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1. BisQue for 3D Materials Science in the Cloud: Microstructure–Property Linkages

   https://doi.org/10.1007/s40192-019-00128-5  

   Latypov, Marat I. ; Khan, Amil ; Lang, Christian A. ; Kvilekval, Kris ; Polonsky, Andrew T. ; Echlin, McLean P. ; Beyerlein, Irene J. ; Manjunath, B. S. ; Pollock, Tresa M. ( March 2019 , Integrating Materials and Manufacturing Innovation)

   Accelerating the design and development of new advanced materials is one of the priorities in modern materials science. These efforts are critically dependent on the development of comprehensive materials cyberinfrastructures which enable efficient data storage, management, sharing, and collaboration as well as integration of computational tools that help establish processing–structure–property relationships. In this contribution, we present implementation of such computational tools into a cloud-based platform called BisQue (Kvilekval et al., Bioinformatics 26(4):554, 2010). We first describe the current state of BisQue as an open-source platform for multidisciplinary research in the cloud and its potential for 3D materials science. We then demonstrate how new computational tools, primarily aimed at processing–structure–property relationships, can be implemented into the system. Specifically, in this work, we develop a module for BisQue that enables microstructure-sensitive predictions of effective yield strength of two-phase materials. Towards this end, we present an implementation of a computationally efficient data-driven model into the BisQue platform. The new module is made available online (web address:https://bisque.ece.ucsb.edu/module_service/Composite_Strength/) and can be used from a web browser without any special software and with minimal computational requirements on the user end. The capabilities of the module for rapid property screening are demonstrated in casemore »studies with two different methodologies based on datasets containing 3D microstructure information from (i) synthetic generation and (ii) sampling large 3D volumes obtained in experiments.

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2. Mining structure–property relationships in polymer nanocomposites using data driven finite element analysis and multi-task convolutional neural networks

   https://doi.org/10.1039/D0ME00020E  

   Wang, Yixing ; Zhang, Min ; Lin, Anqi ; Iyer, Akshay ; Prasad, Aditya Shanker ; Li, Xiaolin ; Zhang, Yichi ; Schadler, Linda S. ; Chen, Wei ; Brinson, L. Catherine ( June 2020 , Molecular Systems Design & Engineering)

   Data-driven methods have attracted increasingly more attention in materials research since the advent of the material genome initiative. The combination of materials science with computer science, statistics, and data-driven methods aims to expediate materials research and applications and can utilize both new and archived research data. In this paper, we present a data driven and deep learning approach that builds a portion of the structure–property relationship for polymer nanocomposites. Analysis of archived experimental data motivates development of a computational model which allows demonstration of the approach and gives flexibility to sufficiently explore a wide range of structures. Taking advantage of microstructure reconstruction methods and finite element simulations, we first explore qualitative relationships between microstructure descriptors and mechanical properties, resulting in new findings regarding the interplay of interphase, volume fraction and dispersion. Then we present a novel deep learning approach that combines convolutional neural networks with multi-task learning for building quantitative correlations between microstructures and property values. The performance of the model is compared with other state-of-the-art strategies including two-point statistics and structure descriptor-based approaches. Lastly, the interpretation of the deep learning model is investigated to show that the model is able to capture physical understandings while learning.
3. A Review of Grain Boundary and Heterointerface Characterization in Polycrystalline Oxides by (Scanning) Transmission Electron Microscopy

   https://doi.org/10.3390/cryst11080878  

   Vahidi, Hasti ; Syed, Komal ; Guo, Huiming ; Wang, Xin ; Wardini, Jenna Laurice ; Martinez, Jenny ; Bowman, William John ( August 2021 , Crystals)

   Interfaces such as grain boundaries (GBs) and heterointerfaces (HIs) are known to play a crucial role in structure-property relationships of polycrystalline materials. While several methods have been used to characterize such interfaces, advanced transmission electron microscopy (TEM) and scanning TEM (STEM) techniques have proven to be uniquely powerful tools, enabling quantification of atomic structure, electronic structure, chemistry, order/disorder, and point defect distributions below the atomic scale. This review focuses on recent progress in characterization of polycrystalline oxide interfaces using S/TEM techniques including imaging, analytical spectroscopies such as energy dispersive X-ray spectroscopy (EDXS) and electron energy-loss spectroscopy (EELS) and scanning diffraction methods such as precession electron nano diffraction (PEND) and 4D-STEM. First, a brief introduction to interfaces, GBs, HIs, and relevant techniques is given. Then, experimental studies which directly correlate GB/HI S/TEM characterization with measured properties of polycrystalline oxides are presented to both strengthen our understanding of these interfaces, and to demonstrate the instrumental capabilities available in the S/TEM. Finally, existing challenges and future development opportunities are discussed. In summary, this article is prepared as a guide for scientists and engineers interested in learning about, and/or using advanced S/TEM techniques to characterize interfaces in polycrystalline materials, particularly ceramic oxides.
4. A Deep Learning-Based Real-time Seizure Detection System

   https://doi.org/10.1109/SPMB50085.2020.9353623  

   Shawki, N. ; Elseify, T. ; Cap, T. ; Shah, V. ; Obeid, I. ; Picone, J. ( December 2020 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, Iyad Selesnick (Ed.)

   Electroencephalography (EEG) is a popular clinical monitoring tool used for diagnosing brain-related disorders such as epilepsy [1]. As monitoring EEGs in a critical-care setting is an expensive and tedious task, there is a great interest in developing real-time EEG monitoring tools to improve patient care quality and efficiency [2]. However, clinicians require automatic seizure detection tools that provide decisions with at least 75% sensitivity and less than 1 false alarm (FA) per 24 hours [3]. Some commercial tools recently claim to reach such performance levels, including the Olympic Brainz Monitor [4] and Persyst 14 [5]. In this abstract, we describe our efforts to transform a high-performance offline seizure detection system [3] into a low latency real-time or online seizure detection system. An overview of the system is shown in Figure 1. The main difference between an online versus offline system is that an online system should always be causal and has minimum latency which is often defined by domain experts. The offline system, shown in Figure 2, uses two phases of deep learning models with postprocessing [3]. The channel-based long short term memory (LSTM) model (Phase 1 or P1) processes linear frequency cepstral coefficients (LFCC) [6] features from each EEGmore »channel separately. We use the hypotheses generated by the P1 model and create additional features that carry information about the detected events and their confidence. The P2 model uses these additional features and the LFCC features to learn the temporal and spatial aspects of the EEG signals using a hybrid convolutional neural network (CNN) and LSTM model. Finally, Phase 3 aggregates the results from both P1 and P2 before applying a final postprocessing step. The online system implements Phase 1 by taking advantage of the Linux piping mechanism, multithreading techniques, and multi-core processors. To convert Phase 1 into an online system, we divide the system into five major modules: signal preprocessor, feature extractor, event decoder, postprocessor, and visualizer. The system reads 0.1-second frames from each EEG channel and sends them to the feature extractor and the visualizer. The feature extractor generates LFCC features in real time from the streaming EEG signal. Next, the system computes seizure and background probabilities using a channel-based LSTM model and applies a postprocessor to aggregate the detected events across channels. The system then displays the EEG signal and the decisions simultaneously using a visualization module. The online system uses C++, Python, TensorFlow, and PyQtGraph in its implementation. The online system accepts streamed EEG data sampled at 250 Hz as input. The system begins processing the EEG signal by applying a TCP montage [8]. Depending on the type of the montage, the EEG signal can have either 22 or 20 channels. To enable the online operation, we send 0.1-second (25 samples) length frames from each channel of the streamed EEG signal to the feature extractor and the visualizer. Feature extraction is performed sequentially on each channel. The signal preprocessor writes the sample frames into two streams to facilitate these modules. In the first stream, the feature extractor receives the signals using stdin. In parallel, as a second stream, the visualizer shares a user-defined file with the signal preprocessor. This user-defined file holds raw signal information as a buffer for the visualizer. The signal preprocessor writes into the file while the visualizer reads from it. Reading and writing into the same file poses a challenge. The visualizer can start reading while the signal preprocessor is writing into it. To resolve this issue, we utilize a file locking mechanism in the signal preprocessor and visualizer. Each of the processes temporarily locks the file, performs its operation, releases the lock, and tries to obtain the lock after a waiting period. The file locking mechanism ensures that only one process can access the file by prohibiting other processes from reading or writing while one process is modifying the file [9]. The feature extractor uses circular buffers to save 0.3 seconds or 75 samples from each channel for extracting 0.2-second or 50-sample long center-aligned windows. The module generates 8 absolute LFCC features where the zeroth cepstral coefficient is replaced by a temporal domain energy term. For extracting the rest of the features, three pipelines are used. The differential energy feature is calculated in a 0.9-second absolute feature window with a frame size of 0.1 seconds. The difference between the maximum and minimum temporal energy terms is calculated in this range. Then, the first derivative or the delta features are calculated using another 0.9-second window. Finally, the second derivative or delta-delta features are calculated using a 0.3-second window [6]. The differential energy for the delta-delta features is not included. In total, we extract 26 features from the raw sample windows which add 1.1 seconds of delay to the system. We used the Temple University Hospital Seizure Database (TUSZ) v1.2.1 for developing the online system [10]. The statistics for this dataset are shown in Table 1. A channel-based LSTM model was trained using the features derived from the train set using the online feature extractor module. A window-based normalization technique was applied to those features. In the offline model, we scale features by normalizing using the maximum absolute value of a channel [11] before applying a sliding window approach. Since the online system has access to a limited amount of data, we normalize based on the observed window. The model uses the feature vectors with a frame size of 1 second and a window size of 7 seconds. We evaluated the model using the offline P1 postprocessor to determine the efficacy of the delayed features and the window-based normalization technique. As shown by the results of experiments 1 and 4 in Table 2, these changes give us a comparable performance to the offline model. The online event decoder module utilizes this trained model for computing probabilities for the seizure and background classes. These posteriors are then postprocessed to remove spurious detections. The online postprocessor receives and saves 8 seconds of class posteriors in a buffer for further processing. It applies multiple heuristic filters (e.g., probability threshold) to make an overall decision by combining events across the channels. These filters evaluate the average confidence, the duration of a seizure, and the channels where the seizures were observed. The postprocessor delivers the label and confidence to the visualizer. The visualizer starts to display the signal as soon as it gets access to the signal file, as shown in Figure 1 using the “Signal File” and “Visualizer” blocks. Once the visualizer receives the label and confidence for the latest epoch from the postprocessor, it overlays the decision and color codes that epoch. The visualizer uses red for seizure with the label SEIZ and green for the background class with the label BCKG. Once the streaming finishes, the system saves three files: a signal file in which the sample frames are saved in the order they were streamed, a time segmented event (TSE) file with the overall decisions and confidences, and a hypotheses (HYP) file that saves the label and confidence for each epoch. The user can plot the signal and decisions using the signal and HYP files with only the visualizer by enabling appropriate options. For comparing the performance of different stages of development, we used the test set of TUSZ v1.2.1 database. It contains 1015 EEG records of varying duration. The any-overlap performance [12] of the overall system shown in Figure 2 is 40.29% sensitivity with 5.77 FAs per 24 hours. For comparison, the previous state-of-the-art model developed on this database performed at 30.71% sensitivity with 6.77 FAs per 24 hours [3]. The individual performances of the deep learning phases are as follows: Phase 1’s (P1) performance is 39.46% sensitivity and 11.62 FAs per 24 hours, and Phase 2 detects seizures with 41.16% sensitivity and 11.69 FAs per 24 hours. We trained an LSTM model with the delayed features and the window-based normalization technique for developing the online system. Using the offline decoder and postprocessor, the model performed at 36.23% sensitivity with 9.52 FAs per 24 hours. The trained model was then evaluated with the online modules. The current performance of the overall online system is 45.80% sensitivity with 28.14 FAs per 24 hours. Table 2 summarizes the performances of these systems. The performance of the online system deviates from the offline P1 model because the online postprocessor fails to combine the events as the seizure probability fluctuates during an event. The modules in the online system add a total of 11.1 seconds of delay for processing each second of the data, as shown in Figure 3. In practice, we also count the time for loading the model and starting the visualizer block. When we consider these facts, the system consumes 15 seconds to display the first hypothesis. The system detects seizure onsets with an average latency of 15 seconds. Implementing an automatic seizure detection model in real time is not trivial. We used a variety of techniques such as the file locking mechanism, multithreading, circular buffers, real-time event decoding, and signal-decision plotting to realize the system. A video demonstrating the system is available at: https://www.isip.piconepress.com/projects/nsf_pfi_tt/resources/videos/realtime_eeg_analysis/v2.5.1/video_2.5.1.mp4. The final conference submission will include a more detailed analysis of the online performance of each module. ACKNOWLEDGMENTS Research reported in this publication was most recently supported by the National Science Foundation Partnership for Innovation award number IIP-1827565 and the Pennsylvania Commonwealth Universal Research Enhancement Program (PA CURE). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the official views of any of these organizations. REFERENCES [1] A. Craik, Y. He, and J. L. Contreras-Vidal, “Deep learning for electroencephalogram (EEG) classification tasks: a review,” J. Neural Eng., vol. 16, no. 3, p. 031001, 2019. https://doi.org/10.1088/1741-2552/ab0ab5. [2] A. C. Bridi, T. Q. Louro, and R. C. L. Da Silva, “Clinical Alarms in intensive care: implications of alarm fatigue for the safety of patients,” Rev. Lat. Am. Enfermagem, vol. 22, no. 6, p. 1034, 2014. https://doi.org/10.1590/0104-1169.3488.2513. [3] M. Golmohammadi, V. Shah, I. Obeid, and J. Picone, “Deep Learning Approaches for Automatic Seizure Detection from Scalp Electroencephalograms,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York, New York, USA: Springer, 2020, pp. 233–274. https://doi.org/10.1007/978-3-030-36844-9_8. [4] “CFM Olympic Brainz Monitor.” [Online]. Available: https://newborncare.natus.com/products-services/newborn-care-products/newborn-brain-injury/cfm-olympic-brainz-monitor. [Accessed: 17-Jul-2020]. [5] M. L. Scheuer, S. B. Wilson, A. Antony, G. Ghearing, A. Urban, and A. I. Bagic, “Seizure Detection: Interreader Agreement and Detection Algorithm Assessments Using a Large Dataset,” J. Clin. Neurophysiol., 2020. https://doi.org/10.1097/WNP.0000000000000709. [6] A. Harati, M. Golmohammadi, S. Lopez, I. Obeid, and J. Picone, “Improved EEG Event Classification Using Differential Energy,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium, 2015, pp. 1–4. https://doi.org/10.1109/SPMB.2015.7405421. [7] V. Shah, C. Campbell, I. Obeid, and J. Picone, “Improved Spatio-Temporal Modeling in Automated Seizure Detection using Channel-Dependent Posteriors,” Neurocomputing, 2021. [8] W. Tatum, A. Husain, S. Benbadis, and P. Kaplan, Handbook of EEG Interpretation. New York City, New York, USA: Demos Medical Publishing, 2007. [9] D. P. Bovet and C. Marco, Understanding the Linux Kernel, 3rd ed. O’Reilly Media, Inc., 2005. https://www.oreilly.com/library/view/understanding-the-linux/0596005652/. [10] V. Shah et al., “The Temple University Hospital Seizure Detection Corpus,” Front. Neuroinform., vol. 12, pp. 1–6, 2018. https://doi.org/10.3389/fninf.2018.00083. [11] F. Pedregosa et al., “Scikit-learn: Machine Learning in Python,” J. Mach. Learn. Res., vol. 12, pp. 2825–2830, 2011. https://dl.acm.org/doi/10.5555/1953048.2078195. [12] J. Gotman, D. Flanagan, J. Zhang, and B. Rosenblatt, “Automatic seizure detection in the newborn: Methods and initial evaluation,” Electroencephalogr. Clin. Neurophysiol., vol. 103, no. 3, pp. 356–362, 1997. https://doi.org/10.1016/S0013-4694(97)00003-9.« less
5. PRECISE 3D STRUCTURING OF POLYMER NANOCOMPOSITES USING TRIAXIAL MAGNETIC FIELDS

   Atescan, Yagmur ; Yamamoto, Namiko. ( January 2019 , Composites)

   Polymer nanocomposites have been sought after for their light weight, high performance (strength-to-mass ratio, renewability, etc.), and multi-functionality (actuation, sensing, protection against lightning strikes, etc.). Nano-/micro-engineering has achieved such advanced properties by controlling crystallinity, phases, and interfaces/interphases; hierarchical structuring, often bio-inspired, has been also implemented. While driven by the advanced properties of nanofillers, properties of polymer nanocomposites are critically affected by their structuring and interfaces/interphases due to their small size (< ~50 nm) and large surface area per volume. Measures of their property improvement by nanofiller addition are often smaller than theoretically predicted. Currently, application of these novel engineered materials is limited because these materials cannot often be made in large sizes without compromising nano-scale organization, and because their multi-scale structure-property relationships are not well understood. In this work, we study precise and fast nanofiller structuring with non-contact and energy-efficient application of oscillating magnetic fields. Magnetic assembly is a promising, scalable method to deliver bulk amount of nanocomposites while maintaining organized nanofiller structure throughout the composite volume. In the past, we have demonstrated controlled alignment of nanofillers with tunable inter-assembly distances with application of oscillating one-dimentional magnetic fields (~100s of G), by taking advantage of both magnetic attraction and repulsion.more »The low oscillation frequency (< 1 Hz) was tuned to achieve maghemite nanofiller alignment patterns, in an epoxy matrix, with different amount of inter-nanofiller contacts with the same nanofiller volume fraction (see Figure 1a). This work was recently expanded to three-dimensional assembly using a triaxial Helmholtz coil system (see Figure 1b); the system can apply the triaxial magnetic fields of varying magnitude (max. ±300G, ±250G, ±180G (x-y-z)) and frequency (0 to 1 Hz, ~0.1 Hz resolution) with controlled phase delay to the sample size of 1.5” x 2.5” x 3.5”(x-y-z). Two model systems are currently studied: maghemite nanofillers in an elastomer for magnetoactuation, and nickel-coated CNTs in an thermoset for mehcniacl and transport property reinforcement. The assembled nanofiller structures are currently characterized by microCT; microCT scan data (see Figure 1b) are segmented through a machine learning algorithm, and will be modeled for their transport properties using a Monte Carlo method. These estimated properties will be compared with the experimentally characterized mechanical, transport, and actuation properties, providing the structure-interphase-property relationships. In future, we plan to integrate these nanocomposites to CFRPs for interlaminar property reinforcement, possibly with an out-of-autoclave composite processing.« less