Longitudinal Feature Selection and Feature Learning for Parkinson’s Disease Diagnosis and Prediction

Haijun Lei, Zhongwei Huang, Xiaohua Xiao, Yi Lei, En-Leng Tan, Baiying Lei, Shiqi Li

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Auto-TLDR; Joint Learning from Multiple Modalities and Relations for Joint Disease Diagnosis and Prediction in Parkinson's Disease

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Parkinson's disease (PD) is an irreversible neurodegenerative disease that seriously affects patients' lives. To provide patients with accurate treatment in time and to reduce deterioration of the disease, it is critical to have an early diagnosis of PD and accurate clinical score predictions. Different from previous studies on PD, most of which only focus on feature selection methods, we propose a network combining joint learning from multiple modalities and relations (JLMMR) with sparse nonnegative autoencoder (SNAE) to further enhance the ability of feature expression. We first preprocess and extract features of the modal neuroimaging data with multiple time points. To extract discriminative and informative features from longitudinal data, we apply JLMMR method for feature selection to avoid over-fitting issues. We further exploit SNAE to learn longitudinal discriminative features for joint disease diagnosis and obtain clinical score predictions. Extensive experiments on the publicly available Parkinson's Progression Markers Initiative (PPMI) dataset show the proposed method produces promising classification and prediction performance, which outperforms state-of-the-art methods as well.

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

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

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

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Analysis of longitudinal changes in brain diseases is essential for a better characterization of pathological processes and evaluation of the prognosis. This is particularly important in Multiple Sclerosis (MS) which is the first traumatic disease in young adults, with unknown etiology and characterized by complex inflammatory and degenerative processes leading to different clinical courses. In this work, we propose a fully automated tensor-based algorithm for the classification of MS clinical forms based on the structural connectivity graph of the white matter (WM) network. Using non-negative tensor factorization (NTF), we first focused on the detection of pathological patterns of the brain WM network affected by significant longitudinal variations. Second, we performed unsupervised classification of different MS phenotypes based on these longitudinal patterns, and finally, we used the latent factors obtained by the factorization algorithm to identify the most affected brain regions.

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

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

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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.

Encoding Brain Networks through Geodesic Clustering of Functional Connectivity for Multiple Sclerosis Classification

Muhammad Abubakar Yamin, Valsasina Paola, Michael Dayan, Sebastiano Vascon, Tessadori Jacopo, Filippi Massimo, Vittorio Murino, A Rocca Maria, Diego Sona

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

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An important task in brain connectivity research is the classification of patients from healthy subjects. In this work, we present a two-step mathematical framework allowing to discriminate between two groups of people with an application to multiple sclerosis. The proposed approach exploits the properties of the connectivity matrices determined using the covariances between signals of a fixed set of brain areas. These positive semi-definite matrices lay on a Riemannian manifold, allowing to use a geodesic distance defined on this space. In order to generate a vector representation useful for classification purpose, but still preserving the network structures, we encoded the data exploiting the network attractors determined by a geodesic clustering of connectivity matrices. Then clustering centroids were used as a dictionary allowing to encode subject’s connectivity matrices as a vector of geodesic distances. A Linear Support Vector Machine was then used to perform classification between subjects. To demonstrate the advantage of using geodesic metrics in this framework, we conducted the same analysis using Euclidean metric. Experimental results validate the fact that employing geodesic metric in this framework leads to a higher classification performance, whereas with Euclidean metric performance was suboptimal.

Exploring Spatial-Temporal Representations for fNIRS-based Intimacy Detection via an Attention-enhanced Cascade Convolutional Recurrent Neural Network

Chao Li, Qian Zhang, Ziping Zhao

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

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

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

Tongxue Zhou, Stéphane Canu, Pierre Vera, Su Ruan

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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.

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

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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.

FMRI Brain Networks As Statistical Mechanical Ensembles

Jianjia Wang, Hui Wu, Edwin Hancock

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

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

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

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.

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

Hermann Jepdjio Nkouanga, Szilard Vajda

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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.

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.

Feature-Aware Unsupervised Learning with Joint Variational Attention and Automatic Clustering

Wang Ru, Lin Li, Peipei Wang, Liu Peiyu

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Auto-TLDR; Deep Variational Attention Encoder-Decoder for Clustering

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Deep clustering aims to cluster unlabeled real-world samples by mining deep feature representation. Most of existing methods remain challenging when handling high-dimensional data and simultaneously exploring the complementarity of deep feature representation and clustering. In this paper, we propose a novel Deep Variational Attention Encoder-decoder for Clustering (DVAEC). Our DVAEC improves the representation learning ability by fusing variational attention. Specifically, we design a feature-aware automatic clustering module to mitigate the unreliability of similarity calculation and guide network learning. Besides, to further boost the performance of deep clustering from a global perspective, we define a joint optimization objective to promote feature representation learning and automatic clustering synergistically. Extensive experimental results show the promising performance achieved by our DVAEC on six datasets comparing with several popular baseline clustering methods.

Using Machine Learning to Refer Patients with Chronic Kidney Disease to Secondary Care

Lee Au-Yeung, Xianghua Xie, Timothy Marcus Scale, James Anthony Chess

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Auto-TLDR; A Machine Learning Approach for Chronic Kidney Disease Prediction using Blood Test Data

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There has been growing interest recently in using machine learning techniques as an aid in clinical medicine. Machine learning offers a range of classification algorithms which can be applied to medical data to aid in making clinical predictions. Recent studies have demonstrated the high predictive accuracy of various classification algorithms applied to clinical data. Several studies have already been conducted in diagnosing or predicting chronic kidney disease at various stages using different sets of variables. In this study we are investigating the use machine learning techniques with blood test data. Such a system could aid renal teams in making recommendations to primary care general practitioners to refer patients to secondary care where patients may benefit from earlier specialist assessment and medical intervention. We are able to achieve an overall accuracy of 88.48\% using logistic regression, 87.12\% using ANN and 85.29\% using SVM. ANNs performed with the highest sensitivity at 89.74\% compared to 86.67\% for logistic regression and 85.51\% for SVM.

Multi-Scale and Attention Based ResNet for Heartbeat Classification

Haojie Zhang, Gongping Yang, Yuwen Huang, Feng Yuan, Yilong Yin

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Auto-TLDR; A Multi-Scale and Attention based ResNet for ECG heartbeat classification in intra-patient and inter-patient paradigms

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This paper presents a novel deep learning framework for the electrocardiogram (ECG) heartbeat classification. Although there have been some studies with excellent overall accuracy, these studies have not been very accurate in the diagnosis of arrhythmia classes especially such as supraventricular ectopic beat (SVEB) and ventricular ectopic beat (VEB). In our work, we propose a Multi-Scale and Attention based ResNet for heartbeat classification in intra-patient and inter-patient paradigms respectively. Firstly, we extract shallow features from a convolutional layer. Secondly, the shallow features are sent into three branches with different convolution kernels in order to combine receptive fields of different sizes. Finally, fully connected layers are used to classify the heartbeat. Besides, we design a new attention mechanism based on the characteristics of heartbeat data. At last, extensive experiments on benchmark dataset demonstrate the effectiveness of our proposed model.

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

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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.

BCAU-Net: A Novel Architecture with Binary Channel Attention Module for MRI Brain Segmentation

Yongpei Zhu, Zicong Zhou, Guojun Liao, Kehong Yuan

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Auto-TLDR; BCAU-Net: Binary Channel Attention U-Net for MRI brain segmentation

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Recently deep learning-based networks have achieved advanced performance in medical image segmentation. However, the development of deep learning is slow in magnetic resonance image (MRI) segmentation of normal brain tissues. In this paper, inspired by channel attention module, we propose a new architecture, Binary Channel Attention U-Net (BCAU-Net), by introducing a novel Binary Channel Attention Module (BCAM) into skip connection of U-Net, which can take full advantages of the channel information extracted from the encoding path and corresponding decoding path. To better aggregate multi-scale spatial information of the feature map, spatial pyramid pooling (SPP) modules with different pooling operations are used in BCAM instead of original average-pooling and max-pooling operations. We verify this model on two datasets including IBSR and MRBrainS18, and obtain better performance on MRI brain segmentation compared with other methods. We believe the proposed method can advance the performance in brain segmentation and clinical diagnosis.

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.

Adversarial Encoder-Multi-Task-Decoder for Multi-Stage Processes

Andre Mendes, Julian Togelius, Leandro Dos Santos Coelho

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Auto-TLDR; Multi-Task Learning and Semi-Supervised Learning for Multi-Stage Processes

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In multi-stage processes, decisions occur in an ordered sequence of stages. Early stages usually have more observations with general information (easier/cheaper to collect), while later stages have fewer observations but more specific data. This situation can be represented by a dual funnel structure, in which the sample size decreases from one stage to the other while the information increases. Training classifiers in this scenario is challenging since information in the early stages may not contain distinct patterns to learn (underfitting). In contrast, the small sample size in later stages can cause overfitting. We address both cases by introducing a framework that combines adversarial autoencoders (AAE), multi-task learning (MTL), and multi-label semi-supervised learning (MLSSL). We improve the decoder of the AAE with an MTL component so it can jointly reconstruct the original input and use feature nets to predict the features for the next stages. We also introduce a sequence constraint in the output of an MLSSL classifier to guarantee the sequential pattern in the predictions. Using real-world data from different domains (selection process, medical diagnosis), we show that our approach outperforms other state-of-the-art methods.

A Riemannian Framework for Detecting Stimulus-Relevant Fiber Pathways

Jingyong Su, Linlin Tang, Zhipeng Yang, Mengmeng Guo

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

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Functional MRI based on blood oxygenation level-dependent (BOLD) contrast is well established as a neuro-imaging technique for detecting neural activity in the cortex of the human brain. Recent studies have shown that variations of BOLD signals in white matter are also related to neural activities both in resting state and under functional loading. We develop a comprehensive framework of detecting task-specific fiber pathways. We not only study fiber tracts as open curves with different physical features (shape, scale, orientation and position), but also incorporate the BOLD signals transmitted along them to find stimulus-relevant pathways. Specifically, we propose a novel Riemannian metric, which is a weighted sum of distances in product space of shapes and functions. This metric provides both a cost function for registration and a proper distance for comparison. Experimental results on real data have shown that we can cluster fiber pathways correctly by evaluating correlations between BOLD signals and stimuli, temporal variations and power spectra of them. The proposed framework can also be easily generalized to various applications where multi-modality data exist.

Prediction of Obstructive Coronary Artery Disease from Myocardial Perfusion Scintigraphy using Deep Neural Networks

Ida Arvidsson, Niels Christian Overgaard, Miguel Ochoa Figueroa, Jeronimo Rose, Anette Davidsson, Kalle Åström, Anders Heyden

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Auto-TLDR; A Deep Learning Algorithm for Multi-label Classification of Myocardial Perfusion Scintigraphy for Stable Ischemic Heart Disease

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For diagnosis and risk assessment in patients with stable ischemic heart disease, myocardial perfusion scintigraphy is one of the most common cardiological examinations performed today. There are however many motivations for why an artificial intelligence algorithm would provide useful input to this task. For example to reduce the subjectiveness and save time for the nuclear medicine physicians working with this time consuming task. In this work we have developed a deep learning algorithm for multi-label classification based on a modified convolutional neural network to estimate probability of obstructive coronary artery disease in the left anterior artery, left circumflex artery and right coronary artery. The prediction is based on data from myocardial perfusion scintigraphy studies conducted in a dedicated Cadmium-Zinc-Telluride cardio camera (D-SPECT Spectrum Dynamics). Data from 588 patients was available, with stress images in both upright and supine position, as well as a number of auxiliary parameters such as angina symptoms and BMI. The data was used to train and evaluate the algorithm using 5-fold cross-validation. We achieve state-of-the-art results for this task with an area under the receiver operating characteristics curve of 0.89 as average on per-vessel level and 0.94 on per-patient level.

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.

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.

Edge-Aware Graph Attention Network for Ratio of Edge-User Estimation in Mobile Networks

Jiehui Deng, Sheng Wan, Xiang Wang, Enmei Tu, Xiaolin Huang, Jie Yang, Chen Gong

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Auto-TLDR; EAGAT: Edge-Aware Graph Attention Network for Automatic REU Estimation in Mobile Networks

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Estimating the Ratio of Edge-Users (REU) is an important issue in mobile networks, as it helps the subsequent adjustment of loads in different cells. However, existing approaches usually determine the REU manually, which are experience-dependent and labor-intensive, and thus the estimated REU might be imprecise. Considering the inherited graph structure of mobile networks, in this paper, we utilize a graph-based deep learning method for automatic REU estimation, where the practical cells are deemed as nodes and the load switchings among them constitute edges. Concretely, Graph Attention Network (GAT) is employed as the backbone of our method due to its impressive generalizability in dealing with networked data. Nevertheless, conventional GAT cannot make full use of the information in mobile networks, since it only incorporates node features to infer the pairwise importance and conduct graph convolutions, while the edge features that are actually critical in our problem are disregarded. To accommodate this issue, we propose an Edge-Aware Graph Attention Network (EAGAT), which is able to fuse the node features and edge features for REU estimation. Extensive experimental results on two real-world mobile network datasets demonstrate the superiority of our EAGAT approach to several state-of-the-art methods.

SAGE: Sequential Attribute Generator for Analyzing Glioblastomas Using Limited Dataset

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

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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.

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.

Joint Learning Multiple Curvature Descriptor for 3D Palmprint Recognition

Lunke Fei, Bob Zhang, Jie Wen, Chunwei Tian, Peng Liu, Shuping Zhao

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Auto-TLDR; Joint Feature Learning for 3D palmprint recognition using curvature data vectors

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3D palmprint-based biometric recognition has drawn growing research attention due to its several merits over 2D counterpart such as robust structural measurement of a palm surface and high anti-counterfeiting capability. However, most existing 3D palmprint descriptors are hand-crafted that usually extract stationary features from 3D palmprint images. In this paper, we propose a feature learning method to jointly learn compact curvature feature descriptor for 3D palmprint recognition. We first form multiple curvature data vectors to completely sample the intrinsic curvature information of 3D palmprint images. Then, we jointly learn a feature projection function that project curvature data vectors into binary feature codes, which have the maximum inter-class variances and minimum intra-class distance so that they are discriminative. Moreover, we learn the collaborative binary representation of the multiple curvature feature codes by minimizing the information loss between the final representation and the multiple curvature features, so that the proposed method is more compact in feature representation and efficient in matching. Experimental results on the baseline 3D palmprint database demonstrate the superiority of the proposed method in terms of recognition performance in comparison with state-of-the-art 3D palmprint descriptors.

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

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

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

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

A Deep Learning Approach for the Segmentation of Myocardial Diseases

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

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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.

CSpA-DN: Channel and Spatial Attention Dense Network for Fusing PET and MRI Images

Bicao Li, Zhoufeng Liu, Shan Gao, Jenq-Neng Hwang, Jun Sun, Zongmin Wang

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Auto-TLDR; CSpA-DN: Unsupervised Fusion of PET and MR Images with Channel and Spatial Attention

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In this paper, we propose a novel unsupervised fusion framework based on a dense network with channel and spatial attention (CSpA-DN) for PET and MR images. In our approach, an encoder composed of the densely connected neural network is constructed to extract features from source images, and a decoder network is leveraged to yield the fused image from these features. Simultaneously, a self-attention mechanism is introduced in the encoder and decoder to further integrate local features along with their global dependencies adaptively. The extracted feature of each spatial position is synthesized by a weighted summation of those features at the same row and column with this position via a spatial attention module. Meanwhile, the interdependent relationship of all feature maps is integrated by a channel attention module. The summation of the outputs of these two attention modules is fed into the decoder and the fused image is generated. Experimental results illustrate the superiorities of our proposed CSpA-DN model compared with state-of-the-art methods in PET and MR images fusion according to both visual perception and objective assessment.

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.

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

Dipayan Das, K.C. Santosh, Umapada Pal

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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.

Attack-Agnostic Adversarial Detection on Medical Data Using Explainable Machine Learning

Matthew Watson, Noura Al Moubayed

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Auto-TLDR; Explainability-based Detection of Adversarial Samples on EHR and Chest X-Ray Data

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Explainable machine learning has become increasingly prevalent, especially in healthcare where explainable models are vital for ethical and trusted automated decision making. Work on the susceptibility of deep learning models to adversarial attacks has shown the ease of designing samples to mislead a model into making incorrect predictions. In this work, we propose an explainability-based method for the accurate detection of adversarial samples on two datasets with different complexity and properties: Electronic Health Record (EHR) and chest X-ray (CXR) data. On the MIMIC-III and Henan-Renmin EHR datasets, we report a detection accuracy of 77% against the Longitudinal Adversarial Attack. On the MIMIC-CXR dataset, we achieve an accuracy of 88%; significantly improving on the state of the art of adversarial detection in both datasets by over 10% in all settings. We propose an anomaly detection based method using explainability techniques to detect adversarial samples which is able to generalise to different attack methods without a need for retraining.

Nonlinear Ranking Loss on Riemannian Potato Embedding

Byung Hyung Kim, Yoonje Suh, Honggu Lee, Sungho Jo

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Auto-TLDR; Riemannian Potato for Rank-based Metric Learning

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We propose a rank-based metric learning method by leveraging a concept of the Riemannian Potato for better separating non-linear data. By exploring the geometric properties of Riemannian manifolds, the proposed loss function optimizes the measure of dispersion using the distribution of Riemannian distances between a reference sample and neighbors and builds a ranked list according to the similarities. We show the proposed function can learn a hypersphere for each class, preserving the similarity structure inside it on Riemannian manifold. As a result, compared with Euclidean distance-based metric, our method can further jointly reduce the intra-class distances and enlarge the inter-class distances for learned features, consistently outperforming state-of-the-art methods on three widely used non-linear datasets.

Constrained Spectral Clustering Network with Self-Training

Xinyue Liu, Shichong Yang, Linlin Zong

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Auto-TLDR; Constrained Spectral Clustering Network: A Constrained Deep spectral clustering network

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Deep spectral clustering networks have shown their superiorities due to the integration of feature learning and cluster assignment, and the ability to deal with non-convex clusters. Nevertheless, deep spectral clustering is still an ill-posed problem. Specifically, the affinity learned by the most remarkable SpectralNet is not guaranteed to be consistent with local invariance and thus hurts the final clustering performance. In this paper, we propose a novel framework of Constrained Spectral Clustering Network (CSCN) by incorporating pairwise constraints and clustering oriented fine-tuning to deal with the ill-posedness. To the best of our knowledge, this is the first constrained deep spectral clustering method. Another advantage of CSCN over existing constrained deep clustering networks is that it propagates pairwise constraints throughout the entire dataset. In addition, we design a clustering oriented loss by self-training to simultaneously finetune feature representations and perform cluster assignments, which further improve the quality of clustering. Extensive experiments on benchmark datasets demonstrate that our approach outperforms the state-of-the-art clustering methods.

A Joint Super-Resolution and Deformable Registration Network for 3D Brain Images

Sheng Lan, Zhenhua Guo

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Auto-TLDR; Joint Super-Resolution and Deformable Image Registration with Super-resolution

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In this paper, we propose a joint network for 3D brain images registration with super-resolution to reduce deformable image registration errors caused by low resolution. Basically, the task of deformable image registration is to find the displacement field between the reference image and the moving image. Many research works have been done for deformable image registration, under the assumption that the image resolution is high enough. However, due to the limited level of current acquisition instruments, the resolution of images is not high enough usually. As low resolution images might cause large registration errors, this paper presents a new approach that performs joint super-resolution and deformable image registration. Experiments with 3D brain images show that the joint network does help to reduce the registration errors significantly.

Assessing the Severity of Health States Based on Social Media Posts

Shweta Yadav, Joy Prakash Sain, Amit Sheth, Asif Ekbal, Sriparna Saha, Pushpak Bhattacharyya

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Auto-TLDR; A Multiview Learning Framework for Assessment of Health State in Online Health Communities

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The unprecedented growth of Internet users has resulted in an abundance of unstructured information on social media including health forums, where patients request health-related information or opinions from other users. Previous studies have shown that online peer support has limited effectiveness without expert intervention. Therefore, a system capable of assessing the severity of health state from the patients' social media posts can help health professionals (HP) in prioritizing the user’s post. In this study, we inspect the efficacy of different aspects of Natural Language Understanding (NLU) to identify the severity of the user’s health state in relation to two perspectives(tasks) (a) Medical Condition (i.e., Recover, Exist, Deteriorate, Other) and (b) Medication (i.e., Effective, Ineffective, Serious Adverse Effect, Other) in online health communities. We propose a multiview learning framework that models both the textual content as well as contextual-information to assess the severity of the user’s health state. Specifically, our model utilizes the NLU views such as sentiment, emotions, personality, and use of figurative language to extract the contextual information. The diverse NLU views demonstrate its effectiveness on both the tasks and as well as on the individual disease to assess a user’s health.

A Systematic Investigation on Deep Architectures for Automatic Skin Lesions Classification

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

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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.

Classification and Feature Selection Using a Primal-Dual Method and Projections on Structured Constraints

Michel Barlaud, Antonin Chambolle, Jean_Baptiste Caillau

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Auto-TLDR; A Constrained Primal-dual Method for Structured Feature Selection on High Dimensional Data

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This paper deals with feature selection using supervised classification on high dimensional datasets. A classical approach is to project data on a low dimensional space and classify by minimizing an appropriate quadratic cost. Our first contribution is to introduce a matrix of centers in the definition of this cost. Moreover, as quadratic costs are not robust to outliers, we propose to use an $\ell_1$ cost instead (or Huber loss to mitigate overfitting issues). While control on sparsity is commonly obtained by adding an $\ell_1$ constraint on the vectorized matrix of weights used for projecting the data, our second contribution is to enforce structured sparsity. To this end we propose constraints that take into account the matrix structure of the data, based either on the nuclear norm, on the $\ell_{2,1}$ norm, or on the $\ell_{1,2}$ norm for which we provide a new projection algorithm. We optimize simultaneously the projection matrix and the matrix of centers thanks to a new tailored constrained primal-dual method. The primal-dual framework is general enough to encompass the various robust losses and structured constraints we use, and allows a convergence analysis. We demonstrate the effectiveness of the approach on three biological datasets. Our primal-dual method with robust losses, adaptive centers and structured constraints does significantly better than classical methods, both in terms of accuracy and computational time.

Confidence Calibration for Deep Renal Biopsy Immunofluorescence Image Classification

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

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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.

Breast Anatomy Enriched Tumor Saliency Estimation

Fei Xu, Yingtao Zhang, Heng-Da Cheng, Jianrui Ding, Boyu Zhang, Chunping Ning, Ying Wang

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Auto-TLDR; Tumor Saliency Estimation for Breast Ultrasound using enriched breast anatomy knowledge

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Breast cancer investigation is of great significance and developing tumor detection methodologies is a critical need. However, it is a challenging task for breast cancer detection using breast ultrasound (BUS) images due to the complicated breast structure and poor quality of the images. In this paper, we propose a novel tumor saliency estimation (TSE) model guided by enriched breast anatomy knowledge to localize the tumor. First, the breast anatomy layers are generated by a deep neural network. Then we refine the layers by integrating a non-semantic breast anatomy model to solve the problems of incomplete mammary layers. Meanwhile, a new background map generation method weighted by the semantic probability and spatial distance is proposed to improve the performance. The experiment demonstrates that the proposed method with the new background map outperforms four state-of-the-art TSE models with increasing 10% of F_meansure on the public BUS dataset.

A Comparison of Neural Network Approaches for Melanoma Classification

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

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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.

Estimation of Clinical Tremor Using Spatio-Temporal Adversarial AutoEncoder

Li Zhang, Vidya Koesmahargyo, Isaac Galatzer-Levy

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Auto-TLDR; ST-AAE: Spatio-temporal Adversarial Autoencoder for Clinical Assessment of Hand Tremor Frequency and Severity

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Collecting sufficient well-labeled training data is a challenging task in many clinical applications. Besides the tremendous efforts required for data collection, clinical assessments are also impacted by raters’ variabilities, which may be significant even among experienced clinicians. The high demands of reproducible and scalable data-driven approaches in these areas necessitates relevant research on learning with limited data. In this work, we propose a spatio-temporal adversarial autoencoder (ST-AAE) for clinical assessment of hand tremor frequency and severity. The ST-AAE integrates spatial and temporal information simultaneously into the original AAE, taking optical flows as inputs. Using only optical flows, irrelevant background or static objects from RGB frames are largely eliminated, so that the AAE is directed to effectively learn key feature representations of the latent space from tremor movements. The ST-AAE was evaluated with both volunteer and clinical data. The volunteer results showed that the ST-AAE improved model performance significantly by 15% increase on accuracy. Leave-one-out (on subjects) cross validation was used to evaluate the accuracy for all the 3068 video segments from 28 volunteers. The weighted average of the AUCs of ROCs is 0.97. The results demonstrated that the ST-AAE model, trained with a small number of subjects, can be generalized well to different subjects. In addition, the model trained only by volunteer data was also evaluated with 32 clinical videos from 9 essential tremor patients, the model predictions correlate well with the clinical ratings: correlation coefficient r = 0.91 and 0.98 for in-person ratings and video watching ratings, respectively.

Feature Extraction by Joint Robust Discriminant Analysis and Inter-Class Sparsity

Fadi Dornaika, Ahmad Khoder

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Auto-TLDR; Robust Discriminant Analysis with Feature Selection and Inter-class Sparsity (RDA_FSIS)

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Feature extraction methods have been successfully applied to many real-world applications. The classical Linear Discriminant Analysis (LDA) and its variants are widely used as feature extraction methods. Although they have been used for different classification tasks, these methods have some shortcomings. The main one is that the projection axes obtained are not informative about the relevance of original features. In this paper, we propose a linear embedding method that merges two interesting properties: Robust LDA and inter-class sparsity. Furthermore, the targeted projection transformation focuses on the most discriminant original features. The proposed method is called Robust Discriminant Analysis with Feature Selection and Inter-class Sparsity (RDA_FSIS). Two kinds of sparsity are explicitly included in the proposed model. The first kind is obtained by imposing the $\ell_{2,1}$ constraint on the projection matrix in order to perform feature ranking. The second kind is obtained by imposing the inter-class sparsity constraint used for getting a common sparsity structure in each class. Comprehensive experiments on five real-world image datasets demonstrate the effectiveness and advantages of our framework over existing linear methods.

More Correlations Better Performance: Fully Associative Networks for Multi-Label Image Classification

Yaning Li, Liu Yang

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Auto-TLDR; Fully Associative Network for Fully Exploiting Correlation Information in Multi-Label Classification

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Recent researches demonstrate that correlation modeling plays a key role in high-performance multi-label classification methods. However, existing methods do not take full advantage of correlation information, especially correlations in feature and label spaces of each image, which limits the performance of correlation-based multi-label classification methods. With more correlations considered, in this study, a Fully Associative Network (FAN) is proposed for fully exploiting correlation information, which involves both visual feature and label correlations. Specifically, FAN introduces a robust covariance pooling to summarize convolution features as global image representation for capturing feature correlation in the multi-label task. Moreover, it constructs an effective label correlation matrix based on a re-weighted scheme, which is fed into a graph convolution network for capturing label correlation. Then, correlation between covariance representations (i.e., feature correlation ) and the outputs of GCN (i.e., label correlation) are modeled for final prediction. Experimental results on two datasets illustrate the effectiveness and efficiency of our proposed FAN compared with state-of-the-art methods.

Saliency Prediction on Omnidirectional Images with Brain-Like Shallow Neural Network

Zhu Dandan, Chen Yongqing, Min Xiongkuo, Zhao Defang, Zhu Yucheng, Zhou Qiangqiang, Yang Xiaokang, Tian Han

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Auto-TLDR; A Brain-like Neural Network for Saliency Prediction of Head Fixations on Omnidirectional Images

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Deep feedforward convolutional neural networks (CNNs) perform well in the saliency prediction of omnidirectional images (ODIs), and have become the leading class of candidate models of the visual processing mechanism in the primate ventral stream. These CNNs have evolved from shallow network architecture to extremely deep and branching architecture to achieve superb performance in various vision tasks, yet it is unclear how brain-like they are. In particular, these deep feedforward CNNs are difficult to mapping to ventral stream structure of the brain visual system due to their vast number of layers and missing biologically-important connections, such as recurrence. To tackle this issue, some brain-like shallow neural networks are introduced. In this paper, we propose a novel brain-like network model for saliency prediction of head fixations on ODIs. Specifically, our proposed model consists of three modules: a CORnet-S module, a template feature extraction module and a ranking attention module (RAM). The CORnet-S module is a lightweight artificial neural network (ANN) with four anatomically mapped areas (V1, V2, V4 and IT) and it can simulate the visual processing mechanism of ventral visual stream in the human brain. The template features extraction module is introduced to extract attention maps of ODIs and provide guidance for the feature ranking in the following RAM module. The RAM module is used to rank and select features that are important for fine-grained saliency prediction. Extensive experiments have validated the effectiveness of the proposed model in predicting saliency maps of ODIs, and the proposed model outperforms other state-of-the-art methods with similar scale.

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

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

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

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

Ancient Document Layout Analysis: Autoencoders Meet Sparse Coding

Homa Davoudi, Marco Fiorucci, Arianna Traviglia

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Auto-TLDR; Unsupervised Unsupervised Representation Learning for Document Layout Analysis

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Layout analysis of historical handwritten documents is a key pre-processing step in document image analysis that, by segmenting the image into its homogeneous regions, facilitates subsequent procedures such as optical character recognition and automatic transcription. Learning-based approaches have shown promising performances in layout analysis, however, the majority of them requires tedious pixel-wise labelled training data to achieve generalisation capabilities, this limitation preventing their application due to the lack of large labelled datasets. This paper proposes a novel unsupervised representation learning method for documents’ layout analysis that reduces the need for labelled data: a sparse autoencoder is first trained in an unsupervised manner on a historical text document’s image; representation of image patches, computed by the sparse encoder, is then used to classify pixels into various region categories of the document using a feed-forward neural network. A new training method, inspired by the ISTA algorithm, is also introduced here to train the sparse encoder. Experimental results on DIVA-HisDB dataset demonstrate that the proposed method outperforms previous approaches based on unsupervised representation learning while achieving performances comparable to the state-of-the-art fully supervised methods.

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

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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%.

Deep Learning Based Sepsis Intervention: The Modelling and Prediction of Severe Sepsis Onset

Gavin Tsang, Xianghua Xie

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Auto-TLDR; Predicting Sepsis onset by up to six hours prior using a boosted cascading training methodology and adjustable margin hinge loss function

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Sepsis presents a significant challenge to healthcare providers during critical care scenarios such as within an intensive care unit. The prognosis of the onset of severe septic shock results in significant increases in mortality rate, length of stay and readmission rates. Continual advancements in health informatics data allows for applications within the machine learning field to predict sepsis onset in a timely manner, allowing for effective preventative intervention of severe septic shock. A novel deep learning application is proposed to provide effective prediction of sepsis onset by up to six hours prior, involving the use of novel concepts such as a boosted cascading training methodology and adjustable margin hinge loss function. The proposed methodology provides statistically significant improvements to that of current machine learning based modelling applications based off the Physionet Computing in Cardiology 2019 challenge. Results show test F1 scores of 0.420, a significant improvement of 0.281 as compared to the next best challenger results.