection when the amount of high-quality labelled data is scarce. Also, we introduce a semi-supervised deep learning boost coefficient which is meant to ease the scalability of our approach and performance comparison.

A Benchmark Dataset for Segmenting Liver, Vasculature and Lesions from Large-Scale Computed Tomography Data

Bo Wang, Zhengqing Xu, Wei Xu, Qingsen Yan, Liang Zhang, Zheng You

Auto-TLDR; The Biggest Treatment-Oriented Liver Cancer Dataset for Segmentation

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How to build a high-performance liver-related computer assisted diagnosis system is an open question of great interest. However, the performance of the state-of-art algorithm is always limited by the amount of data and quality of the label. To address this problem, we propose the biggest treatment-oriented liver cancer dataset for liver surgery and treatment planning. This dataset provides 216 cases (totally about 268K frames) scanned images in contrast-enhanced computed tomography (CT). We labeled all the CT images with the liver, liver vasculature and liver tumor segmentation ground truth for train and tune segmentation algorithms in advance. Based on that, we evaluate several recent and state-of-the-art segmentation algorithms, including 7 deep learning methods, on CT sequences. All results are compared to reference segmentations five error metrics that highlight different aspects of segmentation accuracy. In general, compared with previous datasets, our dataset is really a challenging dataset. To our knowledge, the proposed dataset and benchmark allow for the first time systematic exploration of such issues, and will be made available to allow for further research in this field.

Detail-Revealing Deep Low-Dose CT Reconstruction

Xinchen Ye, Yuyao Xu, Rui Xu, Shoji Kido, Noriyuki Tomiyama

Auto-TLDR; A Dual-branch Aggregation Network for Low-Dose CT Reconstruction

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Low-dose CT imaging emerges with low radiation risk due to the reduction of radiation dose, but brings negative impact on the imaging quality. This paper addresses the problem of low-dose CT reconstruction. Previous methods are unsatisfactory due to the inaccurate recovery of image details under the strong noise generated by the reduction of radiation dose, which directly affects the final diagnosis. To suppress the noise effectively while retain the structures well, we propose a detail-revealing dual-branch aggregation network to effectively reconstruct the degraded CT image. Specifically, the main reconstruction branch iteratively exploits and compensates the reconstruction errors to gradually refine the CT image, while the prior branch is to learn the structure details as prior knowledge to help recover the CT image. A sophisticated detail-revealing loss is designed to fuse the information from both branches and guide the learning to obtain better performance from pixel-wise and holistic perspectives respectively. Experimental results show that our method outperforms the state-of-art methods in both PSNR and SSIM metrics.

Inception Based Deep Learning Architecture for Tuberculosis Screening of Chest X-Rays

Dipayan Das, K.C. Santosh, Umapada Pal

Auto-TLDR; End to End CNN-based Chest X-ray Screening for Tuberculosis positive patients in the severely resource constrained regions of the world

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The motivation for this work is the primary need of screening Tuberculosis (TB) positive patients in the severely resource constrained regions of the world. Chest X-ray (CXR) is considered to be a promising indicator for the onset of TB, but the lack of skilled radiologists in such regions degrades the situation. Therefore, several computer aided diagnosis (CAD) systems have been proposed to solve the decision making problem, which includes hand engineered feature extraction methods to deep learning or Convolutional Neural Network (CNN) based methods. Feature extraction, being a time and resource intensive process, often delays the process of mass screening. Hence an end to end CNN architecture is proposed in this work to solve the problem. Two benchmark CXR datasets have been used in this work, collected from Shenzhen (China) and Montgomery County (USA), on which the proposed methodology achieved a maximum abnormality detection accuracy (ACC) of 91.7\% (0.96 AUC) and 87.47\% (0.92 AUC) respectively. To the greatest of our knowledge, the obtained results are marginally superior to the state of the art results that have solely used deep learning methodologies on the aforementioned datasets.

Automatic Tuberculosis Detection Using Chest X-Ray Analysis with Position Enhanced Structural Information

Hermann Jepdjio Nkouanga, Szilard Vajda

Auto-TLDR; Automatic Chest X-ray Screening for Tuberculosis in Rural Population using Localized Region on Interest

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For Tuberculosis (TB) detection beside the more expensive diagnosis solutions such as culture or sputum smear analysis one could consider the automatic analysis of the chest X-ray (CXR). This could mimic the lung region reading by the radiologist and it could provide a cheap solution to analyze and diagnose pulmonary abnormalities such as TB which often co- occurs with HIV. This software based pulmonary screening can be a reliable and affordable solution for rural population in different parts of the world such as India, Africa, etc. Our fully automatic system is processing the incoming CXR image by applying image processing techniques to detect the region on interest (ROI) followed by a computationally cheap feature extraction involving edge detection using Laplacian of Gaussian which we enrich by counting the local distribution of the intensities. The choice to ”zoom in” the ROI and look for abnormalities locally is motivated by the fact that some pulmonary abnormalities are localized in specific regions of the lungs. Later on the classifiers can decide about the normal or abnormal nature of each lung X-ray. Our goal is to find a simple feature, instead of a combination of several ones, -proposed and promoted in recent years’ literature, which can properly describe the different pathological alterations in the lungs. Our experiments report results on two publicly available data collections1, namely the Shenzhen and the Montgomery collection. For performance evaluation, measures such as area under the curve (AUC), and accuracy (ACC) were considered, achieving AUC = 0.81 (ACC = 83.33%) and AUC = 0.96 (ACC = 96.35%) for the Montgomery and Schenzen collections, respectively. Several comparisons are also provided to other state- of-the-art systems reported recently in the field.

Dual Encoder Fusion U-Net (DEFU-Net) for Cross-manufacturer Chest X-Ray Segmentation

Zhang Lipei, Aozhi Liu, Jing Xiao

Auto-TLDR; Inception Convolutional Neural Network with Dilation for Chest X-Ray Segmentation

Abstract Slides Similar

A number of methods based on the deep learning have been applied to medical image segmentation and have achieved state-of-the-art performance. The most famous technique is U-Net which has been used to many medical datasets including the Chest X-ray. Due to the importance of chest x- ray data in studying COVID-19, there is a demand for state-of- art models capable of precisely segmenting chest x-rays. In this paper, we propose a dual encoder fusion U-Net framework for Chest X-rays based on Inception Convolutional Neural Network with dilation, Densely Connected Recurrent Convolutional Neural Network, which is named DEFU-Net. The densely connected recurrent path extends the network deeper for facilitating context feature extraction. In order to increase the width of network and enrich representation of features, the inception blocks with dilation have been used. The inception blocks can capture globally and locally spatial information with various receptive fields to avoid information loss caused by max-pooling. Meanwhile, the features fusion of two path by summation preserve the context and the spatial information for decoding part. We applied this model in Chest X-ray dataset from two different manufacturers (Montgomery and Shenzhen hospital). The DEFU-Net achieves the better performance than basic U-Net, residual U-Net, BCDU- Net, R2U-Net and attention R2U-Net. This model approaches state-of-the-art in this mixed dataset. The open source code for this proposed framework is public available.

A Deep Learning Approach for the Segmentation of Myocardial Diseases

Khawala Brahim, Abdull Qayyum, Alain Lalande, Arnaud Boucher, Anis Sakly, Fabrice Meriaudeau

Auto-TLDR; Segmentation of Myocardium Infarction Using Late GADEMRI and SegU-Net

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Cardiac left ventricular (LV) segmentation is of paramount essential step for both diagnosis and treatment of cardiac pathologies such as ischemia, myocardial infarction, arrhythmia and myocarditis. However, this segmentation is challenging due to high variability across patients and the potential lack of contrast between structures. In this work, we propose and evaluate a (2.5D) SegU-Net model based on the fusion of two deep learning techniques (U-Net and Seg-Net) for automated LGEMRI (Late gadolinium enhanced magnetic resonance imaging) myocardial disease (infarct core and no reflow region) quantification in a new multifield expert annotated dataset. Given that the scar tissue represents a small part of the whole MRI slices, we focused on myocardium area. Segmentation results show that this preprocessing step facilitate the learning procedure. In order to solve the class imbalance problem, we propose to apply the Jaccard loss and the Focal Loss as optimization loss function and to integrate a class weights strategy into the objective function. Late combination has been used to merge the output of the best trained models on a different set of hyperparameters. The final network segmentation performances will be useful for future comparison of new method to the current related work for this task. A total number of 2237 of slices (320 cases) were used for training/validation and 210 slices (35 cases) were used for testing. Experiments over our proposed dataset, using several evaluation metrics such Jaccard distance (IOU), Accuracy and Dice similarity coefficient (DSC), demonstrate efficiency performance in quantifying different zones of myocardium infarction across various patients. As compared to the second intra-observer study, our testing results showed that the SegUNet prediction model leads to these average dice coefficients over all segmented tissue classes, respectively : 'Background': 0.99999, 'Myocardium': 0.99434, 'Infarctus': 0.95587, 'Noreflow': 0.78187.

CAggNet: Crossing Aggregation Network for Medical Image Segmentation

Xu Cao, Yanghao Lin

Auto-TLDR; Crossing Aggregation Network for Medical Image Segmentation

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In this paper, we present Crossing Aggregation Network (CAggNet), a novel densely connected semantic segmentation method for medical image analysis. The crossing aggregation network absorbs the idea of deep layer aggregation and makes significant innovations in layer connection and semantic information fusion. In this architecture, the traditional skip-connection structure of general U-Net is replaced by aggregations of multi-level down-sampling and up-sampling layers. This enables the network to fuse information interactively flows at different levels of layers in semantic segmentation. It also introduces weighted aggregation module to aggregate multi-scale output information. We have evaluated and compared our CAggNet with several advanced U-Net based methods in two public medical image datasets, including the 2018 Data Science Bowl nuclei detection dataset and the 2015 MICCAI gland segmentation competition dataset. Experimental results indicate that CAggNet improves medical object recognition and achieves a more accurate and efficient segmentation compared to existing improved U-Net and UNet++ structure.

Combining GANs and AutoEncoders for Efficient Anomaly Detection

Fabio Carrara, Giuseppe Amato, Luca Brombin, Fabrizio Falchi, Claudio Gennaro

Auto-TLDR; CBIGAN: Anomaly Detection in Images with Consistency Constrained BiGAN

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In this work, we propose CBiGAN --- a novel method for anomaly detection in images, where a consistency constraint is introduced as a regularization term in both the encoder and decoder of a BiGAN. Our model exhibits fairly good modeling power and reconstruction consistency capability. We evaluate the proposed method on MVTec AD --- a real-world benchmark for unsupervised anomaly detection on high-resolution images --- and compare against standard baselines and state-of-the-art approaches. Experiments show that the proposed method improves the performance of BiGAN formulations by a large margin and performs comparably to expensive state-of-the-art iterative methods while reducing the computational cost. We also observe that our model is particularly effective in texture-type anomaly detection, as it sets a new state of the art in this category. The code will be publicly released.

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

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

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.

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

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.

Semi-Supervised Generative Adversarial Networks with a Pair of Complementary Generators for Retinopathy Screening

Yingpeng Xie, Qiwei Wan, Hai Xie, En-Leng Tan, Yanwu Xu, Baiying Lei

Auto-TLDR; Generative Adversarial Networks for Retinopathy Diagnosis via Fundus Images

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Several typical types of retinopathy are major causes of blindness. However, early detection of retinopathy is quite not easy since few symptoms are observable in the early stage, attributing to the development of non-mydriatic retinal camera. These camera produces high-resolution retinal fundus images provide the possibility of Computer-Aided-Diagnosis (CAD) via deep learning to assist diagnosing retinopathy. Deep learning algorithms usually rely on a great number of labelled images which are expensive and time-consuming to obtain in the medical imaging area. Moreover, the random distribution of various lesions which often vary greatly in size also brings significant challenges to learn discriminative information from high-resolution fundus image. In this paper, we present generative adversarial networks simultaneously equipped with "good" generator and "bad" generator (GBGANs) to make up for the incomplete data distribution provided by limited fundus images. To improve the generative feasibility of generator, we introduce into pre-trained feature extractor to acquire condensed feature for each fundus image in advance. Experimental results on integrated three public iChallenge datasets show that the proposed GBGANs could fully utilize the available fundus images to identify retinopathy with little label cost.

Deep Recurrent-Convolutional Model for AutomatedSegmentation of Craniomaxillofacial CT Scans

Francesca Murabito, Simone Palazzo, Federica Salanitri Proietto, Francesco Rundo, Ulas Bagci, Daniela Giordano, Rosalia Leonardi, Concetto Spampinato

Auto-TLDR; Automated Segmentation of Anatomical Structures in Craniomaxillofacial CT Scans using Fully Convolutional Deep Networks

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In this paper we define a deep learning architecture for automated segmentation of anatomical structures in Craniomaxillofacial (CMF) CT scans that leverages the recent success of encoder-decoder models for semantic segmentation of natural images. In particular, we propose a fully convolutional deep network that combines the advantages of recent fully convolutional models, such as Tiramisu, with squeeze-and-excitation blocks for feature recalibration, integrated with convolutional LSTMs to model spatio-temporal correlations between consecutive slices. The proposed segmentation network shows superior performance and generalization capabilities (to different structures and imaging modalities) than state of the art methods on automated segmentation of CMF structures (e.g., mandibles and airways) in several standard benchmarks (e.g., MICCAI datasets) and on new datasets proposed herein, effectively facing shape variability.

A Novel Computer-Aided Diagnostic System for Early Assessment of Hepatocellular Carcinoma

Ahmed Alksas, Mohamed Shehata, Gehad Saleh, Ahmed Shaffie, Ahmed Soliman, Mohammed Ghazal, Hadil Abukhalifeh, Abdel Razek Ahmed, Ayman El-Baz

Auto-TLDR; Classification of Liver Tumor Lesions from CE-MRI Using Structured Structural Features and Functional Features

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Early assessment of liver cancer patients with hepatocellular carcinoma (HCC) is of immense importance to provide the proper treatment plan. In this paper, we have developed a two-stage classification computer-aided diagnostic (CAD) system that has the ability to detect and grade the liver observations from multiphase contrast enhanced magnetic resonance imaging (CE-MRI). The proposed approach consists of three main steps. First, a pre-processing is applied to the CE-MRI scans to delineate the tumor lesions that will be used as an ROI across the four different phases of the CE-MRI, (namely, the pre-contrast, late-arterial, portal-venous, and delayed-contrast). Second, a group of three features are modeled to provide a quantitative discrimination between the tumor lesions; namely: i) the tumor appearance that is modeled using a set of texture features, (namely; the first-order histogram, second-order gray-level co-occurrence matrix, and second-order gray-level run-length matrix), to capture any discrimination that may appear in the lesion texture, ii) the spherical harmonics (SH) based shape features that have the ability to describe the shape complexity of the liver tumors, and iii) the functional features that are based on the calculation of the wash-in/wash-out through that evaluate the intensity changes across the post-contrast phases. Finally, the aforementioned individual features were then integrated together to obtain the combined features to be fed to a machine learning classifier towards getting the final diagnostic decision. The proposed CAD system has been tested using hepatic observations that was obtained from 85 participating patients, 34 patients with benign tumors, 34 patients with intermediate tumors and 34 with malignant tumors. Using a random forests based classifier with a leave-one-subject-out (LOSO) cross-validation, the developed CAD system achieved an 87.1% accuracy in distinguishing the malignant, intermediate and benign tumors. The classification performance is then evaluated using k-fold (5/10-fold) cross-validation approach to examine the robustness of the system. The LR-1 lesions were classified from LR-2 benign lesions with 91.2% accuracy, while 85.3% accuracy was achieved differentiating between LR-4 and LR-5 malignant tumors. The obtained results hold a promise of the proposed framework to be reliably used as a noninvasive diagnostic tool for the early detection and grading of liver cancer tumors.

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

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.

A Comparison of Neural Network Approaches for Melanoma Classification

Maria Frasca, Michele Nappi, Michele Risi, Genoveffa Tortora, Alessia Auriemma Citarella

Auto-TLDR; Classification of Melanoma Using Deep Neural Network Methodologies

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Melanoma is the deadliest form of skin cancer and it is diagnosed mainly visually, starting from initial clinical screening and followed by dermoscopic analysis, biopsy and histopathological examination. A dermatologist’s recognition of melanoma may be subject to errors and may take some time to diagnose it. In this regard, deep learning can be useful in the study and classification of skin cancer. In particular, by classifying images with Deep Neural Network methodologies, it is possible to obtain comparable or even superior results compared to those of dermatologists. In this paper, we propose a methodology for the classification of melanoma by adopting different deep learning techniques applied to a common dataset, composed of images from the ISIC dataset and consisting of different types of skin diseases, including melanoma on which we applied a specific pre-processing phase. In particular, a comparison of the results is performed in order to select the best effective neural network to be applied to the problem of recognition and classification of melanoma. Moreover, we also evaluate the impact of the pre- processing phase on the final classification. Different metrics such as accuracy, sensitivity, and specificity have been selected to assess the goodness of the adopted neural networks and compare them also with the manual classification of dermatologists.

Super-Resolution Guided Pore Detection for Fingerprint Recognition

Syeda Nyma Ferdous, Ali Dabouei, Jeremy Dawson, Nasser M. Nasarabadi

Auto-TLDR; Super-Resolution Generative Adversarial Network for Fingerprint Recognition Using Pore Features

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Performance of fingerprint recognition algorithms substantially rely on fine features extracted from fingerprints. Apart from minutiae and ridge patterns, pore features have proven to be usable for fingerprint recognition. Although features from minutiae and ridge patterns are quite attainable from low-resolution images, using pore features is practical only if the fingerprint image is of high resolution which necessitates a model that enhances the image quality of the conventional 500 ppi legacy fingerprints preserving the fine details. To find a solution for recovering pore information from low-resolution fingerprints, we adopt a joint learning-based approach that combines both super-resolution and pore detection networks. Our modified single image Super-Resolution Generative Adversarial Network (SRGAN) framework helps to reliably reconstruct high-resolution fingerprint samples from low-resolution ones assisting the pore detection network to identify pores with a high accuracy. The network jointly learns a distinctive feature representation from a real low-resolution fingerprint sample and successfully synthesizes a high-resolution sample from it. To add discriminative information and uniqueness for all the subjects, we have integrated features extracted from a deep fingerprint verifier with the SRGAN quality discriminator. We also add ridge reconstruction loss, utilizing ridge patterns to make the best use of extracted features. Our proposed method solves the recognition problem by improving the quality of fingerprint images. High recognition accuracy of the synthesized samples that is close to the accuracy achieved using the original high-resolution images validate the effectiveness of our proposed model.

SAGE: Sequential Attribute Generator for Analyzing Glioblastomas Using Limited Dataset

Padmaja Jonnalagedda, Brent Weinberg, Jason Allen, Taejin Min, Shiv Bhanu, Bir Bhanu

Auto-TLDR; SAGE: Generative Adversarial Networks for Imaging Biomarker Detection and Prediction

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While deep learning approaches have shown remarkable performance in many imaging tasks, most of these methods rely on availability of large quantities of data. Medical image data, however, is scarce and fragmented. Generative Adversarial Networks (GANs) have recently been very effective in handling such datasets by generating more data. If the datasets are very small, however, GANs cannot learn the data distribution properly, resulting in less diverse or low-quality results. One such limited dataset is that for the concurrent gain of 19/20 chromosomes (19/20 co-gain), a mutation with positive prognostic value in Glioblastomas (GBM). In this paper, we detect imaging biomarkers for the mutation to streamline the extensive and invasive prognosis pipeline. Since this mutation is relatively rare, i.e. small dataset, we propose a novel generative framework – the Sequential Attribute GEnerator (SAGE), that generates detailed tumor imaging features while learning from a limited dataset. Experiments show that not only does SAGE generate high quality tumors when compared to standard Deep Convolutional GAN (DC-GAN) and Wasserstein GAN with Gradient Penalty (WGAN-GP), it also captures the imaging biomarkers accurately.

Dual Stream Network with Selective Optimization for Skin Disease Recognition in Consumer Grade Images

Krishnam Gupta, Jaiprasad Rampure, Monu Krishnan, Ajit Narayanan, Nikhil Narayan

Auto-TLDR; A Deep Network Architecture for Skin Disease Localisation and Classification on Consumer Grade Images

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Skin disease localisation and classification on consumer-grade images is more challenging compared to that on dermoscopic imaging. Consumer grade images refer to the images taken using commonly available imaging devices such as a mobile camera or a hand held digital camera. Such images, in addition to having the skin condition of interest in a very small area of the image, has other noisy non-clinical details introduced due to the lighting conditions and the distance of the hand held device from the anatomy at the time of acquisition. We propose a novel deep network architecture \& a new optimization strategy for classification with implicit localisation of skin diseases from clinical/consumer grade images. A weakly supervised segmentation algorithm is first employed to extract Region of Interests (RoI) from the image, the RoI and the original image form the two input streams of the proposed architecture. Each stream of the architecture learns high level and low level features from the original image and the RoI, respectively. The two streams are independently optimised until the loss stops decreasing after which both the streams are optimised collectively with the help of a third combiner sub-network. Such a strategy resulted in a 5% increase of accuracy over the current state-of-the-art methods on SD-198 dataset, which is publicly available. The proposed algorithm is also validated on a new dataset containing over 12,000 images across 75 different skin conditions. We intend to release this dataset as SD-75 to aid in the advancement of research on skin condition classification on consumer grade images.

3D Medical Multi-Modal Segmentation Network Guided by Multi-Source Correlation Constraint

Tongxue Zhou, Stéphane Canu, Pierre Vera, Su Ruan

Auto-TLDR; Multi-modality Segmentation with Correlation Constrained Network

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In the field of multimodal segmentation, the correlation between different modalities can be considered for improving the segmentation results. In this paper, we propose a multi-modality segmentation network with a correlation constraint. Our network includes N model-independent encoding paths with N image sources, a correlation constrain block, a feature fusion block, and a decoding path. The model-independent encoding path can capture modality-specific features from the N modalities. Since there exists a strong correlation between different modalities, we first propose a linear correlation block to learn the correlation between modalities, then a loss function is used to guide the network to learn the correlated features based on the correlation representation block. This block forces the network to learn the latent correlated features which are more relevant for segmentation. Considering that not all the features extracted from the encoders are useful for segmentation, we propose to use dual attention based fusion block to recalibrate the features along the modality and spatial paths, which can suppress less informative features and emphasize the useful ones. The fused feature representation is finally projected by the decoder to obtain the segmentation result. Our experiment results tested on BraTS-2018 dataset for brain tumor segmentation demonstrate the effectiveness of our proposed method.

A Deep Learning-Based Method for Predicting Volumes of Nasopharyngeal Carcinoma for Adaptive Radiation Therapy Treatment

Bilel Daoud, Ken'Ichi Morooka, Shoko Miyauchi, Ryo Kurazume, Wafa Mnejja, Leila Farhat, Jamel Daoud

Auto-TLDR; TEP-Net: Tumor Evolution Prediction of Nasopharyngeal Carcinoma and Organ-at-risks Using CT Images

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This paper presents a new system for predicting the spatial change of Nasopharyngeal carcinoma(NPC) and organ-at-risks (OARs) volumes over the course of the radiation therapy (RT) treatment for facilitating the workflow of adaptive radiotherapy. The proposed system, called " Tumor Evolution Prediction (TEP-Net)", predicts the spatial distributions of NPC and 5 OARs, separately, in response to RT in the coming week, week n. Here, TEP-Net has (n-1)-inputs that are week 1 to week n-1 of CT axial, coronal or sagittal images acquired once the patient complete the planned RT treatment of the corresponding week. As a result, three predicted results of each target region are obtained from the three-view CT images. To determine the final prediction of NPC and 5 OARs, two integration methods, weighted fully connected layers and weighted voting methods, are introduced. From the experiments using weekly CT images of 140 NPC patients, our proposed system achieves the best performance for predicting NPC and OARs compared with conventional methods.

A Joint Representation Learning and Feature Modeling Approach for One-Class Recognition

Pramuditha Perera, Vishal Patel

Auto-TLDR; Combining Generative Features and One-Class Classification for Effective One-class Recognition

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One-class recognition is traditionally approached either as a representation learning problem or a feature modelling problem. In this work, we argue that both of these approaches have their own limitations; and a more effective solution can be obtained by combining the two. The proposed approach is based on the combination of a generative framework and a one-class classification method. First, we learn generative features using the one-class data with a generative framework. We augment the learned features with the corresponding reconstruction errors to obtain augmented features. Then, we qualitatively identify a suitable feature distribution that reduces the redundancy in the chosen classifier space. Finally, we force the augmented features to take the form of this distribution using an adversarial framework. We test the effectiveness of the proposed method on three one-class classification tasks and obtain state-of-the-art results.

Progressive Adversarial Semantic Segmentation

Abdullah-Al-Zubaer Imran, Demetri Terzopoulos

Auto-TLDR; Progressive Adversarial Semantic Segmentation for End-to-End Medical Image Segmenting

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Medical image computing has advanced rapidly with the advent of deep learning techniques such as convolutional neural networks. Deep convolutional neural networks can perform exceedingly well given full supervision. However, the success of such fully-supervised models for various image analysis tasks (e.g., anatomy or lesion segmentation from medical images) is limited to the availability of massive amounts of labeled data. Given small sample sizes, such models are prohibitively data biased with large domain shift. To tackle this problem, we propose a novel end-to-end medical image segmentation model, namely Progressive Adversarial Semantic Segmentation (PASS), which can make improved segmentation predictions without requiring any domain-specific data during training time. Our extensive experimentation with 8 public diabetic retinopathy and chest X-ray datasets, confirms the effectiveness of PASS for accurate vascular and pulmonary segmentation, both for in-domain and cross-domain evaluations.

Classify Breast Histopathology Images with Ductal Instance-Oriented Pipeline

Beibin Li, Ezgi Mercan, Sachin Mehta, Stevan Knezevich, Corey Arnold, Donald Weaver, Joann Elmore, Linda Shapiro

Auto-TLDR; DIOP: Ductal Instance-Oriented Pipeline for Diagnostic Classification

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In this study, we propose the Ductal Instance-Oriented Pipeline (DIOP) that contains a duct-level instance segmentation model, a tissue-level semantic segmentation model, and three-levels of features for diagnostic classification. Based on recent advancements in instance segmentation and the Mask R-CNN model, our duct-level segmenter tries to identify each ductal individual inside a microscopic image; then, it extracts tissue-level information from the identified ductal instances. Leveraging three levels of information obtained from these ductal instances and also the histopathology image, the proposed DIOP outperforms previous approaches (both feature-based and CNN-based) in all diagnostic tasks; for the four-way classification task, the DIOP achieves comparable performance to general pathologists in this unique dataset. The proposed DIOP only takes a few seconds to run in the inference time, which could be used interactively on most modern computers. More clinical explorations are needed to study the robustness and generalizability of this system in the future.

DA-RefineNet: Dual-Inputs Attention RefineNet for Whole Slide Image Segmentation

Ziqiang Li, Rentuo Tao, Qianrun Wu, Bin Li

Auto-TLDR; DA-RefineNet: A dual-inputs attention network for whole slide image segmentation

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Automatic medical image segmentation techniques have wide applications for disease diagnosing, however, its much more challenging than natural optical image segmentation tasks due to the high-resolution of medical images and the corresponding huge computation cost. Sliding window was a commonly used technique for whole slide image (WSI) segmentation, however, for these methods that based on sliding window, the main drawback was lacking of global contextual information for supervision. In this paper, we proposed a dual-inputs attention network (denoted as DA-RefineNet) for WSI segmentation, where both local fine-grained information and global coarse information can be efficiently utilized. Sufficient comparative experiments were conducted to evaluate the effectiveness of the proposed method, the results proved that the proposed method can achieve better performance on WSI segmentation tasks compared to methods rely on single-input.

BiLuNet: A Multi-Path Network for Semantic Segmentation on X-Ray Images

Van Luan Tran, Huei-Yung Lin, Rachel Liu, Chun-Han Tseng, Chun-Han Tseng

Auto-TLDR; BiLuNet: Multi-path Convolutional Neural Network for Semantic Segmentation of Lumbar vertebrae, sacrum,

Abstract Similar

Semantic segmentation and shape detection of lumbar vertebrae, sacrum, and femoral heads from clinical X-ray images are important and challenging tasks. In this paper, we propose a new multi-path convolutional neural network, BiLuNet, for semantic segmentation on X-ray images. The network is capable of medical image segmentation with very limited training data. With the shape fitting of the bones, we can identify the location of the target regions very accurately for lumbar vertebra inspection. We collected our dataset and annotated by doctors for model training and performance evaluation. Compared to the state-of-the-art methods, the proposed technique provides better mIoUs and higher success rates with the same training data. The experimental results have demonstrated the feasibility of our network to perform semantic segmentation for lumbar vertebrae, sacrum, and femoral heads.

Fused 3-Stage Image Segmentation for Pleural Effusion Cell Clusters

Sike Ma, Meng Zhao, Hao Wang, Fan Shi, Xuguo Sun, Shengyong Chen, Hong-Ning Dai

Auto-TLDR; Coarse Segmentation of Stained and Stained Unstained Cell Clusters in pleural effusion using 3-stage segmentation method

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The appearance of tumor cell clusters in pleural effusion is usually a vital sign of cancer metastasis. Segmentation, as an indispensable basis, is of crucial importance for diagnosing, chemical treatment, and prognosis in patients. However, accurate segmentation of unstained cell clusters containing more detailed features than the fluorescent staining images remains to be a challenging problem due to the complex background and the unclear boundary. Therefore, in this paper, we propose a fused 3-stage image segmentation algorithm, namely Coarse segmentation-Mapping-Fine segmentation (CMF) to achieve unstained cell clusters from whole slide images. Firstly, we establish a tumor cell cluster dataset consisting of 107 sets of images, with each set containing one unstained image, one stained image, and one ground-truth image. Then, according to the features of the unstained and stained cell clusters, we propose a three-stage segmentation method: 1) Coarse segmentation on stained images to extract suspicious cell regions-Region of Interest (ROI); 2) Mapping this ROI to the corresponding unstained image to get the ROI of the unstained image (UI-ROI); 3) Fine Segmentation using improved automatic fuzzy clustering framework (AFCF) on the UI-ROI to get precise cell cluster boundaries. Experimental results on 107 sets of images demonstrate that the proposed algorithm can achieve better performance on unstained cell clusters with an F1 score of 90.40%.

Attention Based Multi-Instance Thyroid Cytopathological Diagnosis with Multi-Scale Feature Fusion

Shuhao Qiu, Yao Guo, Chuang Zhu, Wenli Zhou, Huang Chen

Auto-TLDR; A weakly supervised multi-instance learning framework based on attention mechanism with multi-scale feature fusion for thyroid cytopathological diagnosis

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In recent years, deep learning has been popular in combining with cytopathology diagnosis. Using the whole slide images (WSI) scanned by electronic scanners at clinics, researchers have developed many algorithms to classify the slide (benign or malignant). However, the key area that support the diagnosis result can be relatively small in a thyroid WSI, and only the global label can be acquired, which make the direct use of the strongly supervised learning framework infeasible. What’s more, because the clinical diagnosis of the thyroid cells requires the use of visual features in different scales, a generic feature extraction way may not achieve good performance. In this paper, we propose a weakly supervised multi-instance learning framework based on attention mechanism with multi-scale feature fusion (MSF) using convolutional neural network (CNN) for thyroid cytopathological diagnosis. We take each WSI as a bag, each bag contains multiple instances which are the different regions of the WSI, our framework is trained to learn the key area automatically and make the classification. We also propose a feature fusion structure, merge the low-level features into the final feature map and add an instance-level attention module in it, which improves the classification accuracy. Our model is trained and tested on the collected clinical data, reaches the accuracy of 93.2%, which outperforms the other existing methods. We also tested our model on a public histopathology dataset and achieves better result than the state-of-the-art deep multi-instance method.

Segmenting Kidney on Multiple Phase CT Images Using ULBNet

Yanling Chi, Yuyu Xu, Gang Feng, Jiawei Mao, Sihua Wu, Guibin Xu, Weimin Huang

Auto-TLDR; A ULBNet network for kidney segmentation on multiple phase CT images

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Abstract—Segmentation of kidney on CT images is critical to computer-assisted surgical planning for kidney interventional therapy. Segmenting kidney manually is impractical in clinical, automatic segmentation is desirable. U-Net has been successful in medical image segmentation and is a promising candidate for the task. However, semantic gap still exists, especially when multiple phase images or multiple center images are involved. In this paper, we proposed an ULBNet to reduce the semantic gap and to improve segmentation performance. The proposed architecture includes new skip connections of local binary convolution (LBC). We also proposed a novel strategy of fast retraining a model for a new task without manually labelling required. We evaluated the network for kidney segmentation on multiple phase CT images. ULBNet resulted in an overall accuracy of 98.0% with comparison to Resunet 97.5%. Specifically, on the plain phase CT images, 98.1% resulted from ULBNet and 97.6% from Resunet; on the corticomedullay phase images, 97.8% from ULBNet and 97.2% from Resunet; on the nephrographic phase images, 97.6% from ULBNet and 97.4% from Resunet; on the excretory phase images, 98.1% from ULBNet and 97.4% from Resunet. The proposed network architecture performs better than Resunet on generalizing to multiple phase images.

A Transformer-Based Network for Anisotropic 3D Medical Image Segmentation

Guo Danfeng, Demetri Terzopoulos

Auto-TLDR; A transformer-based model to tackle the anisotropy problem in 3D medical image analysis

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A critical challenge of applying neural networks to 3D medical image analysis is to deal with the anisotropy problem. The inter-slice contextual information contained in medical images is important, especially when the structural information of lesions is needed. However, such information often varies with cases because of variable slice spacing. Image anisotropy downgrades model performance especially when slice spacing varies significantly among training and testing datasets. ExsiWe proposed a transformer-based model to tackle the anisotropy problem. It is adaptable to different levels of anisotropy and is computationally efficient. Experiments are conducted on 3D lung cancer segmentation task. Our model achieves an average Dice score of approximately 0.87, which generally outperforms baseline models.

Cross-View Relation Networks for Mammogram Mass Detection

Ma Jiechao, Xiang Li, Hongwei Li, Ruixuan Wang, Bjoern Menze, Wei-Shi Zheng

Auto-TLDR; Multi-view Modeling for Mass Detection in Mammogram

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In medical image analysis, multi-view modeling is crucial for pathology detection when the target lesion is presented in different views, e.g. mass lesions in breast. Currently mammogram is the most effective imaging modality for mass lesion detection of breast cancer at the early stage. The pathological information from the two paired views (i.e., medio-lateral oblique and cranio-caudal) are highly relational and complementary, which is crucial for diagnosis in clinical practice. Existing mass detection methods do not consider learning synergistic features from the two relational views. For the first time, we propose a novel mass detection framework to capture the latent relation information from the two paired views of a same mass in mammogram. We evaluate our model on a public mammogram dataset and a large-scale private dataset, demonstrating that the proposed method outperforms existing feature fusion approaches and state-of-the-art mass detection methods. We further analyze the performance gains from the relation modeling. Our quantitative and qualitative results suggest that jointly learning cross-view features boosts the detection performance of existing models, which is a promising avenue for mass detection task in mammogram.

Triplet-Path Dilated Network for Detection and Segmentation of General Pathological Images

Jiaqi Luo, Zhicheng Zhao, Fei Su, Limei Guo

Auto-TLDR; Triplet-path Network for One-Stage Object Detection and Segmentation in Pathological Images

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Deep learning has been widely applied in the field of medical image processing. However, compared with flourishing visual tasks in natural images, the progress achieved in pathological images is not remarkable, and detection and segmentation, which are among basic tasks of computer vision, are regarded as two independent tasks. In this paper, we make full use of existing datasets and construct a triplet-path network using dilated convolutions to cooperatively accomplish one-stage object detection and nuclei segmentation for general pathological images. First, in order to meet the requirement of detection and segmentation, a novel structure called triplet feature generation (TFG) is designed to extract high-resolution and multiscale features, where features from different layers can be properly integrated. Second, considering that pathological datasets are usually small, a location-aware and partially truncated loss function is proposed to improve the classification accuracy of datasets with few images and widely varying targets. We compare the performance of both object detection and instance segmentation with state-of-the-art methods. Experimental results demonstrate the effectiveness and efficiency of the proposed network on two datasets collected from multiple organs.

Robust Localization of Retinal Lesions Via Weakly-Supervised Learning

Ruohan Zhao, Qin Li, Jane You

Auto-TLDR; Weakly Learning of Lesions in Fundus Images Using Multi-level Feature Maps and Classification Score

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Retinal fundus images reveal the condition of retina, blood vessels and optic nerve. Retinal imaging is becoming widely adopted in clinical work because any subtle changes to the structures at the back of the eyes can affect the eyes and indicate the overall health. Machine learning, in particular deep learning by convolutional neural network (CNN), has been increasingly adopted for computer-aided detection (CAD) of retinal lesions. However, a significant barrier to the high performance of CNN based CAD approach is caused by the lack of sufficient labeled ground-truth image samples for training. Unlike the fully-supervised learning which relies on pixel-level annotation of pathology in fundus images, this paper presents a new approach to discriminate the location of various lesions based on image-level labels via weakly learning. More specifically, our proposed method leverages multi-level feature maps and classification score to cope with both bright and red lesions in fundus images. To enhance capability of learning less discriminative parts of objects (e.g. small blobs of microaneurysms opposed to bulk of exudates), the classifier is regularized by refining images with corresponding labels. The experimental results of the performance evaluation and benchmarking at both image-level and pixel-level on the public DIARETDB1 dataset demonstrate the feasibility and excellent potentials of our method in practice.

Deep Learning in the Ultrasound Evaluation of Neonatal Respiratory Status

Michela Gravina, Diego Gragnaniello, Giovanni Poggi, Luisa Verdoliva, Carlo Sansone, Iuri Corsini, Carlo Dani, Fabio Meneghin, Gianluca Lista, Salvatore Aversa, Migliaro Migliaro, Raimondi Francesco

Auto-TLDR; Lung Ultrasound Imaging with Deep Learning Networks and Training Strategies: An Analysis and Adaptation

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Lung ultrasound imaging is reaching growing interest from the scientific community. On one side, thanks to its harmlessness and high descriptive power, this kind of diagnostic imaging became largely adopted in sensitive applications, like the diagnosis and follow-up of preterm newborns in neonatal intensive care units. At the same time, novel image analysis and pattern recognition approaches can fully exploit the rich information contained in this data, making them attractive for the research community. In this work, we present a thorough analysis of recent deep learning networks and training strategies conducted on a vast and challenging multicenter dataset comprising 87 patients with different diseases and gestational ages. These approaches are firstly discussed in the context of lung respiratory status assessing through ultrasound imaging and then evaluated against a reference marker. The conducted analysis shed some light on this problem, by relating the criticisms that can mislead the training procedure and proposing some adaptations to the specific problem. The achieved results sensibly outperform that obtained by previous work, based on textural features, and narrow the gap with the visual score predicted by the human experts.

A Multi-Task Contextual Atrous Residual Network for Brain Tumor Detection & Segmentation

Ngan Le, Kashu Yamazaki, Quach Kha Gia, Thanh-Dat Truong, Marios Savvides

Auto-TLDR; Contextual Brain Tumor Segmentation Using 3D atrous Residual Networks and Cascaded Structures

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In recent years, deep neural networks have achieved state-of-the-art performance in a variety of recognition and segmentation tasks in medical imaging including brain tumor segmentation. We investigate that segmenting brain tumor is facing to the imbalanced data problem where the number of pixels belonging to background class (non tumor pixel) is much larger than the number of pixels belonging to foreground class (tumor pixel). To address this problem, we propose a multi-task network which is formed as a cascaded structure and designed to share the feature maps. Our model consists of two targets, i.e., (i) effectively differentiating brain tumor regions and (ii) estimating brain tumor masks. The first task is performed by our proposed contextual brain tumor detection network, which plays the role of an attention gate and focuses on the region around brain tumor only while ignore the background (non tumor area). Instead of processing every pixel, our contextual brain tumor detection network only processes contextual regions around ground-truth instances and this strategy helps to produce meaningful regions proposals. The second task is built upon a 3D atrous residual network and under an encode-decode network in order to effectively segment both large and small objects (brain tumor). Our 3D atrous residual network is designed with a skip connection to enables the gradient from the deep layers to be directly propagated to shallow layers, thus, features of different depths are preserved and used for refining each other. In order to incorporate larger contextual information in volume MRI data, our network is designed by 3D atrous convolution with various kernel sizes, which enlarges the receptive field of filters. Our proposed network has been evaluated on various datasets including BRATS2015, BRATS2017 and BRATS2018 datasets with both validation set and testing set. Our performance has been benchmarked by both region-based metrics and surface-based metrics. We also have conducted comparisons against state-of-the-art approaches.

A Systematic Investigation on Deep Architectures for Automatic Skin Lesions Classification

Pierluigi Carcagni, Marco Leo, Andrea Cuna, Giuseppe Celeste, Cosimo Distante

Auto-TLDR; RegNet: Deep Investigation of Convolutional Neural Networks for Automatic Classification of Skin Lesions

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Computer vision-based techniques are more and more employed in healthcare and medical fields nowadays in order, principally, to be as a support to the experienced medical staff to help them to make a quick and correct diagnosis. One of the hot topics in this arena concerns the automatic classification of skin lesions. Several promising works exist about it, mainly leveraging Convolutional Neural Networks (CNN), but proposed pipeline mainly rely on complex data preprocessing and there is no systematic investigation about how available deep models can actually reach the accuracy needed for real applications. In order to overcome these drawbacks, in this work, an end-to-end pipeline is introduced and some of the most recent Convolutional Neural Networks (CNNs) architectures are included in it and compared on the largest common benchmark dataset recently introduced. To this aim, for the first time in this application context, a new network design paradigm, namely RegNet, has been exploited to get the best models among a population of configurations. The paper introduces a threefold level of contribution and novelty with respect the previous literature: the deep investigation of several CNN architectures driving to a consistent improvement of the lesions recognition accuracy, the exploitation of a new network design paradigm able to study the behavior of populations of models and a deep discussion about pro and cons of each analyzed method paving the path towards new research lines.

One-Stage Multi-Task Detector for 3D Cardiac MR Imaging

Weizeng Lu, Xi Jia, Wei Chen, Nicolò Savioli, Antonio De Marvao, Linlin Shen, Declan O'Regan, Jinming Duan

Auto-TLDR; Multi-task Learning for Real-Time, simultaneous landmark location and bounding box detection in 3D space

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Fast and accurate landmark location and bounding box detection are important steps in 3D medical imaging. In this paper, we propose a novel multi-task learning framework, for real-time, simultaneous landmark location and bounding box detection in 3D space. Our method extends the famous single-shot multibox detector (SSD) from single-task learning to multi-task learning and from 2D to 3D. Furthermore, we propose a post-processing approach to refine the network landmark output, by averaging the candidate landmarks. Owing to these settings, the proposed framework is fast and accurate. For 3D cardiac magnetic resonance (MR) images with size 224 × 224 × 64, our framework runs about 128 volumes per second (VPS) on GPU and achieves 6.75mm average point-to-point distance error for landmark location, which outperforms both state-of-the-art and baseline methods. We also show that segmenting the 3D image cropped with the bounding box results in both improved performance and efficiency.

OCT Image Segmentation Using NeuralArchitecture Search and SRGAN

Saba Heidari, Omid Dehzangi, Nasser M. Nasarabadi, Ali Rezai

Auto-TLDR; Automatic Segmentation of Retinal Layers in Optical Coherence Tomography using Neural Architecture Search

Abstract Poster Similar

Alzheimer’s disease (AD) diagnosis is one of the major research areas in computational medicine. Optical coherence tomography (OCT) is a non-invasive, inexpensive, and timely efficient method that scans the human’s retina with depth. It has been hypothesized that the thickness of the retinal layers extracted from OCTs could be an efficient and effective biomarker for early diagnosis of AD. In this work, we aim to design a self-training model architecture for the task of segmenting the retinal layers in OCT scans. Neural architecture search (NAS) is a subfield of AutoML domain, which has a significant impact on improving the accuracy of machine vision tasks. We integrate the NAS algorithm with a Unet auto-encoder architecture as its backbone. Then, we employ our proposed model to segment the retinal nerve fiber layer in our preprocessed OCT images with the aim of AD diagnosis. In this work, we trained a super-resolution generative adversarial network on the raw OCT scans to improve the quality of the images before the modeling stage. In our architecture search strategy, different primitive operations suggested to find down- \& up-sampling Unet cell blocks and the binary gate method has been applied to make the search strategy more practical. Our architecture search method is empirically evaluated by training on the Unet and NAS-Unet from scratch. Specifically, the proposed NAS-Unet training significantly outperforms the baseline human-designed architecture by achieving 95.1\% in the mean Intersection over Union metric and 79.1\% in the Dice similarity coefﬁcient.

DARN: Deep Attentive Refinement Network for Liver Tumor Segmentation from 3D CT Volume

Yao Zhang, Jiang Tian, Cheng Zhong, Yang Zhang, Zhongchao Shi, Zhiqiang He

Auto-TLDR; Deep Attentive Refinement Network for Liver Tumor Segmentation from 3D Computed Tomography Using Multi-Level Features

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Automatic liver tumor segmentation from 3D Computed Tomography (CT) is a necessary prerequisite in the interventions of hepatic abnormalities and surgery planning. However, accurate liver tumor segmentation remains challenging due to the large variability of tumor sizes and inhomogeneous texture. Recent advances based on Fully Convolutional Network (FCN) in liver tumor segmentation draw on success of learning discriminative multi-level features. In this paper, we propose a Deep Attentive Refinement Network (DARN) for improved liver tumor segmentation from CT volumes by fully exploiting both low and high level features embedded in different layers of FCN. Different from existing works, we exploit attention mechanism to leverage the relation of different levels of features encoded in different layers of FCN. Specifically, we introduce a Semantic Attention Refinement (SemRef) module to selectively emphasize global semantic information in low level features with the guidance of high level ones, and a Spatial Attention Refinement (SpaRef) module to adaptively enhance spatial details in high level features with the guidance of low level ones. We evaluate our network on the public MICCAI 2017 Liver Tumor Segmentation Challenge dataset (LiTS dataset) and it achieves state-of-the-art performance. The proposed refinement modules are an effective strategy to exploit multi-level features and has great potential to generalize to other medical image segmentation tasks.

Confidence Calibration for Deep Renal Biopsy Immunofluorescence Image Classification

Federico Pollastri, Juan Maroñas, Federico Bolelli, Giulia Ligabue, Roberto Paredes, Riccardo Magistroni, Costantino Grana

Auto-TLDR; A Probabilistic Convolutional Neural Network for Immunofluorescence Classification in Renal Biopsy

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With this work we tackle immunofluorescence classification in renal biopsy, employing state-of-the-art Convolutional Neural Networks. In this setting, the aim of the probabilistic model is to assist an expert practitioner towards identifying the location pattern of antibody deposits within a glomerulus. Since modern neural networks often provide overconfident outputs, we stress the importance of having a reliable prediction, demonstrating that Temperature Scaling, a recently introduced re-calibration technique, can be successfully applied to immunofluorescence classification in renal biopsy. Experimental results demonstrate that the designed model yields good accuracy on the specific task, and that Temperature Scaling is able to provide reliable probabilities, which are highly valuable for such a task given the low inter-rater agreement.

IDA-GAN: A Novel Imbalanced Data Augmentation GAN

Hao Yang, Yun Zhou

Auto-TLDR; IDA-GAN: Generative Adversarial Networks for Imbalanced Data Augmentation

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Class imbalance is a widely existed and challenging problem in real-world applications such as disease diagnosis, fraud detection, network intrusion detection and so on. Due to the scarce of data, it could significantly deteriorate the accuracy of classification. To address this challenge, we propose a novel Imbalanced Data Augmentation Generative Adversarial Networks (GAN) named IDA-GAN as an augmentation tool to deal with the imbalanced dataset. This is a great challenge because it is hard to train a GAN model under this situation. We overcome this issue by coupling Variational autoencoder along with GAN training. Specifically, we introduce the Variational autoencoder to learn the majority and minority class distributions in the latent space, and use the generative model to utilize each class distribution for the subsequent GAN training. The generative model learns useful features to generate target minority-class samples. By comparing with the state-of-the-art GAN models, the experimental results demonstrate that our proposed IDA-GAN could generate more diverse minority samples with better qualities, and it consistently benefits the imbalanced classification task in terms of several widely-used evaluation metrics on five benchmark datasets: MNIST, Fashion-MNIST, SVHN, CIFAR-10 and GTRSB.

Fine-Tuning Convolutional Neural Networks: A Comprehensive Guide and Benchmark Analysis for Glaucoma Screening

Amed Mvoulana, Rostom Kachouri, Mohamed Akil

Auto-TLDR; Fine-tuning Convolutional Neural Networks for Glaucoma Screening

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This work aimed at giving a comprehensive and in-detailed guide on the route to fine-tuning Convolutional Neural Networks (CNNs) for glaucoma screening. Transfer learning consists in a promising alternative to train CNNs from stratch, to avoid the huge data and resources requirements. After a thorough study of five state-of-the-art CNNs architectures, a complete and well-explained strategy for fine-tuning these networks is proposed, using hyperparameter grid-searching and two-phase training approach. Excellent performance is reached on model evaluation, with a 0.9772 AUROC validation rate, giving arise to reliable glaucoma diagosis-help systems. Also, a benchmark analysis is conducted across all fine-tuned models, studying them according to performance indices such as model complexity and size, AUROC density and inference time. This in-depth analysis allows a rigorous comparison between model characteristics, and is useful for giving practioners important trademarks for prospective applications and deployments.

Skin Lesion Classification Using Weakly-Supervised Fine-Grained Method

Xi Xue, Sei-Ichiro Kamata, Daming Luo

Auto-TLDR; Different Region proposal module for skin lesion classification

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In recent years, skin cancer has become one of the most common cancers. Among all types of skin cancers, melanoma is the most fatal one and many people die of this disease every year. Early detection can greatly reduce the death rate and save more lives. Skin lesions are one of the early symptoms of melanoma and other types of skin cancer. So accurately recognizing various skin lesions in early stage are of great significance. There have been lots of existing works based on convolutional neural networks (CNN) to solve skin lesion classification but seldom do them involve the similarity among different lesions. For example, we find that some lesions of melanoma and nevi look similar in appearance which is hard for neural network to distinguish categories of skin lesions. Inspired by fine-grained image classification, we propose a novel network to distinguish each category accurately. In our paper, we design an effective module, distinct region proposal module (DRPM), to extract the distinct regions from each image. Spatial attention and channel-wise attention are both utilized to enrich feature maps and guide the network to focus on the highlighted areas in a weakly-supervised way. In addition, two preprocessing steps are added to ensure the network to get better results. We demonstrate the potential of the proposed method on ISIC 2017 dataset. Experiments show that our approach is effective and efficient.

Machine-Learned Regularization and Polygonization of Building Segmentation Masks

Stefano Zorzi, Ksenia Bittner, Friedrich Fraundorfer

Auto-TLDR; Automatic Regularization and Polygonization of Building Segmentation masks using Generative Adversarial Network

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We propose a machine learning based approach for automatic regularization and polygonization of building segmentation masks. Taking an image as input, we first predict building segmentation maps exploiting generic fully convolutional network (FCN). A generative adversarial network (GAN) is then involved to perform a regularization of building boundaries to make them more realistic, i.e., having more rectilinear outlines which construct right angles if required. This is achieved through the interplay between the discriminator which gives a probability of input image being true and generator that learns from discriminator’s response to create more realistic images. Finally, we train the backbone convolutional neural network (CNN) which is adapted to predict sparse outcomes corresponding to building corners out of regularized building segmentation results. Experiments on three building segmentation datasets demonstrate that the proposed method is not only capable of obtaining accurate results, but also of producing visually pleasing building outlines parameterized as polygons.

Early Wildfire Smoke Detection in Videos

Taanya Gupta, Hengyue Liu, Bir Bhanu

Auto-TLDR; Semi-supervised Spatio-Temporal Video Object Segmentation for Automatic Detection of Smoke in Videos during Forest Fire

Abstract Poster Similar

Recent advances in unmanned aerial vehicles and camera technology have proven useful for the detection of smoke that emerges above the trees during a forest fire. Automatic detection of smoke in videos is of great interest to Fire department. To date, in most parts of the world, the fire is not detected in its early stage and generally it turns catastrophic. This paper introduces a novel technique that integrates spatial and temporal features in a deep learning framework using semi-supervised spatio-temporal video object segmentation and dense optical flow. However, detecting this smoke in the presence of haze and without the labeled data is difficult. Considering the visibility of haze in the sky, a dark channel pre-processing method is used that reduces the amount of haze in video frames and consequently improves the detection results. Online training is performed on a video at the time of testing that reduces the need for ground-truth data. Tests using the publicly available video datasets show that the proposed algorithms outperform previous work and they are robust across different wildfire-threatened locations.