arXiv subjects

Arash Mohammadi

Publications and source records attributed to Arash Mohammadi.

At least 73 records · Page 4Linked to original sources

arXiv2021

COVID-Rate: An Automated Framework for Segmentation of COVID-19 Lesions from Chest CT Scans

Novel Coronavirus disease (COVID-19) is a highly contagious respiratory infection that has had devastating effects on the world. Recently, new COVID-19 variants are emerging making the situation more challenging and threatening. Evaluation and quantification of COVID-19 lung abnormalities based on chest Computed Tomography (CT) scans can help determining the disease stage, efficiently allocating limited healthcare resources, and making informed treatment decisions. During pandemic era, however, visual assessment and quantification of COVID-19 lung lesions by expert radiologists become expensive and prone to error, which raises an urgent quest to develop practical autonomous solutions. In this context, first, the paper introduces an open access COVID-19 CT segmentation dataset containing 433 CT images from 82 patients that have been annotated by an expert radiologist. Second, a Deep Neural Network (DNN)-based framework is proposed, referred to as the COVID-Rate, that autonomously segments lung abnormalities associated with COVID-19 from chest CT scans. Performance of the proposed COVID-Rate framework is evaluated through several experiments based on the introduced and external datasets. The results show a dice score of 0:802 and specificity and sensitivity of 0:997 and 0:832, respectively. Furthermore, the results indicate that the COVID-Rate model can efficiently segment COVID-19 lesions in both 2D CT images and whole lung volumes. Results on the external dataset illustrate generalization capabilities of the COVID-Rate model to CT images obtained from a different scanner.

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arXiv2020

Diagnosis/Prognosis of COVID-19 Images: Challenges, Opportunities, and Applications

The novel Coronavirus disease, COVID-19, has rapidly and abruptly changed the world as we knew in 2020. It becomes the most unprecedent challenge to analytic epidemiology in general and signal processing theories in specific. Given its high contingency nature and adverse effects across the world, it is important to develop efficient processing/learning models to overcome this pandemic and be prepared for potential future ones. In this regard, medical imaging plays an important role for the management of COVID-19. Human-centered interpretation of medical images is, however, tedious and can be subjective. This has resulted in a surge of interest to develop Radiomics models for analysis and interpretation of medical images. Signal Processing (SP) and Deep Learning (DL) models can assist in development of robust Radiomics solutions for diagnosis/prognosis, severity assessment, treatment response, and monitoring of COVID-19 patients. In this article, we aim to present an overview of the current state, challenges, and opportunities of developing SP/DL-empowered models for diagnosis (screening/monitoring) and prognosis (outcome prediction and severity assessment) of COVID-19 infection. More specifically, the article starts by elaborating the latest development on the theoretical framework of analytic epidemiology and hypersignal processing for COVID-19. Afterwards, imaging modalities and Radiological characteristics of COVID-19 are discussed. SL/DL-based Radiomic models specific to the analysis of COVID-19 infection are then described covering the following four domains: Segmentation of COVID-19 lesions; Predictive models for outcome prediction; Severity assessment, and; Diagnosis/classification models. Finally, open problems and opportunities are presented in detail.

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arXiv2020

FS-HGR: Few-shot Learning for Hand Gesture Recognition via ElectroMyography

This work is motivated by the recent advances in Deep Neural Networks (DNNs) and their widespread applications in human-machine interfaces. DNNs have been recently used for detecting the intended hand gesture through processing of surface electromyogram (sEMG) signals. The ultimate goal of these approaches is to realize high-performance controllers for prosthetic. However, although DNNs have shown superior accuracy than conventional methods when large amounts of data are available for training, their performance substantially decreases when data are limited. Collecting large datasets for training may be feasible in research laboratories, but it is not a practical approach for real-life applications. Therefore, there is an unmet need for the design of a modern gesture detection technique that relies on minimal training data while providing high accuracy. Here we propose an innovative and novel "Few-Shot Learning" framework based on the formulation of meta-learning, referred to as the FS-HGR, to address this need. Few-shot learning is a variant of domain adaptation with the goal of inferring the required output based on just one or a few training examples. More specifically, the proposed FS-HGR quickly generalizes after seeing very few examples from each class. The proposed approach led to 85.94% classification accuracy on new repetitions with few-shot observation (5-way 5-shot), 81.29% accuracy on new subjects with few-shot observation (5-way 5-shot), and 73.36% accuracy on new gestures with few-shot observation (5-way 5-shot).

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arXiv2020

COVID-FACT: A Fully-Automated Capsule Network-based Framework for Identification of COVID-19 Cases from Chest CT scans

The newly discovered Corona virus Disease 2019 (COVID-19) has been globally spreading and causing hundreds of thousands of deaths around the world as of its first emergence in late 2019. Computed tomography (CT) scans have shown distinctive features and higher sensitivity compared to other diagnostic tests, in particular the current gold standard, i.e., the Reverse Transcription Polymerase Chain Reaction (RT-PCR) test. Current deep learning-based algorithms are mainly developed based on Convolutional Neural Networks (CNNs) to identify COVID-19 pneumonia cases. CNNs, however, require extensive data augmentation and large datasets to identify detailed spatial relations between image instances. Furthermore, existing algorithms utilizing CT scans, either extend slice-level predictions to patient-level ones using a simple thresholding mechanism or rely on a sophisticated infection segmentation to identify the disease. In this paper, we propose a two-stage fully-automated CT-based framework for identification of COVID-19 positive cases referred to as the "COVID-FACT". COVID-FACT utilizes Capsule Networks, as its main building blocks and is, therefore, capable of capturing spatial information. In particular, to make the proposed COVID-FACT independent from sophisticated segmentation of the area of infection, slices demonstrating infection are detected at the first stage and the second stage is responsible for classifying patients into COVID and non-COVID cases. COVID-FACT detects slices with infection, and identifies positive COVID-19 cases using an in-house CT scan dataset, containing COVID-19, community acquired pneumonia, and normal cases. Based on our experiments, COVID-FACT achieves an accuracy of 90.82%, a sensitivity of 94.55%, a specificity of 86.04%, and an Area Under the Curve (AUC) of 0.98, while depending on far less supervision and annotation, in comparison to its counterparts.

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arXiv2020

CT-CAPS: Feature Extraction-based Automated Framework for COVID-19 Disease Identification from Chest CT Scans using Capsule Networks

The global outbreak of the novel corona virus (COVID-19) disease has drastically impacted the world and led to one of the most challenging crisis across the globe since World War II. The early diagnosis and isolation of COVID-19 positive cases are considered as crucial steps towards preventing the spread of the disease and flattening the epidemic curve. Chest Computed Tomography (CT) scan is a highly sensitive, rapid, and accurate diagnostic technique that can complement Reverse Transcription Polymerase Chain Reaction (RT-PCR) test. Recently, deep learning-based models, mostly based on Convolutional Neural Networks (CNN), have shown promising diagnostic results. CNNs, however, are incapable of capturing spatial relations between image instances and require large datasets. Capsule Networks, on the other hand, can capture spatial relations, require smaller datasets, and have considerably fewer parameters. In this paper, a Capsule network framework, referred to as the "CT-CAPS", is presented to automatically extract distinctive features of chest CT scans. These features, which are extracted from the layer before the final capsule layer, are then leveraged to differentiate COVID-19 from Non-COVID cases. The experiments on our in-house dataset of 307 patients show the state-of-the-art performance with the accuracy of 90.8%, sensitivity of 94.5%, and specificity of 86.0%.

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arXiv2020

COVID-CT-MD: COVID-19 Computed Tomography (CT) Scan Dataset Applicable in Machine Learning and Deep Learning

Novel Coronavirus (COVID-19) has drastically overwhelmed more than 200 countries affecting millions and claiming almost 1 million lives, since its emergence in late 2019. This highly contagious disease can easily spread, and if not controlled in a timely fashion, can rapidly incapacitate healthcare systems. The current standard diagnosis method, the Reverse Transcription Polymerase Chain Reaction (RT- PCR), is time consuming, and subject to low sensitivity. Chest Radiograph (CXR), the first imaging modality to be used, is readily available and gives immediate results. However, it has notoriously lower sensitivity than Computed Tomography (CT), which can be used efficiently to complement other diagnostic methods. This paper introduces a new COVID-19 CT scan dataset, referred to as COVID-CT-MD, consisting of not only COVID-19 cases, but also healthy and subjects infected by Community Acquired Pneumonia (CAP). COVID-CT-MD dataset, which is accompanied with lobe-level, slice-level and patient-level labels, has the potential to facilitate the COVID-19 research, in particular COVID-CT-MD can assist in development of advanced Machine Learning (ML) and Deep Neural Network (DNN) based solutions.

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arXiv2020

MIXCAPS: A Capsule Network-based Mixture of Experts for Lung Nodule Malignancy Prediction

Lung diseases including infections such as Pneumonia, Tuberculosis, and novel Coronavirus (COVID-19), together with Lung Cancer are significantly widespread and are, typically, considered life threatening. In particular, lung cancer is among the most common and deadliest cancers with a low 5-year survival rate. Timely diagnosis of lung cancer is, therefore, of paramount importance as it can save countless lives. In this regard, deep learning radiomics solutions have the promise of extracting the most useful features on their own in an end-to-end fashion without having access to the annotated boundaries. Among different deep learning models, Capsule Networks are proposed to overcome shortcomings of the Convolutional Neural Networks (CNN) such as their inability to recognize detailed spatial relations. Capsule networks have so far shown satisfying performance in medical imaging problems. Capitalizing on their success, in this study, we propose a novel capsule network-based mixture of experts, referred to as the MIXCAPS. The proposed MIXCAPS architecture takes advantage of not only the capsule network's capabilities to handle small datasets, but also automatically splitting dataset through a convolutional gating network. MIXCAPS enables capsule network experts to specialize on different subsets of the data. Our results show that MIXCAPS outperforms a single capsule network and a mixture of CNNs, with an accuracy of 92.88%, sensitivity of 93.2%, specificity of 92.3% and area under the curve of 0.963. Our experiments also show that there is a relation between the gate outputs and a couple of hand-crafted features, illustrating explainable nature of the proposed MIXCAPS. To further evaluate generalization capabilities of the proposed MIXCAPS architecture, additional experiments on a brain tumor dataset are performed showing potentials of MIXCAPS for detection of tumors related to other organs.

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arXiv2020

MM-KTD: Multiple Model Kalman Temporal Differences for Reinforcement Learning

There has been an increasing surge of interest on development of advanced Reinforcement Learning (RL) systems as intelligent approaches to learn optimal control policies directly from smart agents' interactions with the environment. Objectives: In a model-free RL method with continuous state-space, typically, the value function of the states needs to be approximated. In this regard, Deep Neural Networks (DNNs) provide an attractive modeling mechanism to approximate the value function using sample transitions. DNN-based solutions, however, suffer from high sensitivity to parameter selection, are prone to overfitting, and are not very sample efficient. A Kalman-based methodology, on the other hand, could be used as an efficient alternative. Such an approach, however, commonly requires a-priori information about the system (such as noise statistics) to perform efficiently. The main objective of this paper is to address this issue. Methods: As a remedy to the aforementioned problems, this paper proposes an innovative Multiple Model Kalman Temporal Difference (MM-KTD) framework, which adapts the parameters of the filter using the observed states and rewards. Moreover, an active learning method is proposed to enhance the sampling efficiency of the system. More specifically, the estimated uncertainty of the value functions are exploited to form the behaviour policy leading to more visits to less certain values, therefore, improving the overall learning sample efficiency. As a result, the proposed MM-KTD framework can learn the optimal policy with significantly reduced number of samples as compared to its DNN-based counterparts. Results: To evaluate performance of the proposed MM-KTD framework, we have performed a comprehensive set of experiments based on three RL benchmarks. Experimental results show superiority of the MM-KTD framework in comparison to its state-of-the-art counterparts.

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arXiv2020

COVID-CAPS: A Capsule Network-based Framework for Identification of COVID-19 cases from X-ray Images

Novel Coronavirus disease (COVID-19) has abruptly and undoubtedly changed the world as we know it at the end of the 2nd decade of the 21st century. COVID-19 is extremely contagious and quickly spreading globally making its early diagnosis of paramount importance. Early diagnosis of COVID-19 enables health care professionals and government authorities to break the chain of transition and flatten the epidemic curve. The common type of COVID-19 diagnosis test, however, requires specific equipment and has relatively low sensitivity. Computed tomography (CT) scans and X-ray images, on the other hand, reveal specific manifestations associated with this disease. Overlap with other lung infections makes human-centered diagnosis of COVID-19 challenging. Consequently, there has been an urgent surge of interest to develop Deep Neural Network (DNN)-based diagnosis solutions, mainly based on Convolutional Neural Networks (CNNs), to facilitate identification of positive COVID-19 cases. CNNs, however, are prone to lose spatial information between image instances and require large datasets. The paper presents an alternative modeling framework based on Capsule Networks, referred to as the COVID-CAPS, being capable of handling small datasets, which is of significant importance due to sudden and rapid emergence of COVID-19. Our results based on a dataset of X-ray images show that COVID-CAPS has advantage over previous CNN-based models. COVID-CAPS achieved an Accuracy of 95.7%, Sensitivity of 90%, Specificity of 95.8%, and Area Under the Curve (AUC) of 0.97, while having far less number of trainable parameters in comparison to its counterparts. To further improve diagnosis capabilities of the COVID-CAPS, pre-training based on a new dataset constructed from an external dataset of X-ray images. Pre-training with a dataset of similar nature further improved accuracy to 98.3% and specificity to 98.6%.

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arXiv2020

Siamese Neural Networks for EEG-based Brain-computer Interfaces

Motivated by the inconceivable capability of the human brain in simultaneously processing multi-modal signals and its real-time feedback to the outer world events, there has been a surge of interest in establishing a communication bridge between the human brain and a computer, which are referred to as Brain-computer Interfaces (BCI). To this aim, monitoring the electrical activity of brain through Electroencephalogram (EEG) has emerged as the prime choice for BCI systems. To discover the underlying and specific features of brain signals for different mental tasks, a considerable number of research works are developed based on statistical and data-driven techniques. However, a major bottleneck in the development of practical and commercial BCI systems is their limited performance when the number of mental tasks for classification is increased. In this work, we propose a new EEG processing and feature extraction paradigm based on Siamese neural networks, which can be conveniently merged and scaled up for multi-class problems. The idea of Siamese networks is to train a double-input neural network based on a contrastive loss-function, which provides the capability of verifying if two input EEG trials are from the same class or not. In this work, a Siamese architecture, which is developed based on Convolutional Neural Networks (CNN) and provides a binary output on the similarity of two inputs, is combined with OVR and OVO techniques to scale up for multi-class problems. The efficacy of this architecture is evaluated on a 4-class Motor Imagery (MI) dataset from BCI Competition IV-2a and the results suggest a promising performance compared to its counterparts.

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arXiv2019

XceptionTime: A Novel Deep Architecture based on Depthwise Separable Convolutions for Hand Gesture Classification

Capitalizing on the need for addressing the existing challenges associated with gesture recognition via sparse multichannel surface Electromyography (sEMG) signals, the paper proposes a novel deep learning model, referred to as the XceptionTime architecture. The proposed innovative XceptionTime is designed by integration of depthwise separable convolutions, adaptive average pooling, and a novel non-linear normalization technique. At the heart of the proposed architecture is several XceptionTime modules concatenated in series fashion designed to capture both temporal and spatial information-bearing contents of the sparse multichannel sEMG signals without the need for data augmentation and/or manual design of feature extraction. In addition, through integration of adaptive average pooling, Conv1D, and the non-linear normalization approach, XceptionTime is less prone to overfitting, more robust to temporal translation of the input, and more importantly is independent from the input window size. Finally, by utilizing the depthwise separable convolutions, the XceptionTime network has far fewer parameters resulting in a less complex network. The performance of XceptionTime is tested on a sub Ninapro dataset, DB1, and the results showed a superior performance in comparison to any existing counterparts. In this regard, 5:71% accuracy improvement, on a window size 200ms, is reported in this paper, for the first time.

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arXiv2019

Performance Constrained Distributed Event-triggered Consensus in Multi-agent Systems

The paper proposes a distributed eventtriggered consensus approach for linear multi-agent systems with guarantees over rate of convergence, resilience to control gain uncertainties, and Pareto optimality of design parameters, namely, the event-triggering threshold (ET) and control gain. The event-triggered consensus problem is first converted to stability problem of an equivalent system. The Lyapunov stability theorem is then used to incorporate the performance constraints with the event-triggered consensus. Using an approximated linear scalarization method, the ET and the control gain are designed simultaneously by solving a convex constrained optimization problem. Followed by some preliminary steps, the optimization can be performed locally, i.e., no global information is required. The effectiveness of the proposed approach is studied through simulations for an experimental multi-agent system.

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arXiv2019

From Hand-Crafted to Deep Learning-based Cancer Radiomics: Challenges and Opportunities

Recent advancements in signal processing and machine learning coupled with developments of electronic medical record keeping in hospitals and the availability of extensive set of medical images through internal/external communication systems, have resulted in a recent surge of significant interest in "Radiomics". Radiomics is an emerging and relatively new research field, which refers to extracting semi-quantitative and/or quantitative features from medical images with the goal of developing predictive and/or prognostic models, and is expected to become a critical component for integration of image-derived information for personalized treatment in the near future. The conventional Radiomics workflow is typically based on extracting pre-designed features (also referred to as hand-crafted or engineered features) from a segmented region of interest. Nevertheless, recent advancements in deep learning have caused trends towards deep learning-based Radiomics (also referred to as discovery Radiomics). Considering the advantages of these two approaches, there are also hybrid solutions developed to exploit the potentials of multiple data sources. Considering the variety of approaches to Radiomics, further improvements require a comprehensive and integrated sketch, which is the goal of this article. This manuscript provides a unique interdisciplinary perspective on Radiomics by discussing state-of-the-art signal processing solutions in the context of Radiomics.

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arXiv2018

Capsule Networks for Brain Tumor Classification based on MRI Images and Course Tumor Boundaries

According to official statistics, cancer is considered as the second leading cause of human fatalities. Among different types of cancer, brain tumor is seen as one of the deadliest forms due to its aggressive nature, heterogeneous characteristics, and low relative survival rate. Determining the type of brain tumor has significant impact on the treatment choice and patient's survival. Human-centered diagnosis is typically error-prone and unreliable resulting in a recent surge of interest to automatize this process using convolutional neural networks (CNNs). CNNs, however, fail to fully utilize spatial relations, which is particularly harmful for tumor classification, as the relation between the tumor and its surrounding tissue is a critical indicator of the tumor's type. In our recent work, we have incorporated newly developed CapsNets to overcome this shortcoming. CapsNets are, however, highly sensitive to the miscellaneous image background. The paper addresses this gap. The main contribution is to equip CapsNet with access to the tumor surrounding tissues, without distracting it from the main target. A modified CapsNet architecture is, therefore, proposed for brain tumor classification, which takes the tumor coarse boundaries as extra inputs within its pipeline to increase the CapsNet's focus. The proposed approach noticeably outperforms its counterparts.

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arXiv2018

WAKE: Wavelet Decomposition Coupled with Adaptive Kalman Filtering for Pathological Tremor Extraction

Pathological Hand Tremor (PHT) is among common symptoms of several neurological movement disorders, which can significantly degrade quality of life of affected individuals. Beside pharmaceutical and surgical therapies, mechatronic technologies have been utilized to control PHTs. Most of these technologies function based on estimation, extraction, and characterization of tremor movement signals. Real-time extraction of tremor signal is of paramount importance because of its application in assistive and rehabilitative devices. In this paper, we propose a novel on-line adaptive method which can adjust the hyper-parameters of the filter to the variable characteristics of the tremor. The proposed "WAKE: Wavelet decomposition coupled with Adaptive Kalman filtering technique for pathological tremor Extraction, referred to as the WAKE framework" is composed of a new adaptive Kalman filter and a wavelet transform core to provide indirect prediction of the tremor, one sample ahead of time, to be used for its suppression. In this paper, the design, implementation and evaluation of WAKE are given. The performance is evaluated based on three different datasets, the first one is a synthetic dataset, developed in this work, that simulates hand tremor under ten different conditions. The second and third ones are real datasets recorded from patients with PHTs. The results obtained from the proposed WAKE framework demonstrate significant improvements in the estimation accuracy in comparison with two well regarded techniques in the literature.

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arXiv2018

Brain Tumor Type Classification via Capsule Networks

Brain tumor is considered as one of the deadliest and most common form of cancer both in children and in adults. Consequently, determining the correct type of brain tumor in early stages is of significant importance to devise a precise treatment plan and predict patient's response to the adopted treatment. In this regard, there has been a recent surge of interest in designing Convolutional Neural Networks (CNNs) for the problem of brain tumor type classification. However, CNNs typically require large amount of training data and can not properly handle input transformations. Capsule networks (referred to as CapsNets) are brand new machine learning architectures proposed very recently to overcome these shortcomings of CNNs, and posed to revolutionize deep learning solutions. Of particular interest to this work is that Capsule networks are robust to rotation and affine transformation, and require far less training data, which is the case for processing medical image datasets including brain Magnetic Resonance Imaging (MRI) images. In this paper, we focus to achieve the following four objectives: (i) Adopt and incorporate CapsNets for the problem of brain tumor classification to design an improved architecture which maximizes the accuracy of the classification problem at hand; (ii) Investigate the over-fitting problem of CapsNets based on a real set of MRI images; (iii) Explore whether or not CapsNets are capable of providing better fit for the whole brain images or just the segmented tumor, and; (iv) Develop a visualization paradigm for the output of the CapsNet to better explain the learned features. Our results show that the proposed approach can successfully overcome CNNs for the brain tumor classification problem.

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arXiv2018

Improved Explainability of Capsule Networks: Relevance Path by Agreement

Recent advancements in signal processing and machine learning domains have resulted in an extensive surge of interest in deep learning models due to their unprecedented performance and high accuracy for different and challenging problems of significant engineering importance. However, when such deep learning architectures are utilized for making critical decisions such as the ones that involve human lives (e.g., in medical applications), it is of paramount importance to understand, trust, and in one word "explain" the rational behind deep models' decisions. Currently, deep learning models are typically considered as black-box systems, which do not provide any clue on their internal processing actions. Although some recent efforts have been initiated to explain behavior and decisions of deep networks, explainable artificial intelligence (XAI) domain is still in its infancy. In this regard, we consider capsule networks (referred to as CapsNets), which are novel deep structures; recently proposed as an alternative counterpart to convolutional neural networks (CNNs), and posed to change the future of machine intelligence. In this paper, we investigate and analyze structures and behaviors of the CapsNets and illustrate potential explainability properties of such networks. Furthermore, we show possibility of transforming deep learning architectures in to transparent networks via incorporation of capsules in different layers instead of convolution layers of the CNNs.

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arXiv2013

Distributed Computation of the Conditional PCRLB for Quantized Decentralized Particle Filters

The conditional posterior Cramer-Rao lower bound (PCRLB) is an effective sensor resource management criteria for large, geographically distributed sensor networks. Existing algorithms for distributed computation of the PCRLB (dPCRLB) are based on raw observations leading to significant communication overhead to the estimation mechanism. This letter derives distributed computational techniques for determining the conditional dPCRLB for quantized, decentralized sensor networks (CQ/dPCRLB). Analytical expressions for the CQ/dPCRLB are derived, which are particularly useful for particle filter-based estimators. The CQ/dPCRLB is compared for accuracy with its centralized counterpart through Monte-Carlo simulations.

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