Supporting Skin Lesion Diagnosis with Content-Based Image Retrieval

Stefano Allegretti, Federico Bolelli, Federico Pollastri, Sabrina Longhitano, Giovanni Pellacani, Costantino Grana

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Auto-TLDR; Skin Images Retrieval Using Convolutional Neural Networks for Skin Lesion Classification and Segmentation

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Given the relevance of skin cancer, many attempts have been dedicated to the creation of automated devices that could assist both expert and beginner dermatologists towards fast and early diagnosis of skin lesions. In recent years, tasks such as skin lesion classification and segmentation have been extensively addressed with deep learning algorithms, which in some cases reach a diagnostic accuracy comparable to that of expert physicians. However, the general lack of interpretability and reliability severely hinders the ability of those approaches to actually support dermatologists in the diagnosis process. In this paper a novel skin images retrieval system is presented, which exploits features extracted by Convolutional Neural Networks to gather similar images from a publicly available dataset, in order to assist the diagnosis process of both expert and novice practitioners. In the proposed framework, Resnet-50 is initially trained for the classification of dermoscopic images; then, the feature extraction part is isolated, and an embedding network is build on top of it. The embedding learns an alternative representation, which allows to check image similarity by means of a distance measure. Experimental results reveal that the proposed method is able to select meaningful images, which can effectively boost the classification accuracy of human dermatologists.

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

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

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

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Auto-TLDR; Fine-tuned Neural Networks for Skin Lesion Classification Using Dermoscopic Images

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

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

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

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

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Auto-TLDR; Self-supervised Contrastive Learning for Deep Representation Learning of Histopathology Images

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

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Nikolaos Passalis, Anastasios Tefas

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Auto-TLDR; Quadratic Mutual Information for Large-Scale Hashing and Information Retrieval

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

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

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

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Thomas E. Koker, Sai Spandana Chintapalli, San Wang, Blake A. Talbot, Daniel Wainstock, Marcelo Cicconet, Mary C. Walsh

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Auto-TLDR; BINDER: Bio-Image Near-Duplicate Examples Repository for Image Identification and Retrieval

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Manipulation and re-use of images in scientific publications is a growing issue, not only for biomedical publishers, but also for the research community in general. In this work we introduce BINDER -- Bio-Image Near-Duplicate Examples Repository, a novel dataset to help researchers develop, train, and test models to detect same-source biomedical images. BINDER contains 7,490 unique image patches for model training, 1,821 same-size patch duplicates for validation and testing, and 868 different-size image/patch pairs for image retrieval validation and testing. Except for the training set, patches already contain manipulations including rotation, translation, scale, perspective transform, contrast adjustment and/or compression artifacts. We further use the dataset to demonstrate how novel adaptations of existing image retrieval and metric learning models can be applied to achieve high-accuracy inference results, creating a baseline for future work. In aggregate, we thus present a supervised protocol for near-duplicate image identification and retrieval without any "real-world" training example. Our dataset and source code are available at hms-idac.github.io/BINDER.

Rotation Invariant Aerial Image Retrieval with Group Convolutional Metric Learning

Hyunseung Chung, Woo-Jeoung Nam, Seong-Whan Lee

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Auto-TLDR; Robust Remote Sensing Image Retrieval Using Group Convolution with Attention Mechanism and Metric Learning

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Classify Breast Histopathology Images with Ductal Instance-Oriented Pipeline

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

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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

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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.

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

Amed Mvoulana, Rostom Kachouri, Mohamed Akil

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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.

VSB^2-Net: Visual-Semantic Bi-Branch Network for Zero-Shot Hashing

Xin Li, Xiangfeng Wang, Bo Jin, Wenjie Zhang, Jun Wang, Hongyuan Zha

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Auto-TLDR; VSB^2-Net: inductive zero-shot hashing for image retrieval

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Deep Convolutional Embedding for Digitized Painting Clustering

Giovanna Castellano, Gennaro Vessio

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Auto-TLDR; A Deep Convolutional Embedding Model for Clustering Artworks

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Hierarchical Deep Hashing for Fast Large Scale Image Retrieval

Yongfei Zhang, Cheng Peng, Zhang Jingtao, Xianglong Liu, Shiliang Pu, Changhuai Chen

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Auto-TLDR; Hierarchical indexed deep hashing for fast large scale image retrieval

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

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

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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.

Exploiting Local Indexing and Deep Feature Confidence Scores for Fast Image-To-Video Search

Savas Ozkan, Gözde Bozdağı Akar

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Auto-TLDR; Fast and Robust Image-to-Video Retrieval Using Local and Global Descriptors

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Cost-effective visual representation and fast query-by-example search are two challenging goals hat should be provided for web-scale visual retrieval task on a moderate hardware. In this paper, we introduce a fast yet robust method that ensures both of these goals by obtaining the state-of-the-art results for an image-to-video search scenario. To this end, we present important enhancements to commonly used indexing and visual representation techniques by promoting faster, better and more moderate retrieval performance. We also boost the effectiveness of the method for visual distortion by exploiting the individual decision results of local and global descriptors in the query time. By this way, local content descriptors effectively represent copied / duplicated scenes with large geometric deformations, while global descriptors for near duplicate and semantic searches are more practical. Experiments are conducted on the large-scale Stanford I2V dataset. The experimental results show that the method is effective in terms of complexity and query processing time for large-scale visual retrieval scenarios, even if local and global representations are used together. In addition, the proposed method is fairly accurate and achieves state-of-the-art performance based on the mAP score of the dataset. Lastly, we report additional mAP scores after updating the ground annotations obtained by the retrieval results of the proposed method showing more clearly the actual performance.

Robust Localization of Retinal Lesions Via Weakly-Supervised Learning

Ruohan Zhao, Qin Li, Jane You

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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.

The Color Out of Space: Learning Self-Supervised Representations for Earth Observation Imagery

Stefano Vincenzi, Angelo Porrello, Pietro Buzzega, Marco Cipriano, Pietro Fronte, Roberto Cuccu, Carla Ippoliti, Annamaria Conte, Simone Calderara

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Auto-TLDR; Satellite Image Representation Learning for Remote Sensing

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The recent growth in the number of satellite images fosters the development of effective deep-learning techniques for Remote Sensing (RS). However, their full potential is untapped due to the lack of large annotated datasets. Such a problem is usually countered by fine-tuning a feature extractor that is previously trained on the ImageNet dataset. Unfortunately, the domain of natural images differs from the RS one, which hinders the final performance. In this work, we propose to learn meaningful representations from satellite imagery, leveraging its high-dimensionality spectral bands to reconstruct the visible colors. We conduct experiments on land cover classification (BigEarthNet) and West Nile Virus detection, showing that colorization is a solid pretext task for training a feature extractor. Furthermore, we qualitatively observe that guesses based on natural images and colorization rely on different parts of the input. This paves the way to an ensemble model that eventually outperforms both the above-mentioned techniques.

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

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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

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

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

Audio-Based Near-Duplicate Video Retrieval with Audio Similarity Learning

Pavlos Avgoustinakis, Giorgos Kordopatis-Zilos, Symeon Papadopoulos, Andreas L. Symeonidis, Ioannis Kompatsiaris

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Auto-TLDR; AuSiL: Audio Similarity Learning for Near-duplicate Video Retrieval

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In this work, we address the problem of audio-based near-duplicate video retrieval. We propose the Audio Similarity Learning (AuSiL) approach that effectively captures temporal patterns of audio similarity between video pairs. For the robust similarity calculation between two videos, we first extract representative audio-based video descriptors by leveraging transfer learning based on a Convolutional Neural Network (CNN) trained on a large scale dataset of audio events, and then we calculate the similarity matrix derived from the pairwise similarity of these descriptors. The similarity matrix is subsequently fed to a CNN network that captures the temporal structures existing within its content. We train our network following a triplet generation process and optimizing the triplet loss function. To evaluate the effectiveness of the proposed approach, we have manually annotated two publicly available video datasets based on the audio duplicity between their videos. The proposed approach achieves very competitive results compared to three state-of-the-art methods. Also, unlike the competing methods, it is very robust for the retrieval of audio duplicates generated with speed transformations.

Learning Embeddings for Image Clustering: An Empirical Study of Triplet Loss Approaches

Kalun Ho, Janis Keuper, Franz-Josef Pfreundt, Margret Keuper

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Auto-TLDR; Clustering Objectives for K-means and Correlation Clustering Using Triplet Loss

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In this work, we evaluate two different image clustering objectives, k-means clustering and correlation clustering, in the context of Triplet Loss induced feature space embeddings. Specifically, we train a convolutional neural network to learn discriminative features by optimizing two popular versions of the Triplet Loss in order to study their clustering properties under the assumption of noisy labels. Additionally, we propose a new, simple Triplet Loss formulation, which shows desirable properties with respect to formal clustering objectives and outperforms the existing methods. We evaluate all three Triplet loss formulations for K-means and correlation clustering on the CIFAR-10 image classification dataset.

End-To-End Training of a Two-Stage Neural Network for Defect Detection

Jakob Božič, Domen Tabernik, Danijel Skocaj

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Auto-TLDR; End-to-End Training of Segmentation-based Neural Network for Surface Defect Detection

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Segmentation-based, two-stage neural network has shown excellent results in the surface defect detection, enabling the network to learn from a relatively small number of samples. In this work, we introduce end-to-end training of the two-stage network together with several extensions to the training process, which reduce the amount of training time and improve results on surface defect detection tasks. To enable end-to-end training we carefully balance the contributions of both the segmentation and the classification loss throughout the learning. We adjust the gradient flow from the classification into the segmentation network in order to prevent the unstable features from corrupting the learning. As additional extension to the learning, we propose frequency-of-use sampling scheme of negative samples to address the issue of over- and under-sampling of images during the training, while we employ the distance transform algorithm on the region-based segmentation masks as weights for positive pixels, giving greater importance to areas with higher probability of presence of defect without requiring a detailed annotation. We demonstrate the performance of the end-to-end training scheme and the proposed extensions on three defect detection datasets---DAGM, KolektorSDD and Severstal Steel defect dataset--- where we show state-of-the-art results. On the DAGM and the KolektorSDD we demonstrate 100\% detection rate, therefore completely solving the datasets. Additional ablation study performed on all three datasets quantitatively demonstrates the contribution to the overall result improvements for each of the proposed extensions.

DFH-GAN: A Deep Face Hashing with Generative Adversarial Network

Bo Xiao, Lanxiang Zhou, Yifei Wang, Qiangfang Xu

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Auto-TLDR; Deep Face Hashing with GAN for Face Image Retrieval

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Face Image retrieval is one of the key research directions in computer vision field. Thanks to the rapid development of deep neural network in recent years, deep hashing has achieved good performance in the field of image retrieval. But for large-scale face image retrieval, the performance needs to be further improved. In this paper, we propose Deep Face Hashing with GAN (DFH-GAN), a novel deep hashing method for face image retrieval, which mainly consists of three components: a generator network for generating synthesized images, a discriminator network with a shared CNN to learn multi-domain face feature, and a hash encoding network to generate compact binary hash codes. The generator network is used to perform data augmentation so that the model could learn from both real images and diverse synthesized images. We adopt a two-stage training strategy. In the first stage, the GAN is trained to generate fake images, while in the second stage, to make the network convergence faster. The model inherits the trained shared CNN of discriminator to train the DFH model by using many different supervised loss functions not only in the last layer but also in the middle layer of the network. Extensive experiments on two widely used datasets demonstrate that DFH-GAN can generate high-quality binary hash codes and exceed the performance of the state-of-the-art model greatly.

Multi-Level Deep Learning Vehicle Re-Identification Using Ranked-Based Loss Functions

Eleni Kamenou, Jesus Martinez-Del-Rincon, Paul Miller, Patricia Devlin - Hill

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Auto-TLDR; Multi-Level Re-identification Network for Vehicle Re-Identification

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Identifying vehicles across a network of cameras with non-overlapping fields of view remains a challenging research problem due to scene occlusions, significant inter-class similarity and intra-class variability. In this paper, we propose an end-to-end multi-level re-identification network that is capable of successfully projecting same identity vehicles closer to one another in the embedding space, compared to vehicles of different identities. Robust feature representations are obtained by combining features at multiple levels of the network. As for the learning process, we employ a recent state-of-the-art structured metric learning loss function previously applied to other retrieval problems and adjust it to the vehicle re-identification task. Furthermore, we explore the cases of image-to-image, image-to-video and video-to-video similarity metric. Finally, we evaluate our system and achieve great performance on two large-scale publicly available datasets, CityFlow-ReID and VeRi-776. Compared to most existing state-of-art approaches, our approach is simpler and more straightforward, utilizing only identity-level annotations, while avoiding post-processing the ranking results (re-ranking) at the testing phase.

Bridging the Gap between Natural and Medical Images through Deep Colorization

Lia Morra, Luca Piano, Fabrizio Lamberti, Tatiana Tommasi

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Auto-TLDR; Transfer Learning for Diagnosis on X-ray Images Using Color Adaptation

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Deep learning has thrived by training on large-scale datasets. However, in many applications, as for medical image diagnosis, getting massive amount of data is still prohibitive due to privacy, lack of acquisition homogeneity and annotation cost. In this scenario transfer learning from natural image collections is a standard practice that attempts to tackle shape, texture and color discrepancy all at once through pretrained model fine-tuning. In this work we propose to disentangle those challenges and design a dedicated network module that focuses on color adaptation. We combine learning from scratch of the color module with transfer learning of different classification backbones obtaining an end-to-end, easy-to-train architecture for diagnostic image recognition on X-ray images. Extensive experiments show how our approach is particularly efficient in case of data scarcity and provides a new path for further transferring the learned color information across multiple medical datasets.

Learn to Segment Retinal Lesions and Beyond

Qijie Wei, Xirong Li, Weihong Yu, Xiao Zhang, Yongpeng Zhang, Bojie Hu, Bin Mo, Di Gong, Ning Chen, Dayong Ding, Youxin Chen

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Auto-TLDR; Multi-task Lesion Segmentation and Disease Classification for Diabetic Retinopathy Grading

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Towards automated retinal screening, this paper makes an endeavor to simultaneously achieve pixel-level retinal lesion segmentation and image-level disease classification. Such a multi-task approach is crucial for accurate and clinically interpretable disease diagnosis. Prior art is insufficient due to three challenges, i.e., lesions lacking objective boundaries, clinical importance of lesions irrelevant to their size, and the lack of one-to-one correspondence between lesion and disease classes. This paper attacks the three challenges in the context of diabetic retinopathy (DR) grading. We propose Lesion-Net, a new variant of fully convolutional networks, with its expansive path re- designed to tackle the first challenge. A dual Dice loss that leverages both semantic segmentation and image classification losses is introduced to resolve the second challenge. Lastly, we build a multi-task network that employs Lesion-Net as a side- attention branch for both DR grading and result interpretation. A set of 12K fundus images is manually segmented by 45 ophthalmologists for 8 DR-related lesions, resulting in 290K manual segments in total. Extensive experiments on this large- scale dataset show that our proposed approach surpasses the prior art for multiple tasks including lesion segmentation, lesion classification and DR grading.

Deep Multiple Instance Learning with Spatial Attention for ROP Case Classification, Instance Selection and Abnormality Localization

Xirong Li, Wencui Wan, Yang Zhou, Jianchun Zhao, Qijie Wei, Junbo Rong, Pengyi Zhou, Limin Xu, Lijuan Lang, Yuying Liu, Chengzhi Niu, Dayong Ding, Xuemin Jin

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Auto-TLDR; MIL-SA: Deep Multiple Instance Learning for Automated Screening of Retinopathy of Prematurity

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This paper tackles automated screening of Retinopathy of Prematurity (ROP), one of the most common causes of visual loss in childhood. Clinically, ROP screening per case requires multiple color fundus images capturing different zones of the premature retina. A desirable model shall not only make a decision at the case level, but also pinpoint which instances and what part of the instances are responsible for the decision. This paper makes the first attempt to accomplish three tasks, i.e, ROP case classification, instance selection and abnormality localization in a unified framework. To that end, we propose a new model that effectively combines instance-attention based deep multiple instance learning (MIL) and spatial attention (SA). The propose model, which we term MIL-SA, identifies positive instances in light of their contributions to case-level decision. Meanwhile, abnormal regions in the identified instances are automatically localized by the SA mechanism. Moreover, MIL-SA is learned from case-level binary labels exclusively, and in an end-to-end manner. Experiments on a large clinical dataset of 2,186 cases with 11,053 fundus images show the viability of the proposed model for all the three tasks.

Explainable Feature Embedding Using Convolutional Neural Networks for Pathological Image Analysis

Kazuki Uehara, Masahiro Murakawa, Hirokazu Nosato, Hidenori Sakanashi

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Auto-TLDR; Explainable Diagnosis Using Convolutional Neural Networks for Pathological Image Analysis

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The development of computer-assisted diagnosis (CAD) algorithms for pathological image analysis constitutes an important research topic. Recently, convolutional neural networks (CNNs) have been used in several studies for the development of CAD algorithms. Such systems are required to be not only accurate but also explainable for their decisions, to ensure reliability. However, a limitation of using CNNs is that the basis of the decisions made by them are incomprehensible to humans. Thus, in this paper, we present an explainable diagnosis method, which comprises of two CNNs for different rolls. This method allows us to interpret the basis of the decisions made by CNN from two perspectives, namely statistics and visualization. For the statistical explanation, the method constructs a dictionary of representative pathological features. It performs diagnoses based on the occurrence and importance of learned features referred from its dictionary. To construct the dictionary, we introduce a vector quantization scheme for CNN. For the visual interpretation, the method provides images of learned features embedded in a high-dimensional feature space as an index of the dictionary by generating them using a conditional autoregressive model. The experimental results showed that the proposed network learned pathological features, which contributed to the diagnosis and yielded an area under the receiver operating curve (AUC) of approximately 0.93 for detecting atypical tissues in pathological images of the uterine cervix. Moreover, the proposed method demonstrated that it could provide visually interpretable images to show the rationales behind its decisions. Thus, the proposed method can serve as a valuable tool for pathological image analysis in terms of both its accuracy and explainability.

End-To-End Triplet Loss Based Emotion Embedding System for Speech Emotion Recognition

Puneet Kumar, Sidharth Jain, Balasubramanian Raman, Partha Pratim Roy, Masakazu Iwamura

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Auto-TLDR; End-to-End Neural Embedding System for Speech Emotion Recognition

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In this paper, an end-to-end neural embedding system based on triplet loss and residual learning has been proposed for speech emotion recognition. The proposed system learns the embeddings from the emotional information of the speech utterances. The learned embeddings are used to recognize the emotions portrayed by given speech samples of various lengths. The proposed system implements Residual Neural Network architecture. It is trained using softmax pre-training and triplet loss function. The weights between the fully connected and embedding layers of the trained network are used to calculate the embedding values. The embedding representations of various emotions are mapped onto a hyperplane, and the angles among them are computed using the cosine similarity. These angles are utilized to classify a new speech sample into its appropriate emotion class. The proposed system has demonstrated 91.67\% and 64.44\% accuracy while recognizing emotions for RAVDESS and IEMOCAP dataset, respectively.

Deep Learning-Based Type Identification of Volumetric MRI Sequences

Jean Pablo De Mello, Thiago Paixão, Rodrigo Berriel, Mauricio Reyes, Alberto F. De Souza, Claudine Badue, Thiago Oliveira-Santos

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Auto-TLDR; Deep Learning for Brain MRI Sequences Identification Using Convolutional Neural Network

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The analysis of Magnetic Resonance Imaging (MRI) sequences enables clinical professionals to monitor the progression of a brain tumor. As the interest for automatizing brain volume MRI analysis increases, it becomes convenient to have each sequence well identified. However, the unstandardized naming of MRI sequences make their identification difficult for automated systems, as well as make it difficult for researches to generate or use datasets for machine learning research. In face of that, we propose a system for identifying types of brain MRI sequences based on deep learning. By training a Convolutional Neural Network (CNN) based on 18-layer ResNet architecture, our system is able to classify a volumetric brain MRI as a T1, T1c, T2 or FLAIR sequence, or whether it does not belong to any of these classes. The network was trained with both pre-processed (BraTS dataset) and non-pre-processed (TCGA-GBM dataset) images with diverse acquisition protocols, requiring only a few layers of the volume for training. Our system is able to classify among sequence types with an accuracy of 96.27%.

Force Banner for the Recognition of Spatial Relations

Robin Deléarde, Camille Kurtz, Laurent Wendling, Philippe Dejean

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Auto-TLDR; Spatial Relation Recognition using Force Banners

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Studying the spatial organization of objects in images is fundamental to increase both the understanding of the sensed scene and the accuracy of the perceived similarity between images. This often leads to the problem of spatial relation recognition: given two objects depicted in an image, what is their spatial relation? In this article, we consider this as a classification problem. Instead of considering directly the original image space (or imaging features) to predict the spatial relation, we propose a novel intermediate representation (called Force Banner) modeling rich spatial information between pairs of objects composing a scene. Such a representation captures the relative position between objects using a panel of forces (attraction and repulsion), that take into account the structural shapes of the objects and their distance in a directional fashion. Force Banners are used to feed a classical 2D Convolutional Neural Network (CNN) for the recognition of spatial relations, benefiting from pre-trained models and fine-tuning. Experimental results obtained on a dataset of images with various shapes highlight the interest of this approach, and in particular its benefit to describe spatial information.

A Lumen Segmentation Method in Ureteroscopy Images Based on a Deep Residual U-Net Architecture

Jorge Lazo, Marzullo Aldo, Sara Moccia, Michele Catellani, Benoit Rosa, Elena De Momi, Michel De Mathelin, Francesco Calimeri

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Auto-TLDR; A Deep Neural Network for Ureteroscopy with Residual Units

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Ureteroscopy is becoming the first surgical treatment option for the majority of urinary affections. This procedure is carried out using an endoscope which provides the surgeon with the visual and spatial information necessary to navigate inside the urinary tract. Having in mind the development of surgical assistance systems, that could enhance the performance of surgeon, the task of lumen segmentation is a fundamental part since this is the visual reference which marks the path that the endoscope should follow. This is something that has not been analyzed in ureteroscopy data before. However, this task presents several challenges given the image quality and the conditions itself of ureteroscopy procedures. In this paper, we study the implementation of a Deep Neural Network which exploits the advantage of residual units in an architecture based on U-Net. For the training of these networks, we analyze the use of two different color spaces: gray-scale and RGB data images. We found that training on gray-scale images gives the best results obtaining mean values of Dice Score, Precision, and Recall of 0.73, 0.58, and 0.92 respectively. The results obtained show that the use of residual U-Net could be a suitable model for further development for a computer-aided system for navigation and guidance through the urinary system.

Automatic Classification of Human Granulosa Cells in Assisted Reproductive Technology Using Vibrational Spectroscopy Imaging

Marina Paolanti, Emanuele Frontoni, Giorgia Gioacchini, Giorgini Elisabetta, Notarstefano Valentina, Zacà Carlotta, Carnevali Oliana, Andrea Borini, Marco Mameli

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Auto-TLDR; Predicting Oocyte Quality in Assisted Reproductive Technology Using Machine Learning Techniques

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In the field of reproductive technology, the biochemical composition of female gametes has been successfully investigated with the use of vibrational spectroscopy. Currently, in assistive reproductive technology (ART), there are no shared criteria for the choice of oocyte, and automatic classification methods for the best quality oocytes have not yet been applied. In this paper, considering the lack of criteria in Assisted Reproductive Technology (ART), we use Machine Learning (ML) techniques to predict oocyte quality for a successful pregnancy. To improve the chances of successful implantation and minimize any complications during the pregnancy, Fourier transform infrared microspectroscopy (FTIRM) analysis has been applied on granulosa cells (GCs) collected along with the oocytes during oocyte aspiration, as it is routinely done in ART, and specific spectral biomarkers were selected by multivariate statistical analysis. A proprietary biological reference dataset (BRD) was successfully collected to predict the best oocyte for a successful pregnancy. Personal health information are stored, maintained and backed up using a cloud computing service. Using a user-friendly interface, the user will evaluate whether or not the selected oocyte will have a positive result. This interface includes a dashboard for retrospective analysis, reporting, real-time processing, and statistical analysis. The experimental results are promising and confirm the efficiency of the method in terms of classification metrics: precision, recall, and F1-score (F1) measures.

TAAN: Task-Aware Attention Network for Few-Shot Classification

Zhe Wang, Li Liu, Fanzhang Li

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Auto-TLDR; TAAN: Task-Aware Attention Network for Few-Shot Classification

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Few-shot classification aims to recognize unlabeled samples from unseen classes given only a few labeled samples.Current approaches of few-shot learning usually employ a metriclearning framework to learn a feature similarity comparison between a query (test) example and the few support (training) examples. However, these approaches all extract features from samples independently without looking at the entire task as a whole, and so fail to provide an enough discrimination to features. Moreover, the existing approaches lack the ability to select the most relevant features for the task at hand. In this work, we propose a novel algorithm called Task-Aware Attention Network (TAAN) to address the above problems in few-shot classification. By inserting a Task-Relevant Channel Attention Module into metric-based few-shot learners, TAAN generates channel attentions for each sample by aggregating the context of the entire support set and identifies the most relevant features for similarity comparison. The experiment demonstrates that TAAN is competitive in overall performance comparing to the recent state-of-the-art systems and improves the performance considerably over baseline systems on both mini-ImageNet and tiered-ImageNet benchmarks.

Loop-closure detection by LiDAR scan re-identification

Jukka Peltomäki, Xingyang Ni, Jussi Puura, Joni-Kristian Kamarainen, Heikki Juhani Huttunen

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Auto-TLDR; Loop-Closing Detection from LiDAR Scans Using Convolutional Neural Networks

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In this work, loop-closure detection from LiDAR scans is defined as an image re-identification problem. Re-identification is performed by computing Euclidean distances of a query scan to a gallery set of previous scans. The distances are computed in a feature embedding space where the scans are mapped by a convolutional neural network (CNN). The network is trained using the triplet loss training strategy. In our experiments we compare different backbone networks, variants of the triplet loss and generic and LiDAR specific data augmentation techniques. With a realistic indoor dataset the best architecture obtains the mean average precision (mAP) above 90%.

Cross-View Relation Networks for Mammogram Mass Detection

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

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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.

A Systematic Investigation on End-To-End Deep Recognition of Grocery Products in the Wild

Marco Leo, Pierluigi Carcagni, Cosimo Distante

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Auto-TLDR; Automatic Recognition of Products on grocery shelf images using Convolutional Neural Networks

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Automatic recognition of products on grocery shelf images is a new and attractive topic in computer vision and machine learning since, it can be exploited in different application areas. This paper introduces a complete end-to-end pipeline (without preliminary radiometric and spatial transformations usually involved while dealing with the considered issue) and it provides a systematic investigation of recent machine learning models based on convolutional neural networks for addressing the product recognition task by exploiting the proposed pipeline on a recent challenging grocery product dataset. The investigated models were never been used in this context: they derive from the successful and more generic object recognition task and have been properly tuned to address this specific issue. Besides, also ensembles of nets built by most advanced theoretical fundaments have been taken into account. Gathered classification results were very encouraging since the recognition accuracy has been improved up to 15\% with respect to the leading approaches in the state of art on the same dataset. A discussion about the pros and cons of the investigated solutions are discussed by paving the path towards new research lines.

Large-Scale Historical Watermark Recognition: Dataset and a New Consistency-Based Approach

Xi Shen, Ilaria Pastrolin, Oumayma Bounou, Spyros Gidaris, Marc Smith, Olivier Poncet, Mathieu Aubry

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Auto-TLDR; Historical Watermark Recognition with Fine-Grained Cross-Domain One-Shot Instance Recognition

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Historical watermark recognition is a highly practical, yet unsolved challenge for archivists and historians. With a large number of well-defined classes, cluttered and noisy samples, different types of representations, both subtle differences between classes and high intra-class variation, historical watermarks are also challenging for pattern recognition. In this paper, overcoming the difficulty of data collection, we present a large public dataset with more than 6k new photographs, allowing for the first time to tackle at scale the scenarios of practical interest for scholars: one-shot instance recognition and cross-domain one-shot instance recognition amongst more than 16k fine-grained classes. We demonstrate that this new dataset is large enough to train modern deep learning approaches, and show that standard methods can be improved considerably by using mid-level deep features. More precisely, we design both a matching score and a feature fine-tuning strategy based on filtering local matches using spatial consistency. This consistency-based approach provides important performance boost compared to strong baselines. Our model achieves 55\% as top-1 accuracy on our very challenging 16,753-class one-shot cross-domain recognition task, each class described by a single drawing from the classic Briquet catalog. In addition to watermark classification, we show our approach provides promising results on fine-grained sketch-based image retrieval.

Transfer Learning through Weighted Loss Function and Group Normalization for Vessel Segmentation from Retinal Images

Abdullah Sarhan, Jon Rokne, Reda Alhajj, Andrew Crichton

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Auto-TLDR; Deep Learning for Segmentation of Blood Vessels in Retinal Images

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The vascular structure of blood vessels is important in diagnosing retinal conditions such as glaucoma and diabetic retinopathy. Accurate segmentation of these vessels can help in detecting retinal objects such as the optic disc and optic cup and hence determine if there are damages to these areas. Moreover, the structure of the vessels can help in diagnosing glaucoma. The rapid development of digital imaging and computer-vision techniques has increased the potential for developing approaches for segmenting retinal vessels. In this paper, we propose an approach for segmenting retinal vessels that uses deep learning along with transfer learning. We adapted the U-Net structure to use a customized InceptionV3 as the encoder and used multiple skip connections to form the decoder. Moreover, we used a weighted loss function to handle the issue of class imbalance in retinal images. Furthermore, we contributed a new dataset to this field. We tested our approach on six publicly available datasets and a newly created dataset. We achieved an average accuracy of 95.60\% and a Dice coefficient of 80.98\%. The results obtained from comprehensive experiments demonstrate the robustness of our approach to the segmentation of blood vessels in retinal images obtained from different sources. Our approach results in greater segmentation accuracy than other approaches.

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

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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.

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

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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.

Leveraging Unlabeled Data for Glioma Molecular Subtype and Survival Prediction

Nicholas Nuechterlein, Beibin Li, Mehmet Saygin Seyfioglu, Sachin Mehta, Patrick Cimino, Linda Shapiro

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Auto-TLDR; Multimodal Brain Tumor Segmentation Using Unlabeled MR Data and Genomic Data for Cancer Prediction

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In this paper, we address two long-standing challenges in neuro-oncology: (1) how to leverage large amounts of unlabeled magnetic resonance (MR) imaging data for radiogenomic tasks and (2) how to unite glioma MR imaging with genomic data. We examine multi-parametric MR data from 542 patients in the combined training, validation, and testing sets of the 2018 Multimodal Brain Tumor Segmentation Challenge and somatic copy number alteration (SCNA) data from 1090 patients in The Cancer Genome Archive's (TCGA) lower-grade glioma and glioblastoma projects. We propose a novel application of multi-task learning (MTL) that leverages unlabeled MR data by jointly learning tumor segmentation masks with glioma molecular subtype markers and allows for SCNA input when available. There are 235 patients in the intersection of these MR and SCNA datasets, which we divide into an unlabeled training set, a labeled training set, and a validation set. Our MTL model significantly outperforms comparable classification models trained only on labeled MR data for both IDH1/2 mutation and 1p/19q co-deletion glioma subtype marker prediction tasks. We also observe that models trained on genomic and imaging data improve survival prediction results achieved by models trained on either alone. We will release our source code for future research.

The DeepHealth Toolkit: A Unified Framework to Boost Biomedical Applications

Michele Cancilla, Laura Canalini, Federico Bolelli, Stefano Allegretti, Salvador Carrión, Roberto Paredes, Jon Ander Gómez, Simone Leo, Marco Enrico Piras, Luca Pireddu, Asaf Badouh, Santiago Marco-Sola, Lluc Alvarez, Miquel Moreto, Costantino Grana

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Auto-TLDR; DeepHealth Toolkit: An Open Source Deep Learning Toolkit for Cloud Computing and HPC

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Given the overwhelming impact of machine learning on the last decade, several libraries and frameworks have been developed in recent years to simplify the design and training of neural networks, providing array-based programming, automatic differentiation and user-friendly access to hardware accelerators. None of those tools, however, was designed with native and transparent support for Cloud Computing or heterogeneous High-Performance Computing (HPC). The DeepHealth Toolkit is an open source deep learning toolkit aimed at boosting productivity of data scientists operating in the medical field by providing a unified framework for the distributed training of neural networks, that is able to leverage hybrid HPC and Cloud environments in a way transparent to the user. The toolkit is composed of a computer vision library, a deep learning library, and a front-end for non-expert users; all of the components are focused on the medical domain, but they are general purpose and can be applied to any other field. In this paper, the principles driving the design of the DeepHealth libraries are described, along with details about the implementation and the interaction between the different elements composing the toolkit. Finally, experiments on common benchmarks prove the efficiency of each separate component, and of the DeepHealth Toolkit overall.