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Attend and Decode: 4D fMRI Task State Decoding Using Attention Models

Source code for Brain Attend and Decode paper. Functional magnetic resonance imaging (fMRI) is a neuroimaging modality that captures the blood oxygen level in a subject's brain while the subject either rests or performs a variety of functional tasks under different conditions. Given fMRI data, the problem of inferring the task, known as task state decoding, is challenging due to the high dimensionality (hundreds of million sampling points per datum) and complex spatio-temporal blood flow patterns inherent in the data. In this work, we propose to tackle the fMRI task state decoding problem by casting it as a 4D spatiotemporal classification problem. We present a novel architecture called Brain Attend and Decode (BAnD), that uses residual convolutional neural networks for spatial feature extraction and self-attention mechanisms for temporal modeling. We achieve significant performance gain compared to previous works on a 7-task benchmark from the large-scale Human Connectome Project-Young Adult (HCP-YA) dataset. We also investigate the transferability of BAnD's extracted features on unseen HCP tasks, either by freezing the spatial feature extraction layers and retraining the temporal model, or finetuning the entire model. The pre-trained features from BAnD are useful on similar tasks while finetuning them yields competitive results on unseen tasks/conditions.

Ng, BrendaM.↗

Dual-Channel Densenet for Hyperspectral Image Classification

Deep neural networks provide deep extracted features for image classification. As a high dimension data, hyperspectral image (HSI) feature extraction is unlike an RGB image whose feature representation could not be simply generated in the spatial domain. To take full advantage of HSI, a dualchannel convolutional neural network (CNN) is applied, 1D convolution for the spectral domain and 2D convolution for spatial domain. For pixel-wise classification of HSI, in our network model, one-dimensional customized DenseNet is for extracting the hierarchical spectral features and another customized DenseNet is applied to extract the hierarchical spatial-related feature. Furthermore, we experimentally tuned the several widen factors and dense-net growth rates to evaluate the impact of hyper-parameter. Furthermore, to compare our proposed method with HSI classification methods, we test other three DNNs based method in two real-world HSI dataset. The result demonstrated our approach outperformed the state-of-art method

97 MATHEMATICS AND COMPUTING↗

SU-E-J-248: Contributions of Tumor and Stroma Phenotyping in Computer-Aided Diagnosis

Purpose: To gain insight into the role of parenchyma stroma in the characterization of breast tumors by incorporating computerized mammographic parenchyma assessment into breast CADx in the task of distinguishing between malignant and benign lesions. Methods: This study was performed on 182 biopsy-proven breast mass lesions, including 76 benign and 106 malignant lesions. For each full-field digital mammogram (FFDM) case, our quantitative imaging analysis was performed on both the tumor and a region-of-interest (ROI) from the normal contralateral breast. The lesion characterization includes automatic lesion segmentation and feature extraction. Radiographic texture analysis (RTA) was applied on the normal ROIs to assess the mammographic parenchymal patterns of these contralateral normal breasts. Classification performance of both individual computer extracted features and the output from a Bayesian artificial neural network (BANN) were evaluated with a leave-one-lesion-out method using receiver operating characteristic (ROC) analysis with area under the curve (AUC) as the figure of merit. Results: Lesion characterization included computer-extracted phenotypes of spiculation, size, shape, and margin. For parenchymal pattern characterization, five texture features were selected, including power law beta, contrast, and edge gradient. Merging of these computer-selected features using BANN classifiers yielded AUC values of 0.79 (SE=0.03) and 0.67 (SE=0.04) in the task of distinguishing between malignant and benign lesions using only tumor phenotypes and texture features from the contralateral breasts, respectively. Incorporation of tumor phenotypes with parenchyma texture features into the BANN yielded improved classification performance with an AUC value of 0.83 (SE=0.03) in the task of differentiating malignant from benign lesions. Conclusion: Combining computerized tumor and parenchyma phenotyping was found to significantly improve breast cancer diagnostic accuracy highlighting the need to consider both tumor and stroma in decision making. Funding: University of Chicago Dean Bridge Fund, NCI U24-CA143848-05, P50-CA58223 Breast SPORE program, and Breast Cancer Research Foundation. COI: MLG is a stockholder in R2 technology/Hologic and receives royalties from Hologic, GE Medical Systems, MEDIAN Technologies, Riverain Medical, Mitsubishi, and Toshiba. MLG is a cofounder and stockholder in Quantitative Insights.

60 APPLIED LIFE SCIENCES↗

Cross-Categorical Transfer Learning based Composite Load Protection Modeling

Protection equipment is used to prevent damage to induction motor loads by isolating them from power systems in the event of severe faults. Modeling the response of induction motor loads and their protection is vital for power system planning and operation, especially in understanding system's dynamic performance and stability after a fault occurs. Induction motors are usually equipped with several types of protection with different operation mechanisms, making it challenging to develop adequate yet not overly complex protection models and determine their parameters for aggregate induction motor models. This paper proposes a novel cross-categorical transfer learning based framework to determine protection model parameters for aggregate induction motor loads in commercial buildings. Introducing a mathematical abstraction, the task of determining a suitable set of parameters for the protection model in composite load models is formulated as a combination of feature extraction using transferable layers, followed by affine operations through non-transferable layers applied on the previous extracted features. Numerical results are provided to illustrate the application of the framework.

transfer learning, Stacked Autoencoder, Composite ↗

Review of In Situ Sensing for Directed Energy Deposition for Industrial Part Quality Assessment

As the use additive manufacturing (AM) processes continues to grow in critical industries, improved quality assurance methods are becoming increasingly sought after for qualification and certification of AM components. Traditional nondestructive evaluation of printed components is often unable to supply the required confidence in print quality to justify qualification and certification, but the layer-by-layer nature of AM provides unprecedented opportunities for in situ quality inspection. This document summarizes recent developments in process monitoring research specifically related to Directed Energy Deposition (DED). Particular attention is given to three aspects of the highlighted manuscripts: (1) the type of sensors used, (2) features extracted from each sensor modality, and (3) analysis of extracted features for AM quality assessment. Based on the review of the state-of-the-art, several observations have been made. First, none of the reviewed works have applied their trained models to real part geometries, with many of the works relying on single track experiments, thin-walled structures, and cubes. Similarly, there have not been any works demonstrating model generalizability, i.e., a model trained on data from one build allows for fruitful analysis of data from another build. Many works used machine learning techniques to distinguish different process regimes (i.e., normal, keyholing, lack-of-fusion), but very few papers have investigated stochastic variation in an already “optimized” process. Sensor fusion approaches are also limited in the DED sensing literature, but the few works that have employed such techniques have demonstrated the benefits. Finally, registration of in situ data to the build coordinate system is of paramount importance to producing industrially relevant in situ monitoring systems. Data registration allows direct correlations between process anomalies detected in the process monitoring data to localized departures in part quality, but such techniques are generally lacking in the current literature.

36 MATERIALS SCIENCE↗

Using computer-extracted image features for modeling of error-making patterns in detection of mammographic masses among radiology residents

Purpose: Mammography is the most widely accepted and utilized screening modality for early breast cancer detection. Providing high quality mammography education to radiology trainees is essential, since excellent interpretation skills are needed to ensure the highest benefit of screening mammography for patients. The authors have previously proposed a computer-aided education system based on trainee models. Those models relate human-assessed image characteristics to trainee error. In this study, the authors propose to build trainee models that utilize features automatically extracted from images using computer vision algorithms to predict likelihood of missing each mass by the trainee. This computer vision-based approach to trainee modeling will allow for automatically searching large databases of mammograms in order to identify challenging cases for each trainee. Methods: The authors’ algorithm for predicting the likelihood of missing a mass consists of three steps. First, a mammogram is segmented into air, pectoral muscle, fatty tissue, dense tissue, and mass using automated segmentation algorithms. Second, 43 features are extracted using computer vision algorithms for each abnormality identified by experts. Third, error-making models (classifiers) are applied to predict the likelihood of trainees missing the abnormality based on the extracted features. The models are developed individually for each trainee using his/her previous reading data. The authors evaluated the predictive performance of the proposed algorithm using data from a reader study in which 10 subjects (7 residents and 3 novices) and 3 experts read 100 mammographic cases. Receiver operating characteristic (ROC) methodology was applied for the evaluation. Results: The average area under the ROC curve (AUC) of the error-making models for the task of predicting which masses will be detected and which will be missed was 0.607 (95% CI,0.564-0.650). This value was statistically significantly different from 0.5 (p < 0.0001). For the 7 residents only, the AUC performance of the models was 0.590 (95% CI,0.537-0.642) and was also significantly higher than 0.5 (p = 0.0009). Therefore, generally the authors’ models were able to predict which masses were detected and which were missed better than chance. Conclusions: The authors proposed an algorithm that was able to predict which masses will be detected and which will be missed by each individual trainee. This confirms existence of error-making patterns in the detection of masses among radiology trainees. Furthermore, the proposed methodology will allow for the optimized selection of difficult cases for the trainees in an automatic and efficient manner.

60 APPLIED LIFE SCIENCES↗

Binary classification of items of interest in a repeatable process

A system includes host and learning machines in electrical communication with sensors positioned with respect to an item of interest, e.g., a weld, and memory. The host executes instructions from memory to predict a binary quality status of the item. The learning machine receives signals from the sensor(s), identifies candidate features, and extracts features from the candidates that are more predictive of the binary quality status relative to other candidate features. The learning machine maps the extracted features to a dimensional space that includes most of the items from a passing binary class and excludes all or most of the items from a failing binary class. The host also compares the received signals for a subsequent item of interest to the dimensional space to thereby predict, in real time, the binary quality status of the subsequent item of interest.

97 MATHEMATICS AND COMPUTING↗

DARHT Multi-intelligence Seismic and Acoustic Data Analysis

The purpose of this report is to document the analysis of seismic and acoustic data collected at the Dual-Axis Radiographic Hydrodynamic Test (DARHT) facility at Los Alamos National Laboratory for robust, multi-intelligence decision making. The data utilized herein is obtained from two tri-axial seismic sensors and three acoustic sensors, resulting in a total of nine data channels. The goal of this analysis is to develop a generalized, automated framework to determine internal operations at DARHT using informative features extracted from measurements collected external of the facility. Our framework involves four components: (1) feature extraction, (2) data fusion, (3) classification, and finally (4) robustness analysis. Two approaches are taken for extracting features from the data. The first of these, generic feature extraction, involves extraction of statistical features from the nine data channels. The second approach, event detection, identifies specific events relevant to traffic entering and leaving the facility as well as explosive activities at DARHT and nearby explosive testing sites. Event detection is completed using a two stage method, first utilizing signatures in the frequency domain to identify outliers and second extracting short duration events of interest among these outliers by evaluating residuals of an autoregressive exogenous time series model. Features extracted from each data set are then fused to perform analysis with a multi-intelligence paradigm, where information from multiple data sets are combined to generate more information than available through analysis of each independently. The fused feature set is used to train a statistical classifier and predict the state of operations to inform a decision maker. We demonstrate this classification using both generic statistical features and event detection and provide a comparison of the two methods. Finally, the concept of decision robustness is presented through a preliminary analysis where uncertainty is added to the system through noise in the measurements.

58 GEOSCIENCES↗

Electronic nose with a new feature reduction method and a multi-linear classifier for Chinese liquor classification

An electronic nose (e-nose) was designed to classify Chinese liquors of the same aroma style. A new method of feature reduction which combined feature selection with feature extraction was proposed. Feature selection method used 8 feature-selection algorithms based on information theory and reduced the dimension of the feature space to 41. Kernel entropy component analysis was introduced into the e-nose system as a feature extraction method and the dimension of feature space was reduced to 12. Classification of Chinese liquors was performed by using back propagation artificial neural network (BP-ANN), linear discrimination analysis (LDA), and a multi-linear classifier. The classification rate of the multi-linear classifier was 97.22%, which was higher than LDA and BP-ANN. Finally the classification of Chinese liquors according to their raw materials and geographical origins was performed using the proposed multi-linear classifier and classification rate was 98.75% and 100%, respectively.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

TU-D-207B-03: Early Assessment of Response to Chemoradiotherapy Based On Textural Analysis of Pre and Mid-Treatment FDG-PET Image in Locally Advanced Head and Neck Cancer

Purpose: To evaluate whether tumor textural features extracted from both pre- and mid-treatment FDG-PET images predict early response to chemoradiotherapy in locally advanced head and neck cancer, and investigate whether they provide complementary value to conventional volume-based measurements. Methods: Ninety-four patients with locally advanced head and neck cancers were retrospectively studied. All patients received definitive chemoradiotherapy and underwent FDG-PET planning scans both before and during treatment. Within the primary tumor we extracted 6 textural features based on gray-level co-occurrence matrices (GLCM): entropy, dissimilarity, contrast, correlation, energy, and homogeneity. These image features were evaluated for their predictive power of treatment response to chemoradiotherapy in terms of local recurrence free survival (LRFS) and progression free survival (PFS). Logrank test were used to assess the statistical significance of the stratification between low- and high-risk groups. P-values were adjusted for multiple comparisons by the false discovery rate (FDR) method. Results: All six textural features extracted from pre-treatment PET images significantly differentiated low- and high-risk patient groups for LRFS (P=0.011–0.038) and PFS (P=0.029–0.034). On the other hand, none of the textural features on mid-treatment PET images was statistically significant in stratifying LRFS (P=0.212–0.445) or PFS (P=0.168–0.299). An imaging signature that combines textural feature (GLCM homogeneity) and metabolic tumor volume showed an improved performance for predicting LRFS (hazard ratio: 22.8, P<0.0001) and PFS (hazard ratio: 13.9, P=0.0005) in leave-one-out cross validation. Intra-tumor heterogeneity measured by textural features was significantly lower in mid-treatment PET images than in pre-treatment PET images (T-test: P<1.4e-6). Conclusion: Tumor textural features on pretreatment FDG-PET images are predictive for response to chemoradiotherapy in locally advanced head and neck cancer. The complementary information offered by textural features improves patient stratification and may potentially aid in personalized risk-adaptive therapy.

60 APPLIED LIFE SCIENCES↗

Pre-trained network-based transfer learning: A small-sample machine learning approach to nuclear power plant classification problem

Some research topics belonging to classification problems in the nuclear industry, such as fault diagnosis and accident identification, can be solved by feature extraction and subsequent application of statistical machine learning classifiers. Recently, deep neural network-based methods with automatic feature extraction and high accuracy have gained wide attention. They usually require large-scale training data, however, plant fault or accident data are scarce or difficult to obtain. Here this paper proposes a convolutional network (CNN)-based transfer learning method to solve this problem. The network's shallow layer is derived from a pre-trained CNN based on the ImageNet database to automatically extract features, and the deep layer is customized to match the classification problem. Data in non-image formats are converted to image formats and subsequently used to train the network. Case studies of rotating machines fault diagnosis show that the proposed method requires only limited training data to achieve high accuracy.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

IBEX: An open infrastructure software platform to facilitate collaborative work in radiomics

Purpose: Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. Methods: The IBEX software package was developed using the MATLAB and C/C++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and C/C++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX’s functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Results: Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the IBEX software to be intuitive, powerful, and easy to use. IBEX can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone IBEX and IBEX’s source code can be downloaded. Conclusions: The authors successfully implemented IBEX, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation.

60 APPLIED LIFE SCIENCES↗

Towards intelligent diagnostic system employing integration of mathematical and engineering model

The development of medical diagnostic system has been one of the main research fields during years. The goal of the medical diagnostic system is to place a nosological system that could ease the diagnostic evaluation normally performed by scientists and doctors. Efficient diagnostic evaluation is essentials and requires broad knowledge in order to improve conventional diagnostic system. Several approaches on developing the medical diagnostic system have been designed and tested since the earliest 60s. Attempts on improving their performance have been made which utilizes the fields of artificial intelligence, statistical analyses, mathematical model and engineering theories. With the availability of the microcomputer and software development as well as the promising aforementioned fields, medical diagnostic prototypes could be developed. In general, the medical diagnostic system consists of several stages, namely the 1) data acquisition, 2) feature extraction, 3) feature selection, and 4) classifications stages. Data acquisition stage plays an important role in converting the inputs measured from the real world physical conditions to the digital numeric values that can be manipulated by the computer system. One of the common medical inputs could be medical microscopic images, radiographic images, magnetic resonance image (MRI) as well as medical signals such as electrocardiogram (ECG) and electroencephalogram (EEG). Normally, the scientist or doctors have to deal with myriad of data and redundant to be processed. In order to reduce the complexity of the diagnosis process, only the significant features of the raw data such as peak value of the ECG signal or size of lesion in the mammogram images will be extracted and considered in the subsequent stages. Mathematical models and statistical analyses will be performed to select the most significant features to be classified. The statistical analyses such as principal component analysis and discriminant analysis as well as mathematical model of clustering technique have been widely used in developing the medical diagnostic systems. The selected features will be classified using mathematical models that embedded engineering theory such as artificial intelligence, support vector machine, neural network and fuzzy-neuro system. These classifiers will provide the diagnostic results without human intervention. Among many publishable researches, several prototypes have been developed namely NeuralPap, Neural Mammo, and Cervix Kit. The former system (NeuralPap) is an automatic intelligent diagnostic system for classifying and distinguishing between the normal and cervical cancerous cells. Meanwhile, the Cervix Kit is a portable Field-programmable gate array (FPGA)-based cervical diagnostic kit that could automatically diagnose the cancerous cell based on the images obtained during sampling test. Besides the cervical diagnostic system, the Neural Mammo system is developed to specifically aid the diagnosis of breast cancer using a fine needle aspiration image.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Early Alarm: Robust Event Analysis for Power Systems using 1-D Fully Convolutional Network

This work presents a novel deep learning model for early, accurate, and robust detection, recognition, and temporal localization of multi-type events in large-scale power systems. The proposed method develops a unified 1-D fully convolutional network (FCN) model that takes time series of raw frequency signals measured from a power system as input, extracts distinguishing features, and predicts at every temporal point in the time series if an event is happening and what the type of the event is. Compared to existing methods, the proposed model eliminates the necessity for hand-crafted feature extraction or complicated data pre-processing, can flexibly handle input signals of arbitrary length, and precisely infer the event occurrence time. Most importantly, the model is intentionally trained with incomplete patterns, such that it is more robust to partial features of an event which is common in real-world online recognition, resulting in early alarm for power system failures. Extensive experimental results demonstrate that the proposed method achieves superior performance to the state-of-the-art, and also shows strong robustness to noise and system oscillations.

Li, Chengcheng↗

PHOTOMETRIC SUPERNOVA CLASSIFICATION WITH MACHINE LEARNING

Automated photometric supernova classification has become an active area of research in recent years in light of current and upcoming imaging surveys such as the Dark Energy Survey (DES) and the Large Synoptic Survey Telescope, given that spectroscopic confirmation of type for all supernovae discovered will be impossible. Here, we develop a multi-faceted classification pipeline, combining existing and new approaches. Our pipeline consists of two stages: extracting descriptive features from the light curves and classification using a machine learning algorithm. Our feature extraction methods vary from model-dependent techniques, namely SALT2 fits, to more independent techniques that fit parametric models to curves, to a completely model-independent wavelet approach. We cover a range of representative machine learning algorithms, including naive Bayes, k -nearest neighbors, support vector machines, artificial neural networks, and boosted decision trees (BDTs). We test the pipeline on simulated multi-band DES light curves from the Supernova Photometric Classification Challenge. Using the commonly used area under the curve (AUC) of the Receiver Operating Characteristic as a metric, we find that the SALT2 fits and the wavelet approach, with the BDTs algorithm, each achieve an AUC of 0.98, where 1 represents perfect classification. We find that a representative training set is essential for good classification, whatever the feature set or algorithm, with implications for spectroscopic follow-up. Importantly, we find that by using either the SALT2 or the wavelet feature sets with a BDT algorithm, accurate classification is possible purely from light curve data, without the need for any redshift information.

79 ASTRONOMY AND ASTROPHYSICS↗

Remote visual analysis of large turbulence databases at multiple scales

The remote analysis and visualization of raw large turbulence datasets is challenging. Current accurate direct numerical simulations (DNS) of turbulent flows generate datasets with billions of points per time-step and several thousand time-steps per simulation. Until recently, the analysis and visualization of such datasets was restricted to scientists with access to large supercomputers. The public Johns Hopkins Turbulence database simplifies access to multi-terabyte turbulence datasets and facilitates the computation of statistics and extraction of features through the use of commodity hardware. In this paper, we present a framework designed around wavelet-based compression for high-speed visualization of large datasets and methods supporting multi-resolution analysis of turbulence. By integrating common technologies, this framework enables remote access to tools available on supercomputers and over 230 terabytes of DNS data over the Web. Finally, the database toolset is expanded by providing access to exploratory data analysis tools, such as wavelet decomposition capabilities and coherent feature extraction.

97 MATHEMATICS AND COMPUTING↗

High-frequency combination coding-based steady-state visual evoked potential for brain computer interface

This study presents a new steady-state visual evoked potential (SSVEP) paradigm for brain computer interface (BCI) systems. The goal of this study is to increase the number of targets using fewer stimulation high frequencies, with diminishing subject’s fatigue and reducing the risk of photosensitive epileptic seizures. The new paradigm is High-Frequency Combination Coding-Based High-Frequency Steady-State Visual Evoked Potential (HFCC-SSVEP).Firstly, we studied SSVEP high frequency(beyond 25 Hz)response of SSVEP, whose paradigm is presented on the LED. The SNR (Signal to Noise Ratio) of high frequency(beyond 40 Hz) response is very low, which is been unable to be distinguished through the traditional analysis method; Secondly we investigated the HFCC-SSVEP response (beyond 25 Hz) for 3 frequencies (25Hz, 33.33Hz, and 40Hz), HFCC-SSVEP produces n{sup n} with n high stimulation frequencies through Frequence Combination Code. Further, Animproved Hilbert-huang transform (IHHT)-based variable frequency EEG feature extraction method and a local spectrum extreme target identification algorithmare adopted to extract time-frequency feature of the proposed HFCC-SSVEP response.Linear predictions and fixed sifting (iterating) 10 time is used to overcome the shortage of end effect and stopping criterion,generalized zero-crossing (GZC) is used to compute the instantaneous frequency of the proposed SSVEP respondent signals, the improved HHT-based feature extraction method for the proposed SSVEP paradigm in this study increases recognition efficiency, so as to improve ITR and to increase the stability of the BCI system. what is more, SSVEPs evoked by high-frequency stimuli (beyond 25Hz) minimally diminish subject’s fatigue and prevent safety hazards linked to photo-induced epileptic seizures, So as to ensure the system efficiency and undamaging.This study tests three subjects in order to verify the feasibility of the proposed method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗