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1. A Coupled SWAT-AEM Modelling Framework for a Comprehensive Hydrologic Assessment

   https://doi.org/10.3390/w14172753  

   Sangeetha, K. ; Narasimhan, Balaji ; Srinivasan, R. ( September 2022 , Water)

   This study attempts to integrate a Surface Water (SW) model Soil and Water Assessment Tool (SWAT) with an existing steady-state, single layer, unconfined heterogeneous aquifer Analytic Element Method (AEM) based Ground Water (GW) model, named Bluebird AEM engine, for a comprehensive assessment of SW and GW resources and its management. The main reason for integrating SWAT with the GW model is that the SWAT model does not simulate the distribution and dynamics of GW levels and recharge rates. To overcome this issue, often the SWAT model is coupled with the numerical GW model (either using MODFLOW or FEFLOW), wherein the spatial and temporal patterns of the interactions are better captured and assessed. However, the major drawback in integrating the two models (SWAT with—MODFLOW/FEM) is its conversion from Hydrological Response Unit’s (HRU)/sub-basins to grid/elements. To couple them, a spatial translation system is necessary to move the inputs and outputs back and forth between the two models due to the difference in discretization. Hence, for effective coupling of SW and GW models, it may be desirable to have both models with a similar spatial discretization and reduce the need for rigorous numerical techniques for solving the PDEs. The objective of this paper is to test the proof of concept of integrating a distributed hydrologic model with an AEM model at the same spatial units, primarily focused on surface water and groundwater interaction with a shallow unconfined aquifer. Analytic Element Method (AEM) based GW models seem to be ideal for coupling with SWAT due to their innate character to consider the HRU, sub-basin, River, and lake boundaries as individual analytic elements directly without the need for any further discretization or modeling units. This study explores the spatio-temporal patterns of groundwater (GW) discharge rates to a river system in a moist-sub humid region with SWAT-AEM applied to the San Jacinto River basin (SJRB) in Texas. The SW-GW interactions are explored throughout the watershed from 2000–2017 using the integrated SWAT-AEM model, which is tested against stream flow and GW levels. The integrated SWAT-AEM model results show good improvement in predicting the stream flow (R2 = 0.65–0.80) and GW levels as compared to the standalone SWAT model. Further, the integrated model predicted the low flows better compared to the standalone SWAT model, thus accounting for the SW-GW interactions. Almost 80% of the stream network experiences an increase in groundwater discharge rate between 2000 and 2017 with an annual average GW discharge rate of 1853 Mm3/year. The result from the study seems promising for potential applications of SWAT-AEM coupling in regions with considerable SW-GW interactions. 

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2. A salinity module for SWAT to simulate salt ion fate and transport at the watershed scale

   https://doi.org/10.5194/hess-23-3155-2019  

   Bailey, Ryan T. ; Tavakoli-Kivi, Saman ; Wei, Xiaolu ( January 2019 , Hydrology and Earth System Sciences)

   Abstract. Salinity is one of the most common water quality threats in riverbasins and irrigated regions worldwide. However, no available numericalmodels simulate all major processes affecting salt ion fate and transport at the watershed scale. This study presents a new salinity module for the SWAT model that simulates the fate and transport of eight major salt ions(SO42-, Ca2+, Mg2+, Na+, K+, Cl−,CO32-, HCO3-) in a watershed system. The module accountsfor salt transport in surface runoff, soil percolation, lateral flow,groundwater, and streams, and equilibrium chemistry reactions in soil layersand the aquifer. The module consists of several new subroutines that areimbedded within the SWAT modelling code and one input file containing soilsalinity and aquifer salinity data for the watershed. The model is appliedto a 732 km2 salinity-impaired irrigated region within the ArkansasRiver Valley in southeastern Colorado and tested against root zone soilsalinity, groundwater salt ion concentration, groundwater salt loadings tothe river network, and in-stream salt ion concentration. The model can be auseful tool in simulating baseline salinity transport and investigatingsalinity best management practices in watersheds of varying spatial scales. 

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3. A Race Against Time: Modeling Time Lags in Watershed Response

   https://doi.org/10.1029/2018WR023815  

   Ilampooranan, Idhayachandhiran ; Van Meter, K. J. ; Basu, Nandita B. ( May 2019 , Water Resources Research)

   Land use change and agricultural intensification have increased food production but at the cost of polluting surface and groundwater. Best management practices implemented to improve water quality have met with limited success. Such lack of success is increasingly attributed to legacy nutrient stores in the subsurface that may act as sources after reduction of external inputs. However, current water‐quality models lack a framework to capture these legacy effects. Here we have modified the SWAT (Soil Water Assessment Tool) model to capture the effects of nitrogen (N) legacies on water quality under multiple land‐management scenarios. Our new SWAT‐LAG model includes (1) a modified carbon‐nitrogen cycling module to capture the dynamics of soil N accumulation, and (2) a groundwater travel time distribution module to capture a range of subsurface travel times. Using a 502‐km²Iowa watershed as a case study, we found that between 1950 and 2016, 25% of the total watershed N surplus (N Deposition + Fertilizer + Manure + N Fixation − Crop N uptake) had accumulated within the root zone, 14% had accumulated in groundwater, while 27% was lost as riverine output, and 34% was denitrified. In future scenarios, a 100% reduction in fertilizer application led to a 79% reduction in stream N load, but the SWAT‐LAG results suggest that it would take 84 years to achieve this reduction, in contrast to the 2 years predicted in the original SWAT model. The framework proposed here constitutes a first step toward modifying a widely used modeling approach to assess the effects of legacy N on the time required to achieve water‐quality goals.

    

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4. Impacts of Land Cover Change on the Spatial Distribution of Nonpoint Source Pollution Based on SWAT Model

   https://doi.org/10.3390/w15061174  

   Zhang, Zeshu ; Montas, Hubert ; Shirmohammadi, Adel ; Leisnham, Paul T. ; Negahban-Azar, Masoud ( March 2023 , Water)

   Nonpoint source (NPS) pollution is a pressing issue worldwide, especially in the Chesapeake Bay, where sediment, nitrogen (N), and phosphorus (P) are the most critical water quality concerns. Despite significant efforts by federal, state, and local governments, the improvement in water quality has been limited. Investigating the spatial distribution of NPS hotspots can help understand NPS pollutant output and guide control measures. We hypothesize that as land cover changes from natural (e.g., forestland) and agricultural to suburban and ultra-urban, the distribution of NPS pollution source areas becomes increasingly spatially uniform. To test this hypothesis, we analyzed three real watersheds with varying land cover (Greensboro watershed for agriculture, Watts Branch watershed for suburban, and Watershed 263 for ultra-urban) and three synthetic watersheds developed based on the Watts Branch watershed, which ranged from forested and agricultural to ultra-urban but had the same soil, slope, and weather conditions. The Soil and Water Assessment Tool (SWAT) was selected as a phenomenological model for the analysis, and SWAT-CUP was used for model calibration and validation. The hydrologic responses of the three real and synthetic watersheds were simulated over ten years (1993–2002 or 2002–2011), and calibration and validation results indicated that SWAT could properly predict the export of runoff and three target NPS pollution constituents (sediment, total nitrogen, and total phosphorus). The results showed that the distribution of NPS pollutant outputs becomes increasingly uniform as land cover changes from agriculture to ultra-urban across watersheds. This research suggests that the spatial distribution of NPS pollution source areas is a function of the major land cover category of study watersheds, and control strategies should be adapted accordingly. If NPS pollution is distributed unevenly across a watershed, hotspot areas output a disproportionate amount of pollution and require more targeted and intensive control measures. Conversely, if the distribution of NPS pollution is more uniform across a watershed, the control strategies need to be more widespread and encompass a larger area. 

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5. 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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