More Like this

1. Correcting for filter-based aerosol light absorption biases at the Atmospheric Radiation Measurement program's Southern Great Plains site using photoacoustic measurements and machine learning

   https://doi.org/10.5194/amt-15-4569-2022  

   Kumar, Joshin ; Paik, Theo ; Shetty, Nishit J. ; Sheridan, Patrick ; Aiken, Allison C. ; Dubey, Manvendra K. ; Chakrabarty, Rajan K. ( January 2022 , Atmospheric Measurement Techniques)

   Abstract. Measurement of light absorption of solar radiation byaerosols is vital for assessing direct aerosol radiative forcing, whichaffects local and global climate. Low-cost and easy-to-operate filter-basedinstruments, such as the Particle Soot Absorption Photometer (PSAP), that collect aerosols on a filter and measure light attenuation through thefilter are widely used to infer aerosol light absorption. However,filter-based absorption measurements are subject to artifacts that aredifficult to quantify. These artifacts are associated with the presence ofthe filter medium and the complex interactions between the filter fibers and accumulated aerosols. Various correction algorithms have been introduced to correct for the filter-based absorption coefficient measurements toward predicting the particle-phase absorption coefficient (Babs). However, the inability of these algorithms to incorporate into their formulations the complex matrix of influencing parameters such as particle asymmetry parameter, particle size, and particle penetration depth results in prediction of particle-phase absorption coefficients with relatively low accuracy. The analytical forms of corrections also suffer from a lack of universal applicability: different corrections are required for rural andurban sites across the world. In this study, we analyzed and compared 3 months of high-time-resolution ambient aerosol absorption data collectedsynchronously using a three-wavelength photoacoustic absorption spectrometer (PASS) and PSAP. Both instruments were operated on the same sampling inletat the Department of Energy's Atmospheric Radiation Measurement program's Southern Great Plains (SGP) user facility in Oklahoma. We implemented the two mostcommonly used analytical correction algorithms, namely, Virkkula (2010) and the average of Virkkula (2010) and Ogren (2010)–Bond et al. (1999) as well as a random forest regression (RFR) machine learning algorithm to predict Babs values from the PSAP's filter-based measurements. The predicted Babs was compared against the reference Babs measured by the PASS. The RFR algorithm performed the best by yielding the lowest root mean squareerror of prediction. The algorithm was trained using input datasets from the PSAP (transmission and uncorrected absorption coefficient), a co-locatednephelometer (scattering coefficients), and the Aerosol Chemical Speciation Monitor (mass concentration of non-refractory aerosol particles). A revisedform of the Virkkula (2010) algorithm suitable for the SGP site has beenproposed; however, its performance yields approximately 2-fold errors when compared to the RFR algorithm. To generalize the accuracy and applicabilityof our proposed RFR algorithm, we trained and tested it on a dataset oflaboratory measurements of combustion aerosols. Input variables to thealgorithm included the aerosol number size distribution from the Scanning Mobility Particle Sizer, absorption coefficients from the filter-basedTricolor Absorption Photometer, and scattering coefficients from amultiwavelength nephelometer. The RFR algorithm predicted Babs values within 5 % of the reference Babs measured by the multiwavelength PASS during the laboratory experiments. Thus, we show that machine learningapproaches offer a promising path to correct for biases in long-termfilter-based absorption datasets and accurately quantify their variabilityand trends needed for robust radiative forcing determination. 

   more » « less
2. A fast asynchronous Markov chain Monte Carlo sampler for sparse Bayesian inference

   https://doi.org/10.1093/jrsssb/qkad078  

   Atchadé, Yves ; Wang, Liwei ( September 2023 , Journal of the Royal Statistical Society Series B: Statistical Methodology)

   We propose a very fast approximate Markov chain Monte Carlo sampling framework that is applicable to a large class of sparse Bayesian inference problems. The computational cost per iteration in several regression models is of order O(n(s+J)), where n is the sample size, s is the underlying sparsity of the model, and J is the size of a randomly selected subset of regressors. This cost can be further reduced by data sub-sampling when stochastic gradient Langevin dynamics are employed. The algorithm is an extension of the asynchronous Gibbs sampler of Johnson et al. [(2013). Analyzing Hogwild parallel Gaussian Gibbs sampling. In Proceedings of the 26th International Conference on Neural Information Processing Systems (NIPS’13) (Vol. 2, pp. 2715–2723)], but can be viewed from a statistical perspective as a form of Bayesian iterated sure independent screening [Fan, J., Samworth, R., & Wu, Y. (2009). Ultrahigh dimensional feature selection: Beyond the linear model. Journal of Machine Learning Research, 10, 2013–2038]. We show that in high-dimensional linear regression problems, the Markov chain generated by the proposed algorithm admits an invariant distribution that recovers correctly the main signal with high probability under some statistical assumptions. Furthermore, we show that its mixing time is at most linear in the number of regressors. We illustrate the algorithm with several models.

    

   more » « less
3. A causality-based learning approach for discovering the underlying dynamics of complex systems from partial observations with stochastic parameterization

   https://doi.org/10.1016/j.physd.2023.133743  

   Chen, Nan ; Zhang, Yinling ( July 2023 , Physica D: Nonlinear Phenomena)

   Discovering the underlying dynamics of complex systems from data is an important practical topic. Constrained optimization algorithms are widely utilized and lead to many successes. Yet, such purely data-driven methods may bring about incorrect physics in the presence of random noise and cannot easily handle the situation with incomplete data. In this paper, a new iterative learning algorithm for complex turbulent systems with partial observations is developed that alternates between identifying model structures, recovering unobserved variables, and estimating parameters. First, a causality-based learning approach is utilized for the sparse identification of model structures, which takes into account certain physics knowledge that is pre-learned from data. It has unique advantages in coping with indirect coupling between features and is robust to stochastic noise. A practical algorithm is designed to facilitate causal inference for high-dimensional systems. Next, a systematic nonlinear stochastic parameterization is built to characterize the time evolution of the unobserved variables. Closed analytic formula via efficient nonlinear data assimilation is exploited to sample the trajectories of the unobserved variables, which are then treated as synthetic observations to advance a rapid parameter estimation. Furthermore, the localization of the state variable dependence and the physics constraints are incorporated into the learning procedure. This mitigates the curse of dimensionality and prevents the finite time blow-up issue. Numerical experiments show that the new algorithm identifies the model structure and provides suitable stochastic parameterizations for many complex nonlinear systems with chaotic dynamics, spatiotemporal multiscale structures, intermittency, and extreme events. 

   more » « less
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 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. 

   more » « less
5. Combining Stochastic Parameterized Reduced‐Order Models With Machine Learning for Data Assimilation and Uncertainty Quantification With Partial Observations

   https://doi.org/10.1029/2022MS003597  

   Mou, Changhong ; Smith, Leslie M. ; Chen, Nan ( October 2023 , Journal of Advances in Modeling Earth Systems)

   A hybrid data assimilation algorithm is developed for complex dynamical systems with partial observations. The method starts with applying a spectral decomposition to the entire spatiotemporal fields, followed by creating a machine learning model that builds a nonlinear map between the coefficients of observed and unobserved state variables for each spectral mode. A cheap low‐order nonlinear stochastic parameterized extended Kalman filter (SPEKF) model is employed as the forecast model in the ensemble Kalman filter to deal with each mode associated with the observed variables. The resulting ensemble members are then fed into the machine learning model to create an ensemble of the corresponding unobserved variables. In addition to the ensemble spread, the training residual in the machine learning‐induced nonlinear map is further incorporated into the state estimation, advancing the diagnostic quantification of the posterior uncertainty. The hybrid data assimilation algorithm is applied to a precipitating quasi‐geostrophic (PQG) model, which includes the effects of water vapor, clouds, and rainfall beyond the classical two‐level QG model. The complicated nonlinearities in the PQG equations prevent traditional methods from building simple and accurate reduced‐order forecast models. In contrast, the SPEKF forecast model is skillful in recovering the intermittent observed states, and the machine learning model effectively estimates the chaotic unobserved signals. Utilizing the calibrated SPEKF and machine learning models under a moderate cloud fraction, the resulting hybrid data assimilation remains reasonably accurate when applied to other geophysical scenarios with nearly clear skies or relatively heavy rainfall, implying the robustness of the algorithm for extrapolation.

    

   more » « less