Disease prediction is a well-known classification problem in medical applications. GCNs provide a powerful tool for analyzing the patients' features relative to each other. This can be achieved by modeling the problem as a graph node classification task, where each node is a patient. Due to the nature of such medical datasets, class imbalance is a prevalent issue in the field of disease prediction, where the distribution of classes is skewed. When the class imbalance is present in the data, the existing graph-based classifiers tend to be biased towards the major class(es) and neglect the samples in the minor class(es). On the other hand, the correct diagnosis of the rare positive cases among all the patients is vital in a healthcare system. In conventional methods, such imbalance is tackled by assigning appropriate weights to classes in the loss function which is still dependent on the relative values of weights, sensitive to outliers, and in some cases biased towards the minor class(es). In this paper, we propose a Re-weighted Adversarial Graph Convolutional Network (RA-GCN) to prevent the graph-based classifier from emphasizing the samples of any particular class. This is accomplished by associating a graph-based neural network to each class, which is responsible for weighting the class samples and changing the importance of each sample for the classifier. Therefore, the classifier adjusts itself and determines the boundary between classes with more attention to the important samples. The parameters of the classifier and weighting networks are trained by an adversarial approach. We show experiments on synthetic and three publicly available medical datasets. RA-GCN demonstrates the superiority compared to recent methods in identifying the patient's status on all three datasets. The detailed analysis is provided as quantitative and qualitative experiments on synthetic datasets.
Image-based characterization and disease understanding involve integrative analysis of morphological, spatial, and topological information across biological scales. The development of graph convolutional networks (GCNs) has created the opportunity to address this information complexity via graph-driven architectures, since GCNs can perform feature aggregation, interaction, and reasoning with remarkable flexibility and efficiency. These GCNs capabilities have spawned a new wave of research in medical imaging analysis with the overarching goal of improving quantitative disease understanding, mon…
University of Science and Technology of China（中国科学技术大学）；The Ohio State University Medical Center（俄亥俄州立大学医学中心）
Deep convolutional neural network (DCNN) models have been widely explored for skin disease diagnosis and some of them have achieved the diagnostic outcomes comparable or even superior to those of dermatologists. However, broad implementation of DCNN in skin disease detection is hindered by small size and data imbalance of the publically accessible skin lesion datasets. This paper proposes a novel single-model based strategy for classification of skin lesions on small and imbalanced datasets. First, various DCNNs are trained on different small and imbalanced datasets to verify that the models w…
University of Engineering and Technology Taxila（塔克西拉工程技术大学）；University of Central Florida（中佛罗里达大学）
Alzheimer's disease (AD) is a progressive and incurable neurodegenerative disease which destroys brain cells and causes loss to patient's memory. An early detection can prevent the patient from further damage of the brain cells and hence avoid permanent memory loss. In past few years, various automatic tools and techniques have been proposed for diagnosis of AD. Several methods focus on fast, accurate and early detection of the disease to minimize the loss to patients mental health. Although machine learning and deep learning techniques have significantly improved medical imaging systems for A…
University of Lugano（卢加诺大学）；Sapienza University of Rome（罗马大学）；Technical University of Munich（慕尼黑工业大学）；Ludwig Maximilians Universität München（慕尼黑大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；Imperial College London（帝国理工学院）；Twitter（推特）
Recently, Graph Convolutional Networks (GCNs) have proven to be a powerful machine learning tool for Computer-Aided Diagnosis (CADx) and disease prediction. A key component in these models is to build a population graph, where the graph adjacency matrix represents pair-wise patient similarities. Until now, the similarity metrics have been defined manually, usually based on meta-features like demographics or clinical scores. The definition of the metric, however, needs careful tuning, as GCNs are very sensitive to the graph structure. In this paper, we demonstrate for the first time in the CADx…
Elliptic；The University of Sheffield（谢菲尔德大学）；Telecom SudParis（南巴黎电信学院）；Polytechnic Institute of Paris（巴黎综合理工学院）
We show that a modification of the first layer of a Graph Convolutional Network (GCN) can be used to effectively propagate label information across neighbor nodes, for binary and multi-class classification problems. This is done by selectively eliminating self-loops for the label features during the training phase of a GCN. The GCN architecture is otherwise unchanged, without any extra hyper-parameters, and can be used in both a transductive and inductive setting. We show through several experiments that, depending on how many labels are available during the inference phase, this strategy can …
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
This paper presents a novel graph convolutional neural network (GCNN)-based approach for improving the diagnosis of neurological diseases using scalp-electroencephalograms (EEGs). Although EEG is one of the main tests used for neurological-disease diagnosis, the sensitivity of EEG-based expert visual diagnosis remains at $\sim$50\%. This indicates a clear need for advanced methodology to reduce the false negative rate in detecting abnormal scalp-EEGs. In that context, we focus on the problem of distinguishing the abnormal scalp EEGs of patients with neurological diseases, which were originally…
Amirkabir University of Technology（阿米尔卡比尔理工大学）；University of Zanjan（赞詹大学）
This paper proposes a new RWO-Sampling (Random Walk Over-Sampling) based on graphs for imbalanced datasets. In this method, two schemes based on under-sampling and over-sampling methods are introduced to keep the proximity information robust to noises and outliers. After constructing the first graph on minority class, RWO-Sampling will be implemented on selected samples, and the rest will remain unchanged. The second graph is constructed for the majority class, and the samples in a low-density area (outliers) are removed. Finally, in the proposed method, samples of the majority class in a high…
OptumLabs at UnitedHealth Group（联合健康集团 OptumLabs）；University of Pennsylvania（宾夕法尼亚大学）
We ascertain and compare the performances of AutoML tools on large, highly imbalanced healthcare datasets. We generated a large dataset using historical administrative claims including demographic information and flags for disease codes in four different time windows prior to 2019. We then trained three AutoML tools on this dataset to predict six different disease outcomes in 2019 and evaluated model performances on several metrics. The AutoML tools showed improvement from the baseline random forest model but did not differ significantly from each other. All models recorded low area under the …
PLA Strategy Support Force Information Engineering University（中国人民解放军战略支援部队信息工程大学）
The Graph Neural Network (GNN) has been widely used for graph data representation. However, the existing researches only consider the ideal balanced dataset, and the imbalanced dataset is rarely considered. Traditional methods such as resampling, reweighting, and synthetic samples that deal with imbalanced datasets are no longer applicable in GNN. This paper proposes an ensemble model called Boosting-GNN, which uses GNNs as the base classifiers during boosting. In Boosting-GNN, higher weights are set for the training samples that are not correctly classified by the previous classifier, thus ac…
UiT The Arctic University of Norway（挪威北极大学）；Technical University of Berlin（柏林工业大学）
The recent trend of integrating multi-source Chest X-Ray datasets to improve automated diagnostics raises concerns that models learn to exploit source-specific correlations to improve performance by recognizing the source domain of an image rather than the medical pathology. We hypothesize that this effect is enforced by and leverages label-imbalance across the source domains, i.e, prevalence of a disease corresponding to a source. Therefore, in this work, we perform a thorough study of the effect of label-imbalance in multi-source training for the task of pneumonia detection on the widely use…
Amasya University（阿马西亚大学）；Bilkent University（比尔肯特大学）；National Magnetic Resonance Research Center, Bilkent University（比尔肯特大学国家磁共振研究中心）；Sabuncu Brain Research Center, Bilkent University（比尔肯特大学萨本朱脑研究中心）
Melanoma is a fatal skin cancer that is curable and has dramatically increasing survival rate when diagnosed at early stages. Learning-based methods hold significant promise for the detection of melanoma from dermoscopic images. However, since melanoma is a rare disease, existing databases of skin lesions predominantly contain highly imbalanced numbers of benign versus malignant samples. In turn, this imbalance introduces substantial bias in classification models due to the statistical dominance of the majority class. To address this issue, we introduce a deep clustering approach based on the …
Queen’s University（女王大学）；University of California, Berkeley（加州大学伯克利分校）；University of Virginia（弗吉尼亚大学）；University of Pittsburgh（匹兹堡大学）
This study proposes an efficient neural network with convolutional layers to classify significantly class-imbalanced clinical data. The data are curated from the National Health and Nutritional Examination Survey (NHANES) with the goal of predicting the occurrence of Coronary Heart Disease (CHD). While the majority of the existing machine learning models that have been used on this class of data are vulnerable to class imbalance even after the adjustment of class-specific weights, our simple two-layer CNN exhibits resilience to the imbalance with fair harmony in class-specific performance. In …
Universidad Politécnica de Madrid（马德里理工大学）；Universidad Autónoma de Madrid（马德里自治大学）；TECNALIA（特克纳利亚研究中心）；Basque Research & Technology Alliance（巴斯克研究与技术联盟）
Over the last few years, convolutional neural networks (CNNs) have dominated the field of computer vision thanks to their ability to extract features and their outstanding performance in classification problems, for example in the automatic analysis of X-rays. Unfortunately, these neural networks are considered black-box algorithms, i.e. it is impossible to understand how the algorithm has achieved the final result. To apply these algorithms in different fields and test how the methodology works, we need to use eXplainable AI techniques. Most of the work in the medical field focuses on binary …
Technical University of Munich（慕尼黑工业大学）；Sharif University of Technology（谢里夫理工大学）；Johns Hopkins University（约翰斯·霍普金斯大学）
Interpretability in Graph Convolutional Networks (GCNs) has been explored to some extent in computer vision in general, yet, in the medical domain, it requires further examination. Moreover, most of the interpretability approaches for GCNs, especially in the medical domain, focus on interpreting the model in a post hoc fashion. In this paper, we propose an interpretable graph learning-based model which 1) interprets the clinical relevance of the input features towards the task, 2) uses the explanation to improve the model performance and, 3) learns a population level latent graph that may be u…
Heart disease is one of the significant challenges in today's world and one of the leading causes of many deaths worldwide. Recent advancement of machine learning (ML) application demonstrates that using electrocardiogram (ECG) and patient data, detecting heart disease during the early stage is feasible. However, both ECG and patient data are often imbalanced, which ultimately raises a challenge for the traditional ML to perform unbiasedly. Over the years, several data level and algorithm level solutions have been exposed by many researchers and practitioners. To provide a broader view of the …
MLC-GCN: Multi-Level Generated Connectome Based GCN for AD Analysis
School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology（上海理工大学光电信息与计算机工程学院）；University of Maryland School of Medicine（马里兰大学医学院）
University of Electronic Science and Technology of China（电子科技大学）；East China Normal University（华东师范大学）；University of British Columbia（不列颠哥伦比亚大学）；Yale University（耶鲁大学）
Graph Convolutional Neural Networks (GCNs) are widely used for graph analysis. Specifically, in medical applications, GCNs can be used for disease prediction on a population graph, where graph nodes represent individuals and edges represent individual similarities. However, GCNs rely on a vast amount of data, which is challenging to collect for a single medical institution. In addition, a critical challenge that most medical institutions continue to face is addressing disease prediction in isolation with incomplete data information. To address these issues, Federated Learning (FL) allows isola…
Carnegie Mellon University（卡内基梅隆大学）；Allegheny Health Network（阿勒格尼健康网络）；University of Colorado（科罗拉多大学）
In this paper, we focus on a new method of data augmentation to solve the data imbalance problem within imbalanced ECG datasets to improve the robustness and accuracy of heart disease detection. By using Optimal Transport, we augment the ECG disease data from normal ECG beats to balance the data among different categories. We build a Multi-Feature Transformer (MF-Transformer) as our classification model, where different features are extracted from both time and frequency domains to diagnose various heart conditions. Learning from 12-lead ECG signals, our model is able to distinguish five categ…
University of Kentucky（肯塔基大学）；Qingdao University（青岛大学）
Alzheimer's disease (AD), as a progressive brain disease, affects cognition, memory, and behavior. Similarly, limbic-predominant age-related TDP-43 encephalopathy (LATE) is a recently defined common neurodegenerative disease that mimics the clinical symptoms of AD. At present, the risk factors implicated in LATE and those distinguishing LATE from AD are largely unknown. We leveraged an integrated feature selection-based algorithmic approach, to identify important factors differentiating subjects with LATE and/or AD from Control on significantly imbalanced data. We analyzed two datasets ROSMAP …
Uncertainty-Aware Multi-Expert Knowledge Distillation for Imbalanced Disease Grading
School of Public Health, Zhejiang University（浙江大学公共卫生学院）；College of Computer Science and Technology, Zhejiang University（浙江大学计算机科学与技术学院）；Liangzhu Laboratory and WeDoctor Cloud（良渚实验室和WeDoctor云）；State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital Zhejiang University School of Medicine（浙江大学医学院第二附属医院心血管植入器械国家重点实验室）；Zhejiang Key Laboratory of Medical Imaging Artificial Intelligence（浙江省医学影像人工智能重点实验室）；School of Electronic Information and Communications, Huazhong University of Science and Technology（华中科技大学电子信息与通信学院）
Technical University of Munich（慕尼黑工业大学）；Sharif University of Technology（谢里夫理工大学）；National Institute of Technology Tiruchirappalli（蒂鲁吉拉伯利国家理工学院）；Ludwig Maximilians Universität München（路德维希-马克西米利安慕尼黑大学）；Klinikum der Universität München（慕尼黑大学医院）；Johns Hopkins University（约翰斯·霍普金斯大学）
Geometric deep learning provides a principled and versatile manner for the integration of imaging and non-imaging modalities in the medical domain. Graph Convolutional Networks (GCNs) in particular have been explored on a wide variety of problems such as disease prediction, segmentation, and matrix completion by leveraging large, multimodal datasets. In this paper, we introduce a new spectral domain architecture for deep learning on graphs for disease prediction. The novelty lies in defining geometric 'inception modules' which are capable of capturing intra- and inter-graph structural heteroge…
Southern University of Science and Technology（南方科技大学）；The University of Queensland（昆士兰大学）
Imbalanced classification on graphs is ubiquitous yet challenging in many real-world applications, such as fraudulent node detection. Recently, graph neural networks (GNNs) have shown promising performance on many network analysis tasks. However, most existing GNNs have almost exclusively focused on the balanced networks, and would get unappealing performance on the imbalanced networks. To bridge this gap, in this paper, we present a generative adversarial graph network model, called ImGAGN to address the imbalanced classification problem on graphs. It introduces a novel generator for graph st…
Interpretable Information-Decomposed Brain Graph Learning for fMRI-based Disease Diagnosis
School of Mathematics and Statistics, Shandong University（山东大学数学与统计学院）；Data Science Institute, Shandong University（山东大学数据科学研究院）；Academy of Mathematics and Systems Science, University of Chinese Academy of Sciences（中国科学院大学数学与系统科学研究院）
Lehigh University（里海大学）；University of Pennsylvania（宾夕法尼亚大学）
Identification of brain regions related to the specific neurological disorders are of great importance for biomarker and diagnostic studies. In this paper, we propose an interpretable Graph Convolutional Network (GCN) framework for the identification and classification of Alzheimer's disease (AD) using multi-modality brain imaging data. Specifically, we extended the Gradient Class Activation Mapping (Grad-CAM) technique to quantify the most discriminative features identified by GCN from brain connectivity patterns. We then utilized them to find signature regions of interest (ROIs) by detecting…
School of Professional Studies（专业研究学院）；Northwestern University（西北大学）
Artificial intelligence (AI) is disrupting the medical field as advances in modern technology allow common household computers to learn anatomical and pathological features that distinguish between healthy and disease with the accuracy of highly specialized, trained physicians. Computer vision AI applications use medical imaging, such as lung chest X-Rays (LCXRs), to facilitate diagnoses by providing second-opinions in addition to a physician's or radiologist's interpretation. Considering the advent of the current Coronavirus disease (COVID-19) pandemic, LCXRs may provide rapid insights to ind…
Medical image classification is often challenging for two reasons: a lack of labelled examples due to expensive and time-consuming annotation protocols, and imbalanced class labels due to the relative scarcity of disease-positive individuals in the wider population. Semi-supervised learning (SSL) methods exist for dealing with a lack of labels, but they generally do not address the problem of class imbalance. In this study we propose Adaptive Blended Consistency Loss (ABCL), a drop-in replacement for consistency loss in perturbation-based SSL methods. ABCL counteracts data skew by adaptively m…
University of Electronic Science and Technology of China（电子科技大学）；East China Normal University（华东师范大学）；University of British Columbia（不列颠哥伦比亚大学）
In this work, we focus on the challenging task, neuro-disease classification, using functional magnetic resonance imaging (fMRI). In population graph-based disease analysis, graph convolutional neural networks (GCNs) have achieved remarkable success. However, these achievements are inseparable from abundant labeled data and sensitive to spurious signals. To improve fMRI representation learning and classification under a label-efficient setting, we propose a novel and theory-driven self-supervised learning (SSL) framework on GCNs, namely Graph CCA for Temporal self-supervised learning on fMRI a…
Exploiting the wealth of imaging and non-imaging information for disease prediction tasks requires models capable of representing, at the same time, individual features as well as data associations between subjects from potentially large populations. Graphs provide a natural framework for such tasks, yet previous graph-based approaches focus on pairwise similarities without modelling the subjects' individual characteristics and features. On the other hand, relying solely on subject-specific imaging feature vectors fails to model the interaction and similarity between subjects, which can reduce…
Simon Fraser University（西蒙弗雷泽大学）；MetaOptima Technology Inc（MetaOptima科技公司）；University of British Columbia（不列颠哥伦比亚大学）
Medical image diagnosis can be achieved by deep neural networks, provided there is enough varied training data for each disease class. However, a hitherto unknown disease class not encountered during training will inevitably be misclassified, even if predicted with low probability. This problem is especially important for medical image diagnosis, when an image of a hitherto unknown disease is presented for diagnosis, especially when the images come from the same image domain, such as dermoscopic skin images. Current out-of-distribution detection algorithms act unfairly when the in-distribution…
Technological University of the Philippines（菲律宾技术大学）；College of Engineering, Technological University of the Philippines（菲律宾技术大学工程学院）；Center for Engineering Design, Fabrication, and Innovation（工程设计、制造与创新中心）
The MobileNet model was used by applying transfer learning on the 7 skin diseases to create a skin disease classification system on Android application. The proponents gathered a total of 3,406 images and it is considered as imbalanced dataset because of the unequal number of images on its classes. Using different sampling method and preprocessing of input data was explored to further improved the accuracy of the MobileNet. Using under-sampling method and the default preprocessing of input data achieved an 84.28% accuracy. While, using imbalanced dataset and default preprocessing of input data…
The University of Sydney（悉尼大学）；Medicinovo Inc.（Medicinovo公司）
In medical real-world study (RWS), how to fully utilize the fragmentary and scarce information in model training to generate the solid diagnosis results is a challenging task. In this work, we introduce a novel multi-instance neural network, AMI-Net+, to train and predict from the incomplete and extremely imbalanced data. It is more effective than the state-of-art method, AMI-Net. First, we also implement embedding, multi-head attention and gated attention-based multi-instance pooling to capture the relations of symptoms themselves and with the given disease. Besides, we propose var-ious impro…
Alzheimer's disease (AD) is the most prevalent form of dementia. Traditional methods cannot achieve efficient and accurate diagnosis of AD. In this paper, we introduce a novel method based on dynamic functional connectivity (dFC) that can effectively capture changes in the brain. We compare and combine four different types of features including amplitude of low-frequency fluctuation (ALFF), regional homogeneity (ReHo), dFC and the adjacency matrix of different brain structures between subjects. We use graph convolution network (GCN) which consider the similarity of brain structure between pati…
Rutgers University - New Brunswick（罗格斯大学新布朗斯维克分校）；Weifang Medical University（潍坊医学院）
The paper presents Imbalance-XGBoost, a Python package that combines the powerful XGBoost software with weighted and focal losses to tackle binary label-imbalanced classification tasks. Though a small-scale program in terms of size, the package is, to the best of the authors' knowledge, the first of its kind which provides an integrated implementation for the two losses on XGBoost and brings a general-purpose extension on XGBoost for label-imbalanced scenarios. In this paper, the design and usage of the package are described with exemplar code listings, and its convenience to be integrated int…
Class imbalanced datasets are common in real-world applications that range from credit card fraud detection to rare disease diagnostics. Several popular classification algorithms assume that classes are approximately balanced, and hence build the accompanying objective function to maximize an overall accuracy rate. In these situations, optimizing the overall accuracy will lead to highly skewed predictions towards the majority class. Moreover, the negative business impact resulting from false positives (positive samples incorrectly classified as negative) can be detrimental. Many methods have b…
In rare disease physician targeting, a major challenge is how to identify physicians who are treating diagnosed or underdiagnosed rare diseases patients. Rare diseases have extremely low incidence rate. For a specified rare disease, only a small number of patients are affected and a fractional of physicians are involved. The existing targeting methodologies, such as segmentation and profiling, are developed under mass market assumption. They are not suitable for rare disease market where the target classes are extremely imbalanced. The authors propose a graphical model approach to predict targ…
School of Computing Science, Newcastle University（纽卡斯尔大学计算科学学院）；University Medical Center Utrecht（乌得勒支大学医学中心）；Merck（默克公司）；Bioscience Institute, Newcastle University（纽卡斯尔大学生物科学研究所）；Institut de Recherches Internationales Servier（赛诺菲国际研究所）；GlaxoSmithKline（葛兰素史克公司）；Delft University of Technology（代尔夫特理工大学）；State Research Institute Centre for Innovative Medicine（创新医学国家研究中心）；University of Oulu（奥卢大学）；Versus Arthritis（对抗关节炎组织）
Conventional inclusion criteria used in osteoarthritis clinical trials are not very effective in selecting patients who would benefit from a therapy being tested. Typically majority of selected patients show no or limited disease progression during a trial period. As a consequence, the effect of the tested treatment cannot be observed, and the efforts and resources invested in running the trial are not rewarded. This could be avoided, if selection criteria were more predictive of the future disease progression. In this article, we formulated the patient selection problem as a multi-class class…
Mobility-GCN: a human mobility-based graph convolutional network for tracking and analyzing the spatial dynamics of the synthetic opioid crisis in the USA, 2013-2020
