Unsupervised Multivariate Time Series Clustering

Clustering is widely used in unsupervised machine learning to partition a given set of data into non-overlapping groups. Many real-world applications require processing more complex multivariate time series data characterized by more than one dependent variables. A few works in literature reported multivariate classification using Shapelet learning. However, the clustering of multivariate time series signals using Shapelet learning has not explored yet. Shapelet learning is a process of discovering those Shapelets which contain the most informative features of the time series signal. Discovering suitable Shapelets from many candidates Shapelet has been broadly studied for classification and clustering of univariate time series signals. Shapelet learning has shown promising results in the case of univariate time series analysis. The analysis of multivariate time series signals is not widely explored because of the dimensionality issue. This work proposes a generalized Shapelet learning method for unsupervised multivariate time series clustering. The proposed method utilizes spectral clustering and Shapelet similarity minimization with least square regularization to obtain the optimal Shapelets for unsupervised clustering. The proposed method is evaluated using an in-house multivariate time series dataset on detection of radio frequency (RF) faults in the Jefferson Labs Continuous Beam Accelerator Facility (CEBAF). The dataset constitutes of three-dimensional time series recordings of three RF fault types. The proposed method shows successful clustering performance with average value of a precision of 0.732, recall of 0.717, F-score of 0.732, a rand index (RI) score of 0.812 and normalize mutual information (NMI) of 0.56 with overall less than 3% standard deviation in a five-fold cross validation evaluation.https://digitalcommons.odu.edu/gradposters2021_engineering/1004/thumbnail.jp

Context Aware Deep Learning for Brain Tumor Segmentation, Subtype Classification, and Survival Prediction Using Radiology Images

A brain tumor is an uncontrolled growth of cancerous cells in the brain. Accurate segmentation and classification of tumors are critical for subsequent prognosis and treatment planning. This work proposes context aware deep learning for brain tumor segmentation, subtype classification, and overall survival prediction using structural multimodal magnetic resonance images (mMRI). We first propose a 3D context aware deep learning, that considers uncertainty of tumor location in the radiology mMRI image sub-regions, to obtain tumor segmentation. We then apply a regular 3D convolutional neural network (CNN) on the tumor segments to achieve tumor subtype classification. Finally, we perform survival prediction using a hybrid method of deep learning and machine learning. To evaluate the performance, we apply the proposed methods to the Multimodal Brain Tumor Segmentation Challenge 2019 (BraTS 2019) dataset for tumor segmentation and overall survival prediction, and to the dataset of the Computational Precision Medicine Radiology-Pathology (CPM-RadPath) Challenge on Brain Tumor Classification 2019 for tumor classification. We also perform an extensive performance evaluation based on popular evaluation metrics, such as Dice score coefficient, Hausdorff distance at percentile 95 (HD95), classification accuracy, and mean square error. The results suggest that the proposed method offers robust tumor segmentation and survival prediction, respectively. Furthermore, the tumor classification results in this work is ranked at second place in the testing phase of the 2019 CPM-RadPath global challenge

Deep Learning with Context Encoding for Semantic Brain Tumor Segmentation and Patient Survival Prediction

One of the most challenging problems encountered in deep learning-based brain tumor segmentation models is the misclassification of tumor tissue classes due to the inherent imbalance in the class representation. Consequently, strong regularization methods are typically considered when training large-scale deep learning models for brain tumor segmentation to overcome undue bias towards representative tissue types. However, these regularization methods tend to be computationally exhaustive, and may not guarantee the learning of features representing all tumor tissue types that exist in the input MRI examples. Recent work in context encoding with deep CNN models have shown promise for semantic segmentation of natural scenes, with particular improvements in small object segmentation due to improved representative feature learning. Accordingly, we propose a novel, efficient 3DCNN based deep learning framework with context encoding for semantic brain tumor segmentation using multimodal magnetic resonance imaging (mMRI). The context encoding module in the proposed model enforces rich, class-dependent feature learning to improve the overall multi-label segmentation performance. We subsequently utilize context augmented features in a machine-learning based survival prediction pipeline to improve the prediction performance. The proposed method is evaluated using the publicly available 2019 Brain Tumor Segmentation (BraTS) and survival prediction challenge dataset. The results show that the proposed method significantly improves the tumor tissue segmentation performance and the overall survival prediction performance

Initial Studies of Cavity Fault Prediction at Jefferson Laboratory

The Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Laboratory is a CW recirculating linac that utilizes over 400 superconducting radio-frequency (SRF) cavities to accelerate electrons up to 12 GeV through 5-passes. Recent work has shown that, given RF signals from a cavity during a fault as input, machine learning approaches can accurately classify the fault type. In this paper we report on initial results of predicting a fault onset using only data prior to the failure event. A data set was constructed using time-series data immediately before a fault (’unstable’) and 1.5 seconds prior to a fault (’stable’) gathered from over 5,000 saved fault events. The data was used to train a binary classifier. The results gave key insights into the behavior of several fault types and provided motivation to investigate whether data prior to a failure event could also predict the type of fault. We discuss our method using a sliding window approach and report on initial results. Recent modifications to the low-level RF control system will provide access to streaming signals and we outline a path forward for leveraging deep learning on streaming dat

Deep Learning Based Superconducting Radio-Frequency Cavity Fault Classification at Jefferson Laboratory

This work investigates the efficacy of deep learning (DL) for classifying C100 superconducting radio-frequency (SRF) cavity faults in the Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Lab. CEBAF is a large, high-power continuous wave recirculating linac that utilizes 418 SRF cavities to accelerate electrons up to 12 GeV. Recent upgrades to CEBAF include installation of 11 new cryomodules (88 cavities) equipped with a low-level RF system that records RF time-series data from each cavity at the onset of an RF failure. Typically, subject matter experts (SME) analyze this data to determine the fault type and identify the cavity of origin. This information is subsequently utilized to identify failure trends and to implement corrective measures on the offending cavity. Manual inspection of large-scale, time-series data, generated by frequent system failures is tedious and time consuming, and thereby motivates the use of machine learning (ML) to automate the task. This study extends work on a previously developed system based on traditional ML methods (Tennant and Carpenter and Powers and Shabalina Solopova and Vidyaratne and Iftekharuddin, Phys. Rev. Accel. Beams, 2020, 23, 114601), and investigates the effectiveness of deep learning approaches. The transition to a DL model is driven by the goal of developing a system with sufficiently fast inference that it could be used to predict a fault event and take actionable information before the onset (on the order of a few hundred milliseconds). Because features are learned, rather than explicitly computed, DL offers a potential advantage over traditional ML. Specifically, two seminal DL architecture types are explored: deep recurrent neural networks (RNN) and deep convolutional neural networks (CNN). We provide a detailed analysis on the performance of individual models using an RF waveform dataset built from past operational runs of CEBAF. In particular, the performance of RNN models incorporating long short-term memory (LSTM) are analyzed along with the CNN performance. Furthermore, comparing these DL models with a state-of-the-art fault ML model shows that DL architectures obtain similar performance for cavity identification, do not perform quite as well for fault classification, but provide an advantage in inference speed

Using AI for Management of Field Emission in SRF Linacs

Field emission control, mitigation, and reduction is critical for reliable operation of high gradient superconducting radio-frequency (SRF) accelerators. With the SRF cavities at high gradients, the field emission of electrons from cavity walls can occur and will impact the operational gradient, radiological environment via activated components, and reliability of CEBAF’s two linacs. A new effort has started to minimize field emission in the CEBAF linacs by re-distributing cavity gradients. To measure radiation levels, newly designed neutron and gamma radiation dose rate monitors have been installed in both linacs. Artificial intelligence (AI) techniques will be used to identify cavities with high levels of field emission based on control system data such as radiation levels, cryogenic readbacks, and vacuum loads. The gradients on the most offending cavities will be reduced and compensated for by increasing the gradients on least offensive cavities. Training data will be collected during this year’s operational program and initial implementation of AI models will be deployed. Preliminary results and future plans are presented

QU-BraTS : MICCAI BraTS 2020 Challenge on QuantifyingUncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results

Deep learning (DL) models have provided the state-of-the-art performance in a wide variety of medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder the translation of DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties, could enable clinical review of the most uncertain regions, thereby building trust and paving the way towards clinical translation. Recently, a number of uncertainty estimation methods have been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019-2020 task on uncertainty quantification (QU-BraTS), and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions, and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentages of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, and hence highlight the need for uncertainty quantification in medical image analyses. Our evaluation code is made publicly available at https://github.com/RagMeh11/QU-BraT

QU-BraTS : MICCAI BraTS 2020 Challenge on QuantifyingUncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results

Deep learning (DL) models have provided the state-of-the-art performance in a wide variety of medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder the translation of DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties, could enable clinical review of the most uncertain regions, thereby building trust and paving the way towards clinical translation. Recently, a number of uncertainty estimation methods have been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019-2020 task on uncertainty quantification (QU-BraTS), and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions, and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentages of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, and hence highlight the need for uncertainty quantification in medical image analyses. Our evaluation code is made publicly available at https://github.com/RagMeh11/QU-BraT