arXiv subjects

Shadi Albarqouni

Publications and source records attributed to Shadi Albarqouni.

At least 37 records · Page 2Linked to original sources

arXiv2022

Semi-Supervised Federated Peer Learning for Skin Lesion Classification

Globally, Skin carcinoma is among the most lethal diseases. Millions of people are diagnosed with this cancer every year. Sill, early detection can decrease the medication cost and mortality rate substantially. The recent improvement in automated cancer classification using deep learning methods has reached a human-level performance requiring a large amount of annotated data assembled in one location, yet, finding such conditions usually is not feasible. Recently, federated learning (FL) has been proposed to train decentralized models in a privacy-preserved fashion depending on labeled data at the client-side, which is usually not available and costly. To address this, we propose \verb!FedPerl!, a semi-supervised federated learning method. Our method is inspired by peer learning from educational psychology and ensemble averaging from committee machines. FedPerl builds communities based on clients' similarities. Then it encourages communities members to learn from each other to generate more accurate pseudo labels for the unlabeled data. We also proposed the peer anonymization (PA) technique to anonymize clients. As a core component of our method, PA is orthogonal to other methods without additional complexity and reduces the communication cost while enhancing performance. Finally, we propose a dynamic peer-learning policy that controls the learning stream to avoid any degradation in the performance, especially for individual clients. Our experimental setup consists of 71,000 skin lesion images collected from 5 publicly available datasets. We test our method in four different scenarios in SSFL. With few annotated data, FedPerl is on par with a state-of-the-art method in skin lesion classification in the standard setup while outperforming SSFLs and the baselines by 1.8% and 15.8%, respectively. Also, it generalizes better to unseen clients while being less sensitive to noisy ones.

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arXiv2021

Sickle Cell Disease Severity Prediction from Percoll Gradient Images using Graph Convolutional Networks

Sickle cell disease (SCD) is a severe genetic hemoglobin disorder that results in premature destruction of red blood cells. Assessment of the severity of the disease is a challenging task in clinical routine since the causes of broad variance in SCD manifestation despite the common genetic cause remain unclear. Identification of the biomarkers that would predict the severity grade is of importance for prognosis and assessment of responsiveness of patients to therapy. Detection of the changes in red blood cell (RBC) density through separation of Percoll density gradient could be such marker as it allows to resolve intercellular differences and follow the most damaged dense cells prone to destruction and vaso-occlusion. Quantification of the images obtained from the distribution of RBCs in Percoll gradient and interpretation of the obtained is an important prerequisite for establishment of this approach. Here, we propose a novel approach combining a graph convolutional network, a convolutional neural network, fast Fourier transform, and recursive feature elimination to predict the severity of SCD directly from a Percoll image. Two important but expensive laboratory blood test parameters measurements are used for training the graph convolutional network. To make the model independent from such tests during prediction, the two parameters are estimated by a neural network from the Percoll image directly. On a cohort of 216 subjects, we achieve a prediction performance that is only slightly below an approach where the groundtruth laboratory measurements are used. Our proposed method is the first computational approach for the difficult task of SCD severity prediction. The two-step approach relies solely on inexpensive and simple blood analysis tools and can have a significant impact on the patients' survival in underdeveloped countries where access to medical instruments and doctors is limited

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arXiv2021

The Federated Tumor Segmentation (FeTS) Challenge

This manuscript describes the first challenge on Federated Learning, namely the Federated Tumor Segmentation (FeTS) challenge 2021. International challenges have become the standard for validation of biomedical image analysis methods. However, the actual performance of participating (even the winning) algorithms on "real-world" clinical data often remains unclear, as the data included in challenges are usually acquired in very controlled settings at few institutions. The seemingly obvious solution of just collecting increasingly more data from more institutions in such challenges does not scale well due to privacy and ownership hurdles. Towards alleviating these concerns, we are proposing the FeTS challenge 2021 to cater towards both the development and the evaluation of models for the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas. Specifically, the FeTS 2021 challenge uses clinically acquired, multi-institutional magnetic resonance imaging (MRI) scans from the BraTS 2020 challenge, as well as from various remote independent institutions included in the collaborative network of a real-world federation (https://www.fets.ai/). The goals of the FeTS challenge are directly represented by the two included tasks: 1) the identification of the optimal weight aggregation approach towards the training of a consensus model that has gained knowledge via federated learning from multiple geographically distinct institutions, while their data are always retained within each institution, and 2) the federated evaluation of the generalizability of brain tumor segmentation models "in the wild", i.e. on data from institutional distributions that were not part of the training datasets.

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arXiv2021

Fourier Transform of Percoll Gradients Boosts CNN Classification of Hereditary Hemolytic Anemias

Hereditary hemolytic anemias are genetic disorders that affect the shape and density of red blood cells. Genetic tests currently used to diagnose such anemias are expensive and unavailable in the majority of clinical labs. Here, we propose a method for identifying hereditary hemolytic anemias based on a standard biochemistry method, called Percoll gradient, obtained by centrifuging a patient's blood. Our hybrid approach consists on using spatial data-driven features, extracted with a convolutional neural network and spectral handcrafted features obtained from fast Fourier transform. We compare late and early feature fusion with AlexNet and VGG16 architectures. AlexNet with late fusion of spectral features performs better compared to other approaches. We achieved an average F1-score of 88% on different classes suggesting the possibility of diagnosing of hereditary hemolytic anemias from Percoll gradients. Finally, we utilize Grad-CAM to explore the spatial features used for classification.

cs.CV↗

arXiv2021

FedDis: Disentangled Federated Learning for Unsupervised Brain Pathology Segmentation

In recent years, data-driven machine learning (ML) methods have revolutionized the computer vision community by providing novel efficient solutions to many unsolved (medical) image analysis problems. However, due to the increasing privacy concerns and data fragmentation on many different sites, existing medical data are not fully utilized, thus limiting the potential of ML. Federated learning (FL) enables multiple parties to collaboratively train a ML model without exchanging local data. However, data heterogeneity (non-IID) among the distributed clients is yet a challenge. To this end, we propose a novel federated method, denoted Federated Disentanglement (FedDis), to disentangle the parameter space into shape and appearance, and only share the shape parameter with the clients. FedDis is based on the assumption that the anatomical structure in brain MRI images is similar across multiple institutions, and sharing the shape knowledge would be beneficial in anomaly detection. In this paper, we leverage healthy brain scans of 623 subjects from multiple sites with real data (OASIS, ADNI) in a privacy-preserving fashion to learn a model of normal anatomy, that allows to segment abnormal structures. We demonstrate a superior performance of FedDis on real pathological databases containing 109 subjects; two publicly available MS Lesions (MSLUB, MSISBI), and an in-house database with MS and Glioblastoma (MSI and GBI). FedDis achieved an average dice performance of 0.38, outperforming the state-of-the-art (SOTA) auto-encoder by 42% and the SOTA federated method by 11%. Further, we illustrate that FedDis learns a shape embedding that is orthogonal to the appearance and consistent under different intensity augmentations.

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arXiv2021

Semi-Supervised Few-Shot Learning with Prototypical Random Walks

Recent progress has shown that few-shot learning can be improved with access to unlabelled data, known as semi-supervised few-shot learning(SS-FSL). We introduce an SS-FSL approach, dubbed as Prototypical Random Walk Networks(PRWN), built on top of Prototypical Networks (PN). We develop a random walk semi-supervised loss that enables the network to learn representations that are compact and well-separated. Our work is related to the very recent development of graph-based approaches for few-shot learning. However, we show that compact and well-separated class representations can be achieved by modeling our prototypical random walk notion without needing additional graph-NN parameters or requiring a transductive setting where a collective test set is provided. Our model outperforms baselines in most benchmarks with significant improvements in some cases. Our model, trained with 40$\%$ of the data as labeled, compares competitively against fully supervised prototypical networks, trained on 100$\%$ of the labels, even outperforming it in the 1-shot mini-Imagenet case with 50.89$\%$ to 49.4$\%$ accuracy. We also show that our loss is resistant to distractors, unlabeled data that does not belong to any of the training classes, and hence reflecting robustness to labeled/unlabeled class distribution mismatch. Associated GitHub page can be found at https://prototypical-random-walk.github.io.

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arXiv2021

The Future of Digital Health with Federated Learning

Data-driven Machine Learning has emerged as a promising approach for building accurate and robust statistical models from medical data, which is collected in huge volumes by modern healthcare systems. Existing medical data is not fully exploited by ML primarily because it sits in data silos and privacy concerns restrict access to this data. However, without access to sufficient data, ML will be prevented from reaching its full potential and, ultimately, from making the transition from research to clinical practice. This paper considers key factors contributing to this issue, explores how Federated Learning (FL) may provide a solution for the future of digital health and highlights the challenges and considerations that need to be addressed.

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arXiv2020

An Uncertainty-Driven GCN Refinement Strategy for Organ Segmentation

Organ segmentation in CT volumes is an important pre-processing step in many computer assisted intervention and diagnosis methods. In recent years, convolutional neural networks have dominated the state of the art in this task. However, since this problem presents a challenging environment due to high variability in the organ's shape and similarity between tissues, the generation of false negative and false positive regions in the output segmentation is a common issue. Recent works have shown that the uncertainty analysis of the model can provide us with useful information about potential errors in the segmentation. In this context, we proposed a segmentation refinement method based on uncertainty analysis and graph convolutional networks. We employ the uncertainty levels of the convolutional network in a particular input volume to formulate a semi-supervised graph learning problem that is solved by training a graph convolutional network. To test our method we refine the initial output of a 2D U-Net. We validate our framework with the NIH pancreas dataset and the spleen dataset of the medical segmentation decathlon. We show that our method outperforms the state-of-the-art CRF refinement method by improving the dice score by 1% for the pancreas and 2% for spleen, with respect to the original U-Net's prediction. Finally, we perform a sensitivity analysis on the parameters of our proposal and discuss the applicability to other CNN architectures, the results, and current limitations of the model for future work in this research direction. For reproducibility purposes, we make our code publicly available at https://github.com/rodsom22/gcn_refinement.

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arXiv2020

ROAM: Random Layer Mixup for Semi-Supervised Learning in Medical Imaging

Medical image segmentation is one of the major challenges addressed by machine learning methods. Yet, deep learning methods profoundly depend on a large amount of annotated data, which is time-consuming and costly. Though, semi-supervised learning methods approach this problem by leveraging an abundant amount of unlabeled data along with a small amount of labeled data in the training process. Recently, MixUp regularizer has been successfully introduced to semi-supervised learning methods showing superior performance. MixUp augments the model with new data points through linear interpolation of the data at the input space. We argue that this option is limited. Instead, we propose ROAM, a RandOm lAyer Mixup, which encourages the network to be less confident for interpolated data points at randomly selected space. ROAM generates more data points that have never seen before, and hence it avoids over-fitting and enhances the generalization ability. We conduct extensive experiments to validate our method on three publicly available datasets on whole-brain image segmentation. ROAM achieves state-of-the-art (SOTA) results in fully supervised (89.5%) and semi-supervised (87.0%) settings with a relative improvement of up to 2.40% and 16.50%, respectively for the whole-brain segmentation.

cs.CV↗

arXiv2020

Polyp-artifact relationship analysis using graph inductive learned representations

The diagnosis process of colorectal cancer mainly focuses on the localization and characterization of abnormal growths in the colon tissue known as polyps. Despite recent advances in deep object localization, the localization of polyps remains challenging due to the similarities between tissues, and the high level of artifacts. Recent studies have shown the negative impact of the presence of artifacts in the polyp detection task, and have started to take them into account within the training process. However, the use of prior knowledge related to the spatial interaction of polyps and artifacts has not yet been considered. In this work, we incorporate artifact knowledge in a post-processing step. Our method models this task as an inductive graph representation learning problem, and is composed of training and inference steps. Detected bounding boxes around polyps and artifacts are considered as nodes connected by a defined criterion. The training step generates a node classifier with ground truth bounding boxes. In inference, we use this classifier to analyze a second graph, generated from artifact and polyp predictions given by region proposal networks. We evaluate how the choices in the connectivity and artifacts affect the performance of our method and show that it has the potential to reduce the false positives in the results of a region proposal network.

cs.CV↗

arXiv2020

Uncertainty-based graph convolutional networks for organ segmentation refinement

Organ segmentation in CT volumes is an important pre-processing step in many computer assisted intervention and diagnosis methods. In recent years, convolutional neural networks have dominated the state of the art in this task. However, since this problem presents a challenging environment due to high variability in the organ's shape and similarity between tissues, the generation of false negative and false positive regions in the output segmentation is a common issue. Recent works have shown that the uncertainty analysis of the model can provide us with useful information about potential errors in the segmentation. In this context, we proposed a segmentation refinement method based on uncertainty analysis and graph convolutional networks. We employ the uncertainty levels of the convolutional network in a particular input volume to formulate a semi-supervised graph learning problem that is solved by training a graph convolutional network. To test our method we refine the initial output of a 2D U-Net. We validate our framework with the NIH pancreas dataset and the spleen dataset of the medical segmentation decathlon. We show that our method outperforms the state-of-the art CRF refinement method by improving the dice score by 1% for the pancreas and 2% for spleen, with respect to the original U-Net's prediction. Finally, we discuss the results and current limitations of the model for future work in this research direction. For reproducibility purposes, we make our code publicly available.

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arXiv2020

Understanding the effects of artifacts on automated polyp detection and incorporating that knowledge via learning without forgetting

Survival rates for colorectal cancer are higher when polyps are detected at an early stage and can be removed before they develop into malignant tumors. Automated polyp detection, which is dominated by deep learning based methods, seeks to improve early detection of polyps. However, current efforts rely heavily on the size and quality of the training datasets. The quality of these datasets often suffers from various image artifacts that affect the visibility and hence, the detection rate. In this work, we conducted a systematic analysis to gain a better understanding of how artifacts affect automated polyp detection. We look at how six different artifact classes, and their location in an image, affect the performance of a RetinaNet based polyp detection model. We found that, depending on the artifact class, they can either benefit or harm the polyp detector. For instance, bubbles are often misclassified as polyps, while specular reflections inside of a polyp region can improve detection capabilities. We then investigated different strategies, such as a learning without forgetting framework, to leverage artifact knowledge to improve automated polyp detection. Our results show that such models can mitigate some of the harmful effects of artifacts, but require more work to significantly improve polyp detection capabilities.

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arXiv2020

Inverse Distance Aggregation for Federated Learning with Non-IID Data

Federated learning (FL) has been a promising approach in the field of medical imaging in recent years. A critical problem in FL, specifically in medical scenarios is to have a more accurate shared model which is robust to noisy and out-of distribution clients. In this work, we tackle the problem of statistical heterogeneity in data for FL which is highly plausible in medical data where for example the data comes from different sites with different scanner settings. We propose IDA (Inverse Distance Aggregation), a novel adaptive weighting approach for clients based on meta-information which handles unbalanced and non-iid data. We extensively analyze and evaluate our method against the well-known FL approach, Federated Averaging as a baseline.

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arXiv2020

Attention based Multiple Instance Learning for Classification of Blood Cell Disorders

Red blood cells are highly deformable and present in various shapes. In blood cell disorders, only a subset of all cells is morphologically altered and relevant for the diagnosis. However, manually labeling of all cells is laborious, complicated and introduces inter-expert variability. We propose an attention based multiple instance learning method to classify blood samples of patients suffering from blood cell disorders. Cells are detected using an R-CNN architecture. With the features extracted for each cell, a multiple instance learning method classifies patient samples into one out of four blood cell disorders. The attention mechanism provides a measure of the contribution of each cell to the overall classification and significantly improves the network's classification accuracy as well as its interpretability for the medical expert.

cs.CV↗

arXiv2020

6D Camera Relocalization in Ambiguous Scenes via Continuous Multimodal Inference

We present a multimodal camera relocalization framework that captures ambiguities and uncertainties with continuous mixture models defined on the manifold of camera poses. In highly ambiguous environments, which can easily arise due to symmetries and repetitive structures in the scene, computing one plausible solution (what most state-of-the-art methods currently regress) may not be sufficient. Instead we predict multiple camera pose hypotheses as well as the respective uncertainty for each prediction. Towards this aim, we use Bingham distributions, to model the orientation of the camera pose, and a multivariate Gaussian to model the position, with an end-to-end deep neural network. By incorporating a Winner-Takes-All training scheme, we finally obtain a mixture model that is well suited for explaining ambiguities in the scene, yet does not suffer from mode collapse, a common problem with mixture density networks. We introduce a new dataset specifically designed to foster camera localization research in ambiguous environments and exhaustively evaluate our method on synthetic as well as real data on both ambiguous scenes and on non-ambiguous benchmark datasets. We plan to release our code and dataset under $\href{https://multimodal3dvision.github.io}{multimodal3dvision.github.io}$.

cs.CV↗

arXiv2020

Fairness by Learning Orthogonal Disentangled Representations

Learning discriminative powerful representations is a crucial step for machine learning systems. Introducing invariance against arbitrary nuisance or sensitive attributes while performing well on specific tasks is an important problem in representation learning. This is mostly approached by purging the sensitive information from learned representations. In this paper, we propose a novel disentanglement approach to invariant representation problem. We disentangle the meaningful and sensitive representations by enforcing orthogonality constraints as a proxy for independence. We explicitly enforce the meaningful representation to be agnostic to sensitive information by entropy maximization. The proposed approach is evaluated on five publicly available datasets and compared with state of the art methods for learning fairness and invariance achieving the state of the art performance on three datasets and comparable performance on the rest. Further, we perform an ablative study to evaluate the effect of each component.

cs.CV↗

arXiv2020

Scale-Space Autoencoders for Unsupervised Anomaly Segmentation in Brain MRI

Brain pathologies can vary greatly in size and shape, ranging from few pixels (i.e. MS lesions) to large, space-occupying tumors. Recently proposed Autoencoder-based methods for unsupervised anomaly segmentation in brain MRI have shown promising performance, but face difficulties in modeling distributions with high fidelity, which is crucial for accurate delineation of particularly small lesions. Here, similar to these previous works, we model the distribution of healthy brain MRI to localize pathologies from erroneous reconstructions. However, to achieve improved reconstruction fidelity at higher resolutions, we learn to compress and reconstruct different frequency bands of healthy brain MRI using the laplacian pyramid. In a range of experiments comparing our method to different State-of-the-Art approaches on three different brain MR datasets with MS lesions and tumors, we show improved anomaly segmentation performance and the general capability to obtain much more crisp reconstructions of input data at native resolution. The modeling of the laplacian pyramid further enables the delineation and aggregation of lesions at multiple scales, which allows to effectively cope with different pathologies and lesion sizes using a single model.

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arXiv2020

Autoencoders for Unsupervised Anomaly Segmentation in Brain MR Images: A Comparative Study

Deep unsupervised representation learning has recently led to new approaches in the field of Unsupervised Anomaly Detection (UAD) in brain MRI. The main principle behind these works is to learn a model of normal anatomy by learning to compress and recover healthy data. This allows to spot abnormal structures from erroneous recoveries of compressed, potentially anomalous samples. The concept is of great interest to the medical image analysis community as it i) relieves from the need of vast amounts of manually segmented training data---a necessity for and pitfall of current supervised Deep Learning---and ii) theoretically allows to detect arbitrary, even rare pathologies which supervised approaches might fail to find. To date, the experimental design of most works hinders a valid comparison, because i) they are evaluated against different datasets and different pathologies, ii) use different image resolutions and iii) different model architectures with varying complexity. The intent of this work is to establish comparability among recent methods by utilizing a single architecture, a single resolution and the same dataset(s). Besides providing a ranking of the methods, we also try to answer questions like i) how many healthy training subjects are needed to model normality and ii) if the reviewed approaches are also sensitive to domain shift. Further, we identify open challenges and provide suggestions for future community efforts and research directions.

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