810 results on '"Najarian, Kayvan"'
Search Results
2. Enhancing heart failure treatment decisions: interpretable machine learning models for advanced therapy eligibility prediction using EHR data
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Zhang, Yufeng, Golbus, Jessica R., Wittrup, Emily, Aaronson, Keith D., and Najarian, Kayvan
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- 2024
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3. Tensor Denoising via Amplification and Stable Rank Methods
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Gryak, Jonathan, Najarian, Kayvan, and Derksen, Harm
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Computer Science - Machine Learning ,Electrical Engineering and Systems Science - Signal Processing - Abstract
Tensors in the form of multilinear arrays are ubiquitous in data science applications. Captured real-world data, including video, hyperspectral images, and discretized physical systems, naturally occur as tensors and often come with attendant noise. Under the additive noise model and with the assumption that the underlying clean tensor has low rank, many denoising methods have been created that utilize tensor decomposition to effect denoising through low rank tensor approximation. However, all such decomposition methods require estimating the tensor rank, or related measures such as the tensor spectral and nuclear norms, all of which are NP-hard problems. In this work we leverage our previously developed framework of $\textit{tensor amplification}$, which provides good approximations of the spectral and nuclear tensor norms, to denoising synthetic tensors of various sizes, ranks, and noise levels, along with real-world tensors derived from physiological signals. We also introduce two new notions of tensor rank -- $\textit{stable slice rank}$ and $\textit{stable }$$X$$\textit{-rank}$ -- and new denoising methods based on their estimation. The experimental results show that in the low rank context, tensor-based amplification provides comparable denoising performance in high signal-to-noise ratio (SNR) settings and superior performance in noisy (i.e., low SNR) settings, while the stable $X$-rank method achieves superior denoising performance on the physiological signal data.
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- 2023
4. Prediction of Oral Food Challenge Outcomes via Ensemble Learning
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Zhang, Justin, Lee, Deborah, Jungles, Kylie, Shaltis, Diane, Najarian, Kayvan, Ravikumar, Rajan, Sanders, Georgiana, and Gryak, Jonathan
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Computer Science - Machine Learning - Abstract
Oral Food Challenges (OFCs) are essential to accurately diagnosing food allergy due to the limitations of existing clinical testing. However, some patients are hesitant to undergo OFCs, while those willing suffer from limited access to allergists in rural/community healthcare settings. Despite its success in predicting patient outcomes in other clinical settings, few applications of machine learning to food allergy have been developed. Thus, in this study, we seek to leverage machine learning methodologies for OFC outcome prediction. Retrospective data was gathered from 1,112 patients who collectively underwent a total of 1,284 OFCs, and consisted of clinical factors including serum-specific Immunoglobulin E (IgE), total IgE, skin prick tests (SPTs), comorbidities, sex, and age. Using these features, multiple machine learning models were constructed to predict OFC outcomes for three common allergens: peanut, egg, and milk. The best performing model for each allergen was an ensemble of random forest (egg) or Learning Using Concave and Convex Kernels (LUCCK) (peanut, milk) models, which achieved an Area under the Curve (AUC) of 0.91, 0.96, and 0.94, in predicting OFC outcomes for peanut, egg, and milk, respectively. Moreover, all such models had sensitivity and specificity values 89%. Model interpretation via SHapley Additive exPlanations (SHAP) indicates that specific IgE, along with wheal and flare values from SPTs, are highly predictive of OFC outcomes. The results of this analysis suggest that ensemble learning has the potential to predict OFC outcomes and reveal relevant clinical factors for further study.
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- 2022
5. Learning using privileged information with logistic regression on acute respiratory distress syndrome detection
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Gao, Zijun, Cheng, Shuyang, Wittrup, Emily, Gryak, Jonathan, and Najarian, Kayvan
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- 2024
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6. A Novel Tropical Geometry-based Interpretable Machine Learning Method: Application in Prognosis of Advanced Heart Failure
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Yao, Heming, Derksen, Harm, Golbus, Jessica R., Zhang, Justin, Aaronson, Keith D., Gryak, Jonathan, and Najarian, Kayvan
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Computer Science - Machine Learning - Abstract
A model's interpretability is essential to many practical applications such as clinical decision support systems. In this paper, a novel interpretable machine learning method is presented, which can model the relationship between input variables and responses in humanly understandable rules. The method is built by applying tropical geometry to fuzzy inference systems, wherein variable encoding functions and salient rules can be discovered by supervised learning. Experiments using synthetic datasets were conducted to investigate the performance and capacity of the proposed algorithm in classification and rule discovery. Furthermore, the proposed method was applied to a clinical application that identified heart failure patients that would benefit from advanced therapies such as heart transplant or durable mechanical circulatory support. Experimental results show that the proposed network achieved great performance on the classification tasks. In addition to learning humanly understandable rules from the dataset, existing fuzzy domain knowledge can be easily transferred into the network and used to facilitate model training. From our results, the proposed model and the ability of learning existing domain knowledge can significantly improve the model generalizability. The characteristics of the proposed network make it promising in applications requiring model reliability and justification.
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- 2021
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7. Prediction of pediatric peanut oral food challenge outcomes using machine learning
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Gryak, Jonathan, Georgievska, Aleksandra, Zhang, Justin, Najarian, Kayvan, Ravikumar, Rajan, Sanders, Georgiana, and Schuler, Charles F., IV
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- 2024
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8. Motion-based Camera Localization System in Colonoscopy Videos
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Yao, Heming, Stidham, Ryan W., Gao, Zijun, Gryak, Jonathan, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence - Abstract
Optical colonoscopy is an essential diagnostic and prognostic tool for many gastrointestinal diseases, including cancer screening and staging, intestinal bleeding, diarrhea, abdominal symptom evaluation, and inflammatory bowel disease assessment. Automated assessment of colonoscopy is of interest considering the subjectivity present in qualitative human interpretations of colonoscopy findings. Localization of the camera is essential to interpreting the meaning and context of findings for diseases evaluated by colonoscopy. In this study, we propose a camera localization system to estimate the relative location of the camera and classify the colon into anatomical segments. The camera localization system begins with non-informative frame detection and removal. Then a self-training end-to-end convolutional neural network is built to estimate the camera motion, where several strategies are proposed to improve its robustness and generalization on endoscopic videos. Using the estimated camera motion a camera trajectory can be derived and a relative location index calculated. Based on the estimated location index, anatomical colon segment classification is performed by constructing a colon template. The proposed motion estimation algorithm was evaluated on an external dataset containing the ground truth for camera pose. The experimental results show that the performance of the proposed method is superior to other published methods. The relative location index estimation and anatomical region classification were further validated using colonoscopy videos collected from routine clinical practice. This validation yielded an average accuracy in classification of 0.754, which is substantially higher than the performances obtained using location indices built from other methods.
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- 2020
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9. Using Computer Vision to Improve Endoscopic Disease Quantification in Therapeutic Clinical Trials of Ulcerative Colitis
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Stidham, Ryan W., Cai, Lingrui, Cheng, Shuyang, Rajaei, Flora, Hiatt, Tadd, Wittrup, Emily, Rice, Michael D., Bishu, Shrinivas, Wehkamp, Jan, Schultz, Weiwei, Khan, Najat, Stojmirovic, Aleksandar, Ghanem, Louis R., and Najarian, Kayvan
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- 2024
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10. Radial basis function kernel optimization for Support Vector Machine classifiers
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Thurnhofer-Hemsi, Karl, López-Rubio, Ezequiel, Molina-Cabello, Miguel A., and Najarian, Kayvan
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Computer Science - Machine Learning ,Statistics - Machine Learning ,I.5.3 - Abstract
Support Vector Machines (SVMs) are still one of the most popular and precise classifiers. The Radial Basis Function (RBF) kernel has been used in SVMs to separate among classes with considerable success. However, there is an intrinsic dependence on the initial value of the kernel hyperparameter. In this work, we propose OKSVM, an algorithm that automatically learns the RBF kernel hyperparameter and adjusts the SVM weights simultaneously. The proposed optimization technique is based on a gradient descent method. We analyze the performance of our approach with respect to the classical SVM for classification on synthetic and real data. Experimental results show that OKSVM performs better irrespective of the initial values of the RBF hyperparameter., Comment: 9 pages, 5 figures, 1 table (main paper), 8 pages, 6 figures, 2 tables (supplementary material). To be submitted to IEEE Transactions on Neural Networks and Learning Systems
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- 2020
11. Algebraic Methods for Tensor Data
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Tokcan, Neriman, Gryak, Jonathan, Najarian, Kayvan, and Derksen, Harm
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Mathematics - Representation Theory ,Mathematics - Combinatorics ,Mathematics - Numerical Analysis ,14-XX, 15A72, 15A69, 62-07, 22E45, 20G05, 5-XX, 90-XX - Abstract
We develop algebraic methods for computations with tensor data. We give 3 applications: extracting features that are invariant under the orthogonal symmetries in each of the modes, approximation of the tensor spectral norm, and amplification of low rank tensor structure. We introduce colored Brauer diagrams, which are used for algebraic computations and in analyzing their computational complexity. We present numerical experiments whose results show that the performance of the alternating least square algorithm for the low rank approximation of tensors can be improved using tensor amplification.
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- 2020
12. Gland Segmentation in Histopathology Images Using Deep Networks and Handcrafted Features
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Rezaei, Safiyeh, Emami, Ali, Zarrabi, Hamidreza, Rafiei, Shima, Najarian, Kayvan, Karimi, Nader, Samavi, Shadrokh, and Soroushmehr, S. M. Reza
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
Histopathology images contain essential information for medical diagnosis and prognosis of cancerous disease. Segmentation of glands in histopathology images is a primary step for analysis and diagnosis of an unhealthy patient. Due to the widespread application and the great success of deep neural networks in intelligent medical diagnosis and histopathology, we propose a modified version of LinkNet for gland segmentation and recognition of malignant cases. We show that using specific handcrafted features such as invariant local binary pattern drastically improves the system performance. The experimental results demonstrate the competency of the proposed system against state-of-the-art methods. We achieved the best results in testing on section B images of the Warwick-QU dataset and obtained comparable results on section A images.
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- 2019
13. Fetal Ultrasound Image Segmentation for Measuring Biometric Parameters Using Multi-Task Deep Learning
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Sobhaninia, Zahra, Rafiei, Shima, Emami, Ali, Karimi, Nader, Najarian, Kayvan, Samavi, Shadrokh, and Soroushmehr, S. M. Reza
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
Ultrasound imaging is a standard examination during pregnancy that can be used for measuring specific biometric parameters towards prenatal diagnosis and estimating gestational age. Fetal head circumference (HC) is one of the significant factors to determine the fetus growth and health. In this paper, a multi-task deep convolutional neural network is proposed for automatic segmentation and estimation of HC ellipse by minimizing a compound cost function composed of segmentation dice score and MSE of ellipse parameters. Experimental results on fetus ultrasound dataset in different trimesters of pregnancy show that the segmentation results and the extracted HC match well with the radiologist annotations. The obtained dice scores of the fetal head segmentation and the accuracy of HC evaluations are comparable to the state-of-the-art.
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- 2019
14. An Unsupervised Feature Learning Approach to Reduce False Alarm Rate in ICUs
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Ghazanfari, Behzad, Afghah, Fatemeh, Najarian, Kayvan, Mousavi, Sajad, Gryak, Jonathan, and Todd, James
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
The high rate of false alarms in intensive care units (ICUs) is one of the top challenges of using medical technology in hospitals. These false alarms are often caused by patients' movements, detachment of monitoring sensors, or different sources of noise and interference that impact the collected signals from different monitoring devices. In this paper, we propose a novel set of high-level features based on unsupervised feature learning technique in order to effectively capture the characteristics of different arrhythmia in electrocardiogram (ECG) signal and differentiate them from irregularity in signals due to different sources of signal disturbances. This unsupervised feature learning technique, first extracts a set of low-level features from all existing heart cycles of a patient, and then clusters these segments for each individual patient to provide a set of prominent high-level features. The objective of the clustering phase is to enable the classification method to differentiate between the high-level features extracted from normal and abnormal cycles (i.e., either due to arrhythmia or different sources of distortions in signal) in order to put more attention to the features extracted from abnormal portion of the signal that contribute to the alarm. The performance of this method is evaluated using the 2015 PhysioNet/Computing in Cardiology Challenge dataset for reducing false arrhythmia alarms in the ICUs. As confirmed by the experimental results, the proposed method offers a considerable performance in terms of accuracy, sensitivity and specificity of alarm detection only using a few high-level features that are extracted from one single lead ECG signal.
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- 2019
15. Transcranial Color-Coded Sonography With Angle Correction As a Screening Tool for Raised Intracranial Pressure
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Rajajee, Venkatakrishna, Soroushmehr, Reza, Williamson, Craig A., Najarian, Kayvan, Ward, Kevin, and Tiba, Hakam
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- 2023
- Full Text
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16. Prediction of oral food challenge outcomes via ensemble learning
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Zhang, Justin, Lee, Deborah, Jungles, Kylie, Shaltis, Diane, Najarian, Kayvan, Ravikumar, Rajan, Sanders, Georgiana, and Gryak, Jonathan
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- 2023
- Full Text
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17. ReDMark: Framework for Residual Diffusion Watermarking on Deep Networks
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Ahmadi, Mahdi, Norouzi, Alireza, Soroushmehr, S. M. Reza, Karimi, Nader, Najarian, Kayvan, Samavi, Shadrokh, and Emami, Ali
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Computer Science - Multimedia ,Computer Science - Cryptography and Security ,Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
Due to the rapid growth of machine learning tools and specifically deep networks in various computer vision and image processing areas, application of Convolutional Neural Networks for watermarking have recently emerged. In this paper, we propose a deep end-to-end diffusion watermarking framework (ReDMark) which can be adapted for any desired transform space. The framework is composed of two Fully Convolutional Neural Networks with the residual structure for embedding and extraction. The whole deep network is trained end-to-end to conduct a blind secure watermarking. The framework is customizable for the level of robustness vs. imperceptibility. It is also adjustable for the trade-off between capacity and robustness. The proposed framework simulates various attacks as a differentiable network layer to facilitate end-to-end training. For JPEG attack, a differentiable approximation is utilized, which drastically improves the watermarking robustness to this attack. Another important characteristic of the proposed framework, which leads to improved security and robustness, is its capability to diffuse watermark information among a relatively wide area of the image. Comparative results versus recent state-of-the-art researches highlight the superiority of the proposed framework in terms of imperceptibility and robustness., Comment: 33 pages (Single column), 10 figures, 5 tables, one appendix
- Published
- 2018
18. Multiple Abnormality Detection for Automatic Medical Image Diagnosis Using Bifurcated Convolutional Neural Network
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Hajabdollahi, Mohsen, Esfandiarpoor, Reza, Sabeti, Elyas, Karimi, Nader, Najarian, Kayvan, Soroushmehr, S. M. Reza, and Samavi, Shadrokh
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Automating classification and segmentation process of abnormal regions in different body organs has a crucial role in most of medical imaging applications such as funduscopy, endoscopy, and dermoscopy. Detecting multiple abnormalities in each type of images is necessary for better and more accurate diagnosis procedure and medical decisions. In recent years portable medical imaging devices such as capsule endoscopy and digital dermatoscope have been introduced and made the diagnosis procedure easier and more efficient. However, these portable devices have constrained power resources and limited computational capability. To address this problem, we propose a bifurcated structure for convolutional neural networks performing both classification and segmentation of multiple abnormalities simultaneously. The proposed network is first trained by each abnormality separately. Then the network is trained using all abnormalities. In order to reduce the computational complexity, the network is redesigned to share some features which are common among all abnormalities. Later, these shared features are used in different settings (directions) to segment and classify the abnormal region of the image. Finally, results of the classification and segmentation directions are fused to obtain the classified segmentation map. Proposed framework is simulated using four frequent gastrointestinal abnormalities as well as three dermoscopic lesions and for evaluation of the proposed framework the results are compared with the corresponding ground truth map. Properties of the bifurcated network like low complexity and resource sharing make it suitable to be implemented as a part of portable medical imaging devices.
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- 2018
19. Segmentation of Bleeding Regions in Wireless Capsule Endoscopy for Detection of Informative Frames
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Hajabdollahi, Mohsen, Esfandiarpoor, Reza, Khadivi, Pejman, Soroushmehr, S. M. Reza, Karimi, Nader, Najarian, Kayvan, and Samavi, Shadrokh
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Wireless capsule endoscopy (WCE) is an effective mean for diagnosis of gastrointestinal disorders. Detection of informative scenes in WCE video could reduce the length of transmitted videos and help the diagnosis procedure. In this paper, we investigate the problem of simplification of neural networks for automatic bleeding region detection inside capsule endoscopy device. Suitable color channels are selected as neural networks inputs, and image classification is conducted using a multi-layer perceptron (MLP) and a convolutional neural network (CNN) separately. Both CNN and MLP structures are simplified to reduce the number of computational operations. Performances of two simplified networks are evaluated on a WCE bleeding image dataset using the DICE score. Simulation results show that applying simplification methods on both MLP and CNN structures reduces the number of computational operations significantly with AUC greater than 0.97. Although CNN performs better in comparison with simplified MLP, the simplified MLP segments bleeding regions with a significantly smaller number of computational operations. Concerning the importance of having a simple structure or a more accurate model, each of the designed structures could be selected for inside capsule implementation.
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- 2018
20. Left ventricle segmentation By modelling uncertainty in prediction of deep convolutional neural networks and adaptive thresholding inference
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Norouzi, Alireza, Emami, Ali, Soroushmehr, S. M. Reza, Karimi, Nader, Samavi, Shadrokh, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Deep neural networks have shown great achievements in solving complex problems. However, there are fundamental problems that limit their real world applications. Lack of measurable criteria for estimating uncertainty in the network outputs is one of these problems. In this paper, we address this limitation by introducing deformation to the network input and measuring the level of stability in the network's output. We calculate simple random transformations to estimate the prediction uncertainty of deep convolutional neural networks. For a real use-case, we apply this method to left ventricle segmentation in MRI cardiac images. We also propose an adaptive thresholding method to consider the deep neural network uncertainty. Experimental results demonstrate state-of-the-art performance and highlight the capabilities of simple methods in conjunction with deep neural networks., Comment: 5 pages, 3 figures
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- 2018
21. Adaptive specular reflection detection and inpainting in colonoscopy video frames
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Akbari, Mojtaba, Mohrekesh, Majid, Soroushmehr, S. M. Reza, Karimi, Nader, Samavi, Shadrokh, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Colonoscopy video frames might be contaminated by bright spots with unsaturated values known as specular reflection. Detection and removal of such reflections could enhance the quality of colonoscopy images and facilitate diagnosis procedure. In this paper we propose a novel two-phase method for this purpose, consisting of detection and removal phases. In the detection phase, we employ both HSV and RGB color space information for segmentation of specular reflections. We first train a non-linear SVM for selecting a color space based on image statistical features extracted from each channel of the color spaces. Then, a cost function for detection of specular reflections is introduced. In the removal phase, we propose a two-step inpainting method which consists of appropriate replacement patch selection and removal of the blockiness effects. The proposed method is evaluated by testing on an available colonoscopy image database where accuracy and Dice score of 99.68% and 71.79% are achieved respectively., Comment: 5 pages, 5 figures
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- 2018
22. Liver Segmentation in Abdominal CT Images by Adaptive 3D Region Growing
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Rafiei, Shima, Karimi, Nader, Mirmahboub, Behzad, Soroushmehr, S. M. Reza, Felfelian, Banafsheh, Samavi, Shadrokh, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Automatic liver segmentation plays an important role in computer-aided diagnosis and treatment. Manual segmentation of organs is a difficult and tedious task and so prone to human errors. In this paper, we propose an adaptive 3D region growing with subject-specific conditions. For this aim we use the intensity distribution of most probable voxels in prior map along with location prior. We also incorporate the boundary of target organs to restrict the region growing. In order to obtain strong edges and high contrast, we propose an effective contrast enhancement algorithm to facilitate more accurate segmentation. In this paper, 92.56% Dice score is achieved. We compare our method with the method of hard thresholding on Deeds prior map and also with the majority voting on Deeds registration with 13 organs., Comment: Table 1 of the paper contains comparisons and results that are not correct
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- 2018
23. Lossless Image Compression Algorithm for Wireless Capsule Endoscopy by Content-Based Classification of Image Blocks
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Rajaeefar, Atefe, Emami, Ali, Soroushmehr, S. M. Reza, Karimi, Nader, Samavi, Shadrokh, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Recent advances in capsule endoscopy systems have introduced new methods and capabilities. The capsule endoscopy system, by observing the entire digestive tract, has significantly improved diagnosing gastrointestinal disorders and diseases. The system has challenges such as the need to enhance the quality of the transmitted images, low frame rates of transmission, and battery lifetime that need to be addressed. One of the important parts of a capsule endoscopy system is the image compression unit. Better compression of images increases the frame rate and hence improves the diagnosis process. In this paper a high precision compression algorithm with high compression ratio is proposed. In this algorithm we use the similarity between frames to compress the data more efficiently., Comment: 4 pages, 5 figures
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- 2018
24. Segmentation of Bleeding Regions in Wireless Capsule Endoscopy Images an Approach for inside Capsule Video Summarization
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Hajabdollahi, Mohsen, Esfandiarpoor, Reza, Soroushmehr, S. M. Reza, Karimi, Nader, Samavi, Shadrokh, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Wireless capsule endoscopy (WCE) is an effective means of diagnosis of gastrointestinal disorders. Detection of informative scenes by WCE could reduce the length of transmitted videos and can help with the diagnosis. In this paper we propose a simple and efficient method for segmentation of the bleeding regions in WCE captured images. Suitable color channels are selected and classified by a multi-layer perceptron (MLP) structure. The MLP structure is quantized such that the implementation does not require multiplications. The proposed method is tested by simulation on WCE bleeding image dataset. The proposed structure is designed considering hardware resource constrains that exist in WCE systems., Comment: 4 pages, 3 figures
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- 2018
25. Reversible Image Watermarking for Health Informatics Systems Using Distortion Compensation in Wavelet Domain
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Zarrabi, Hamidreza, Hajabdollahi, Mohsen, Soroushmehr, S. M. Reza, Karimi, Nader, Samavi, Shadrokh, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Reversible image watermarking guaranties restoration of both original cover and watermark logo from the watermarked image. Capacity and distortion of the image under reversible watermarking are two important parameters. In this study a reversible watermarking is investigated with focusing on increasing the embedding capacity and reducing the distortion in medical images. Integer wavelet transform is used for embedding where in each iteration, one watermark bit is embedded in one transform coefficient. We devise a novel approach that when a coefficient is modified in an iteration, the produced distortion is compensated in the next iteration. This distortion compensation method would result in low distortion rate. The proposed method is tested on four types of medical images including MRI of brain, cardiac MRI, MRI of breast, and intestinal polyp images. Using a one-level wavelet transform, maximum capacity of 1.5 BPP is obtained. Experimental results demonstrate that the proposed method is superior to the state-of-the-art works in terms of capacity and distortion., Comment: 4 pages, 5 figures
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- 2018
26. Left Ventricle Segmentation in Cardiac MR Images Using Fully Convolutional Network
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Nasr-Esfahani, Mina, Mohrekesh, Majid, Akbari, Mojtaba, Soroushmehr, S. M. Reza, Nasr-Esfahani, Ebrahim, Karimi, Nader, Samavi, Shadrokh, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Medical image analysis, especially segmenting a specific organ, has an important role in developing clinical decision support systems. In cardiac magnetic resonance (MR) imaging, segmenting the left and right ventricles helps physicians diagnose different heart abnormalities. There are challenges for this task, including the intensity and shape similarity between left ventricle and other organs, inaccurate boundaries and presence of noise in most of the images. In this paper we propose an automated method for segmenting the left ventricle in cardiac MR images. We first automatically extract the region of interest, and then employ it as an input of a fully convolutional network. We train the network accurately despite the small number of left ventricle pixels in comparison with the whole image. Thresholding on the output map of the fully convolutional network and selection of regions based on their roundness are performed in our proposed post-processing phase. The Dice score of our method reaches 87.24% by applying this algorithm on the York dataset of heart images., Comment: 4 pages, 3 figures
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- 2018
27. Lossless Compression of Angiogram Foreground with Visual Quality Preservation of Background
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Ahmadi, Mahdi, Emami, Ali, Hajabdollahi, Mohsen, Soroushmehr, S. M. Reza, Karimi, Nader, Samavi, Shadrokh, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
By increasing the volume of telemedicine information, the need for medical image compression has become more important. In angiographic images, a small ratio of the entire image usually belongs to the vasculature that provides crucial information for diagnosis. Other parts of the image are diagnostically less important and can be compressed with higher compression ratio. However, the quality of those parts affect the visual perception of the image as well. Existing methods compress foreground and background of angiographic images using different techniques. In this paper we first utilize convolutional neural network to segment vessels and then represent a hierarchical block processing algorithm capable of both eliminating the background redundancies and preserving the overall visual quality of angiograms., Comment: 4 pages , 7 figures
- Published
- 2018
28. Liver segmentation in CT images using three dimensional to two dimensional fully convolutional network
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Rafiei, Shima, Nasr-Esfahani, Ebrahim, Soroushmehr, S. M. Reza, Karimi, Nader, Samavi, Shadrokh, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
The need for CT scan analysis is growing for pre-diagnosis and therapy of abdominal organs. Automatic organ segmentation of abdominal CT scan can help radiologists analyze the scans faster and segment organ images with fewer errors. However, existing methods are not efficient enough to perform the segmentation process for victims of accidents and emergencies situations. In this paper we propose an efficient liver segmentation with our 3D to 2D fully connected network (3D-2D-FCN). The segmented mask is enhanced by means of conditional random field on the organ's border. Consequently, we segment a target liver in less than a minute with Dice score of 93.52., Comment: 5 pages, 2 figures
- Published
- 2018
29. Classification of Informative Frames in Colonoscopy Videos Using Convolutional Neural Networks with Binarized Weights
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Akbari, Mojtaba, Mohrekesh, Majid, Rafiei, Shima, Soroushmehr, S. M. Reza, Karimi, Nader, Samavi, Shadrokh, and Najarian, Kayvan
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Electrical Engineering and Systems Science - Image and Video Processing - Abstract
Colorectal cancer is one of the common cancers in the United States. Polyp is one of the main causes of the colonic cancer and early detection of polyps will increase chance of cancer treatments. In this paper, we propose a novel classification of informative frames based on a convolutional neural network with binarized weights. The proposed CNN is trained with colonoscopy frames along with the labels of the frames as input data. We also used binarized weights and kernels to reduce the size of CNN and make it suitable for implementation in medical hardware. We evaluate our proposed method using Asu Mayo Test clinic database, which contains colonoscopy videos of different patients. Our proposed method reaches a dice score of 71.20% and accuracy of more than 90% using the mentioned dataset.
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- 2018
30. Polyp Segmentation in Colonoscopy Images Using Fully Convolutional Network
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Akbari, Mojtaba, Mohrekesh, Majid, Nasr-Esfahani, Ebrahim, Soroushmehr, S. M. Reza, Karimi, Nader, Samavi, Shadrokh, and Najarian, Kayvan
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Electrical Engineering and Systems Science - Image and Video Processing - Abstract
Colorectal cancer is a one of the highest causes of cancer-related death, especially in men. Polyps are one of the main causes of colorectal cancer and early diagnosis of polyps by colonoscopy could result in successful treatment. Diagnosis of polyps in colonoscopy videos is a challenging task due to variations in the size and shape of polyps. In this paper we proposed a polyp segmentation method based on convolutional neural network. Performance of the method is enhanced by two strategies. First, we perform a novel image patch selection method in the training phase of the network. Second, in the test phase, we perform an effective post processing on the probability map that is produced by the network. Evaluation of the proposed method using the CVC-ColonDB database shows that our proposed method achieves more accurate results in comparison with previous colonoscopy video-segmentation methods.
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- 2018
31. Deep Learning in Pharmacogenomics: From Gene Regulation to Patient Stratification
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Kalinin, Alexandr A., Higgins, Gerald A., Reamaroon, Narathip, Soroushmehr, S. M. Reza, Allyn-Feuer, Ari, Dinov, Ivo D., Najarian, Kayvan, and Athey, Brian D.
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Quantitative Biology - Quantitative Methods ,Computer Science - Learning ,Statistics - Machine Learning - Abstract
This Perspective provides examples of current and future applications of deep learning in pharmacogenomics, including: (1) identification of novel regulatory variants located in noncoding domains and their function as applied to pharmacoepigenomics; (2) patient stratification from medical records; and (3) prediction of drugs, targets, and their interactions. Deep learning encapsulates a family of machine learning algorithms that over the last decade has transformed many important subfields of artificial intelligence (AI) and has demonstrated breakthrough performance improvements on a wide range of tasks in biomedicine. We anticipate that in the future deep learning will be widely used to predict personalized drug response and optimize medication selection and dosing, using knowledge extracted from large and complex molecular, epidemiological, clinical, and demographic datasets., Comment: Alexandr A. Kalinin and Gerald A. Higgins contributed equally to this work. Corresponding author: Brian D. Athey,
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- 2018
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32. Dense Pooling layers in Fully Convolutional Network for Skin Lesion Segmentation
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Nasr-Esfahani, Ebrahim, Rafiei, Shima, Jafari, Mohammad H., Karimi, Nader, Wrobel, James S., Soroushmehr, S. M. Reza, Samavi, Shadrokh, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
One of the essential tasks in medical image analysis is segmentation and accurate detection of borders. Lesion segmentation in skin images is an essential step in the computerized detection of skin cancer. However, many of the state-of-the-art segmentation methods have deficiencies in their border detection phase. In this paper, a new class of fully convolutional network is proposed, with new dense pooling layers for segmentation of lesion regions in skin images. This network leads to highly accurate segmentation of lesions on skin lesion datasets which outperforms state-of-the-art algorithms in the skin lesion segmentation.
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- 2017
33. On diabetic foot ulcer knowledge gaps, innovation, evaluation, prediction markers, and clinical needs
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Schmidt, Brian M., Holmes, Crystal M., Najarian, Kayvan, Gallagher, Katherine, Haus, Jacob M., Shadiow, James, Ye, Wen, Ang, Lynn, Burant, Aaron, Baker, Nicole, Katona, Aimee, Martin, Catherine L., and Pop-Busui, Rodica
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- 2022
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34. A deep learning framework for automated detection and quantitative assessment of liver trauma
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Farzaneh, Negar, Stein, Erica B., Soroushmehr, Reza, Gryak, Jonathan, and Najarian, Kayvan
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- 2022
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35. An interpretable neural network for outcome prediction in traumatic brain injury
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Minoccheri, Cristian, Williamson, Craig A., Hemmila, Mark, Ward, Kevin, Stein, Erica B., Gryak, Jonathan, and Najarian, Kayvan
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- 2022
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36. Prediction of postoperative cardiac events in multiple surgical cohorts using a multimodal and integrative decision support system
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Kim, Renaid B., Alge, Olivia P., Liu, Gang, Biesterveld, Ben E., Wakam, Glenn, Williams, Aaron M., Mathis, Michael R., Najarian, Kayvan, and Gryak, Jonathan
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- 2022
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37. Vessel segmentation for X-ray coronary angiography using ensemble methods with deep learning and filter-based features
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Gao, Zijun, Wang, Lu, Soroushmehr, Reza, Wood, Alexander, Gryak, Jonathan, Nallamothu, Brahmajee, and Najarian, Kayvan
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- 2022
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38. Vessel Segmentation and Catheter Detection in X-Ray Angiograms Using Superpixels
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Fazlali, Hamid R., Karimi, Nader, Soroushmehr, S. M. Reza, Shirani, Shahram, Nallamothu, Brahmajee. K., Ward, Kevin R., Samavi, Shadrokh, and Najarian, Kayvan
- Subjects
Computer Science - Computer Vision and Pattern Recognition - Abstract
Coronary artery disease (CAD) is the leading causes of death around the world. One of the most common imaging methods for diagnosing this disease is X-ray angiography. Diagnosing using these images is usually challenging due to non-uniform illumination, low contrast, presence of other body tissues, presence of catheter etc. These challenges make the diagnoses task of cardiologists tougher and more prone to misdiagnosis. In this paper we propose a new automated framework for coronary arteries segmentation, catheter detection and center-line extraction in x-ray angiography images. Our proposed segmentation method is based on superpixels. In this method at first three different superpixel scales are exploited and a measure for vesselness probability of each superpixel is determined. A majority voting is used for obtaining an initial segmentation map from these three superpixel scales. This initial segmentation is refined by finding the orthogonal line on each ridge pixel of vessel region. In this framework we use our catheter detection and tracking method which detects the catheter by finding its ridge in the first frame and traces in other frames by fitting a second order polynomial on it. Also we use the image ridges for extracting the coronary arteries centerlines. We evaluated our method qualitatively and quantitatively on two different challenging datasets and compared it with one of the previous well-known coronary arteries segmentation methods. Our method could detect the catheter and reduced the false positive rate in addition to achieving better segmentation results. The evaluation results prove that our method performs better in a much shorter time., Comment: 14 Pages, 19 figures, 2 tables
- Published
- 2017
39. Adaptive Real-Time Removal of Impulse Noise in Medical Images
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HosseinKhani, Zohreh, Hajabdollahi, Mohsen, Karimi, Nader, Soroushmehr, Reza, Shirani, Shahram, Najarian, Kayvan, and Samavi, Shadrokh
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Noise is an important factor that degrades the quality of medical images. Impulse noise is a common noise, which is caused by malfunctioning of sensor elements or errors in the transmission of images. In medical images due to presence of white foreground and black background, many pixels have intensities similar to impulse noise and distinction between noisy and regular pixels is difficult. In software techniques, the accuracy of the noise removal is more important than the algorithm's complexity. But for hardware implementation having a low complexity algorithm with an acceptable accuracy is essential. In this paper a low complexity de-noising method is proposed that removes the noise by local analysis of the image blocks. The proposed method distinguishes non-noisy pixels that have noise-like intensities. All steps are designed to have low hardware complexity. Simulation results show that for different magnetic resonance images, the proposed method removes impulse noise with an acceptable accuracy., Comment: 9 pages, 12 figures, 2 tables
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- 2017
40. Adaptive Blind Image Watermarking Using Fuzzy Inference System Based on Human Visual Perception
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Jamali, Maedeh, Rafiei, Shima, Soroushmehr, S. M. Reza, Karimi, Nader, Shirani, Shahram, Najarian, Kayvan, and Samavi, Shadrokh
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Computer Science - Multimedia - Abstract
Development of digital content has increased the necessity of copyright protection by means of watermarking. Imperceptibility and robustness are two important features of watermarking algorithms. The goal of watermarking methods is to satisfy the tradeoff between these two contradicting characteristics. Recently watermarking methods in transform domains have displayed favorable results. In this paper, we present an adaptive blind watermarking method which has high transparency in areas that are important to human visual system. We propose a fuzzy system for adaptive control of the embedding strength factor. Features such as saliency, intensity, and edge-concentration, are used as fuzzy attributes. Redundant embedding in discrete cosine transform (DCT) of wavelet domain has increased the robustness of our method. Experimental results show the efficiency of the proposed method and better results are obtained as compared to comparable methods with same size of watermark logo., Comment: 11 pages, 11 figures
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- 2017
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41. Blind Stereo Image Quality Assessment Inspired by Brain Sensory-Motor Fusion
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Karimi, Maryam, Soltanian, Najmeh, Samavi, Shadrokh, Karimi, Nader, Soroushmehr, S. M. Reza, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
The use of 3D and stereo imaging is rapidly increasing. Compression, transmission, and processing could degrade the quality of stereo images. Quality assessment of such images is different than their 2D counterparts. Metrics that represent 3D perception by human visual system (HVS) are expected to assess stereoscopic quality more accurately. In this paper, inspired by brain sensory/motor fusion process, two stereo images are fused together. Then from every fused image two synthesized images are extracted. Effects of different distortions on statistical distributions of the synthesized images are shown. Based on the observed statistical changes, features are extracted from these synthesized images. These features can reveal type and severity of distortions. Then, a stacked neural network model is proposed, which learns the extracted features and accurately evaluates the quality of stereo images. This model is tested on 3D images of popular databases. Experimental results show the superiority of this method over state of the art stereo image quality assessment approaches, Comment: 11 pages, 13 figures, 3 tables
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- 2017
42. Real-Time Impulse Noise Removal from MR Images for Radiosurgery Applications
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HosseinKhani, Zohreh, Hajabdollahi, Mohsen, Karimi, Nader, Soroushmehr, S. M. Reza, Shirani, Shahram, Samavi, Shadrokh, and Najarian, Kayvan
- Subjects
Computer Science - Hardware Architecture ,Physics - Medical Physics - Abstract
In the recent years image processing techniques are used as a tool to improve detection and diagnostic capabilities in the medical applications. Medical applications have been so much affected by these techniques which some of them are embedded in medical instruments such as MRI, CT and other medical devices. Among these techniques, medical image enhancement algorithms play an essential role in removal of the noise which can be produced by medical instruments and during image transfer. It has been proved that impulse noise is a major type of noise, which is produced during medical operations, such as MRI, CT, and angiography, by their image capturing devices. An embeddable hardware module which is able to denoise medical images before and during surgical operations could be very helpful. In this paper an accurate algorithm is proposed for real-time removal of impulse noise in medical images. All image blocks are divided into three categories of edge, smooth, and disordered areas. A different reconstruction method is applied to each category of blocks for the purpose of noise removal. The proposed method is tested on MR images. Simulation results show acceptable denoising accuracy for various levels of noise. Also an FPAG implementation of our denoising algorithm shows acceptable hardware resource utilization. Hence, the algorithm is suitable for embedding in medical hardware instruments such as radiosurgery devices., Comment: 12 pages, 13 figures, 2 tables
- Published
- 2017
43. Can Machine Learning Overcome the 95% Failure Rate and Reality that Only 30% of Approved Cancer Drugs Meaningfully Extend Patient Survival?
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Sun, Duxin, Macedonia, Christian, Chen, Zhigang, Chandrasekaran, Sriram, Najarian, Kayvan, Zhou, Simon, Cernak, Tim, Ellingrod, Vicki L., Jagadish, H. V., Marini, Bernard, Pai, Manjunath, Violi, Angela, Rech, Jason C., Wang, Shaomeng, Li, Yan, Athey, Brian, and Omenn, Gilbert S.
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- 2024
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44. Feature Selection for Privileged Modalities in Disease Classification
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Zhang, Winston, Turkestani, Najla Al, Bianchi, Jonas, Le, Celia, Deleat-Besson, Romain, Ruellas, Antonio, Cevidanes, Lucia, Yatabe, Marilia, Gonçalves, Joao, Benavides, Erika, Soki, Fabiana, Prieto, Juan, Paniagua, Beatriz, Gryak, Jonathan, Najarian, Kayvan, Soroushmehr, Reza, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Syeda-Mahmood, Tanveer, editor, Li, Xiang, editor, Madabhushi, Anant, editor, Greenspan, Hayit, editor, Li, Quanzheng, editor, Leahy, Richard, editor, Dong, Bin, editor, and Wang, Hongzhi, editor
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- 2021
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45. Merging and Annotating Teeth and Roots from Automated Segmentation of Multimodal Images
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Deleat-Besson, Romain, Le, Celia, Zhang, Winston, Turkestani, Najla Al, Cevidanes, Lucia, Bianchi, Jonas, Ruellas, Antonio, Gurgel, Marcela, Massaro, Camila, Del Castillo, Aron Aliaga, Ioshida, Marcos, Yatabe, Marilia, Benavides, Erika, Rios, Hector, Soki, Fabiana, Neiva, Gisele, Najarian, Kayvan, Gryak, Jonathan, Styner, Martin, Aristizabal, Juan Fernando, Rey, Diego, Alvarez, Maria Antonia, Bert, Loris, Soroushmehr, Reza, Prieto, Juan, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Syeda-Mahmood, Tanveer, editor, Li, Xiang, editor, Madabhushi, Anant, editor, Greenspan, Hayit, editor, Li, Quanzheng, editor, Leahy, Richard, editor, Dong, Bin, editor, and Wang, Hongzhi, editor
- Published
- 2021
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46. Patient Specific Classification of Dental Root Canal and Crown Shape
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Dumont, Maxime, Prieto, Juan Carlos, Brosset, Serge, Cevidanes, Lucia, Bianchi, Jonas, Ruellas, Antonio, Gurgel, Marcela, Massaro, Camila, Del Castillo, Aron Aliaga, Ioshida, Marcos, Yatabe, Marilia, Benavides, Erika, Rios, Hector, Soki, Fabiana, Neiva, Gisele, Aristizabal, Juan Fernando, Rey, Diego, Alvarez, Maria Antonia, Najarian, Kayvan, Gryak, Jonathan, Styner, Martin, Fillion-Robin, Jean-Christophe, Paniagua, Beatriz, Soroushmehr, Reza, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Reuter, Martin, editor, Wachinger, Christian, editor, Lombaert, Hervé, editor, Paniagua, Beatriz, editor, Goksel, Orcun, editor, and Rekik, Islem, editor
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- 2020
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47. Motion-based camera localization system in colonoscopy videos
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Yao, Heming, Stidham, Ryan W., Gao, Zijun, Gryak, Jonathan, and Najarian, Kayvan
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- 2021
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48. Hand Gesture Recognition for Contactless Device Control in Operating Rooms
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Nasr-Esfahani, Ebrahim, Karimi, Nader, Soroushmehr, S. M. Reza, Jafari, M. Hossein, Khorsandi, M. Amin, Samavi, Shadrokh, and Najarian, Kayvan
- Subjects
Computer Science - Computer Vision and Pattern Recognition - Abstract
Hand gesture is one of the most important means of touchless communication between human and machines. There is a great interest for commanding electronic equipment in surgery rooms by hand gesture for reducing the time of surgery and the potential for infection. There are challenges in implementation of a hand gesture recognition system. It has to fulfill requirements such as high accuracy and fast response. In this paper we introduce a system of hand gesture recognition based on a deep learning approach. Deep learning is known as an accurate detection model, but its high complexity prevents it from being fabricated as an embedded system. To cope with this problem, we applied some changes in the structure of our work to achieve low complexity. As a result, the proposed method could be implemented on a naive embedded system. Our experiments show that the proposed system results in higher accuracy while having less complexity in comparison with the existing comparable methods.
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- 2016
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49. Extraction of Skin Lesions from Non-Dermoscopic Images Using Deep Learning
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Jafari, Mohammad H., Nasr-Esfahani, Ebrahim, Karimi, Nader, Soroushmehr, S. M. Reza, Samavi, Shadrokh, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Melanoma is amongst most aggressive types of cancer. However, it is highly curable if detected in its early stages. Prescreening of suspicious moles and lesions for malignancy is of great importance. Detection can be done by images captured by standard cameras, which are more preferable due to low cost and availability. One important step in computerized evaluation of skin lesions is accurate detection of lesion region, i.e. segmentation of an image into two regions as lesion and normal skin. Accurate segmentation can be challenging due to burdens such as illumination variation and low contrast between lesion and healthy skin. In this paper, a method based on deep neural networks is proposed for accurate extraction of a lesion region. The input image is preprocessed and then its patches are fed to a convolutional neural network (CNN). Local texture and global structure of the patches are processed in order to assign pixels to lesion or normal classes. A method for effective selection of training patches is used for more accurate detection of a lesion border. The output segmentation mask is refined by some post processing operations. The experimental results of qualitative and quantitative evaluations demonstrate that our method can outperform other state-of-the-art algorithms exist in the literature.
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- 2016
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50. A Shapley Value Solution to Game Theoretic-based Feature Reduction in False Alarm Detection
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Afghah, Fatemeh, Razi, Abolfazl, and Najarian, Kayvan
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Computer Science - Computer Vision and Pattern Recognition - Abstract
False alarm is one of the main concerns in intensive care units and can result in care disruption, sleep deprivation, and insensitivity of care-givers to alarms. Several methods have been proposed to suppress the false alarm rate through improving the quality of physiological signals by filtering, and developing more accurate sensors. However, significant intrinsic correlation among the extracted features limits the performance of most currently available data mining techniques, as they often discard the predictors with low individual impact that may potentially have strong discriminatory power when grouped with others. We propose a model based on coalition game theory that considers the inter-features dependencies in determining the salient predictors in respect to false alarm, which results in improved classification accuracy. The superior performance of this method compared to current methods is shown in simulation results using PhysionNet's MIMIC II database., Comment: Neural Information Processing Systems (NIPS'15), Workshop on Machine Learning in Healthcare
- Published
- 2015
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