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1. 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 EEG 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. 

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2. Assessing the Physical Realism of Deep Learning Hydrologic Model Projections Under Climate Change

   https://doi.org/10.1029/2022WR032123  

   Wi, Sungwook ; Steinschneider, Scott ( September 2022 , Water Resources Research)

   This study examines whether deep learning models can produce reliable future projections of streamflow under warming. We train a regional long short‐term memory network (LSTM) to daily streamflow in 15 watersheds in California and develop three process models (HYMOD, SAC‐SMA, and VIC) as benchmarks. We force all models with scenarios of warming and assess their hydrologic response, including shifts in the hydrograph and total runoff ratio. All process models show a shift to more winter runoff, reduced summer runoff, and a decline in the runoff ratio due to increased evapotranspiration. The LSTM predicts similar hydrograph shifts but in some watersheds predicts an unrealistic increase in the runoff ratio. We then test two alternative versions of the LSTM in which process model outputs are used as either additional training targets (i.e., multi‐output LSTM) or input features. Results indicate that the multi‐output LSTM does not correct the unrealistic streamflow projections under warming. The hybrid LSTM using estimates of evapotranspiration from SAC‐SMA as an additional input feature produces more realistic streamflow projections, but this does not hold for VIC or HYMOD. This suggests that the hybrid method depends on the fidelity of the process model. Finally, we test climate change responses under an LSTM trained to over 500 watersheds across the United States and find more realistic streamflow projections under warming. Ultimately, this work suggests that hybrid modeling may support the use of LSTMs for hydrologic projections under climate change, but so may training LSTMs to a large, diverse set of watersheds.

    

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3. Meta-learning biologically plausible plasticity rules with random feedback pathways

   https://doi.org/10.1038/s41467-023-37562-1  

   Shervani-Tabar, Navid ; Rosenbaum, Robert ( March 2023 , Nature Communications)

   Backpropagation is widely used to train artificial neural networks, but its relationship to synaptic plasticity in the brain is unknown. Some biological models of backpropagation rely on feedback projections that are symmetric with feedforward connections, but experiments do not corroborate the existence of such symmetric backward connectivity. Random feedback alignment offers an alternative model in which errors are propagated backward through fixed, random backward connections. This approach successfully trains shallow models, but learns slowly and does not perform well with deeper models or online learning. In this study, we develop a meta-learning approach to discover interpretable, biologically plausible plasticity rules that improve online learning performance with fixed random feedback connections. The resulting plasticity rules show improved online training of deep models in the low data regime. Our results highlight the potential of meta-learning to discover effective, interpretable learning rules satisfying biological constraints.

    

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4. Predicting Water Temperature Dynamics of Unmonitored Lakes With Meta‐Transfer Learning

   https://doi.org/10.1029/2021WR029579  

   Willard, Jared D. ; Read, Jordan S. ; Appling, Alison P. ; Oliver, Samantha K. ; Jia, Xiaowei ; Kumar, Vipin ( June 2021 , Water Resources Research)

   Most environmental data come from a minority of well‐monitored sites. An ongoing challenge in the environmental sciences is transferring knowledge from monitored sites to unmonitored sites. Here, we demonstrate a novel transfer‐learning framework that accurately predicts depth‐specific temperature in unmonitored lakes (targets) by borrowing models from well‐monitored lakes (sources). This method, meta‐transfer learning (MTL), builds a meta‐learning model to predict transfer performance from candidate source models to targets using lake attributes and candidates' past performance. We constructed source models at 145 well‐monitored lakes using calibrated process‐based (PB) modeling and a recently developed approach called process‐guided deep learning (PGDL). We applied MTL to either PB or PGDL source models (PB‐MTL or PGDL‐MTL, respectively) to predict temperatures in 305 target lakes treated as unmonitored in the Upper Midwestern United States. We show significantly improved performance relative to the uncalibrated PB General Lake Model, where the median root mean squared error (RMSE) for the target lakes is 2.52°C. PB‐MTL yielded a median RMSE of 2.43°C; PGDL‐MTL yielded 2.16°C; and a PGDL‐MTL ensemble of nine sources per target yielded 1.88°C. For sparsely monitored target lakes, PGDL‐MTL often outperformed PGDL models trained on the target lakes themselves. Differences in maximum depth between the source and target were consistently the most important predictors. Our approach readily scales to thousands of lakes in the Midwestern United States, demonstrating that MTL with meaningful predictor variables and high‐quality source models is a promising approach for many kinds of unmonitored systems and environmental variables.

    

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5. Exploring the exceptional performance of a deep learning stream temperature model and the value of streamflow data

   https://doi.org/10.1088/1748-9326/abd501  

   Rahmani, Farshid ; Lawson, Kathryn ; Ouyang, Wenyu ; Appling, Alison ; Oliver, Samantha ; Shen, Chaopeng ( December 2020 , Environmental Research Letters)

   null (Ed.)

   Stream water temperature (Ts) is a variable of critical importance for aquatic ecosystem health. Ts is strongly affected by groundwater-surface water interactions which can be learned from streamflow records, but previously such information was challenging to effectively absorb with process-based models due to parameter equifinality. Based on the long short-term memory (LSTM) deep learning architecture, we developed a basin-centric lumped daily mean Ts model, which was trained over 118 data-rich basins with no major dams in the conterminous United States, and showed strong results. At a national scale, we obtained a median root-mean-square error (RMSE) of 0.69oC, Nash-Sutcliffe model efficiency coefficient (NSE) of 0.985, and correlation of 0.994, which are marked improvements over previous values reported in literature. The addition of streamflow observations as a model input strongly elevated the performance of this model. In the absence of measured streamflow, we showed that a two-stage model can be used where simulated streamflow from a pre-trained LSTM model (Qsim) still benefits the Ts model, even though no new information was brought directly in the inputs of the Ts model; the model indirectly used information learned from streamflow observations provided during the training of Qsim, potentially to improve internal representation of physically meaningful variables. Our results indicate that strong relationships exist between basin-averaged forcing variables, catchment attributes, and Ts that can be simulated by a single model trained by data on the continental scale. 

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