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1. Feature-Wise Bias Amplification

   Leino, Klas ; Fredrikson, Matt ; Black, Emily ; Sen, Shayak ; Datta, Anupam ( January 2019 , International Conference on Learning Representations (ICLR))

   We study the phenomenon of bias amplification in classifiers, wherein a machine learning model learns to predict classes with a greater disparity than the underlying ground truth. We demonstrate that bias amplification can arise via inductive bias in gradient descent methods resulting in overestimation of importance of moderately-predictive weak'' features if insufficient training data is available. This overestimation gives rise to feature-wise bias amplification -- a previously unreported form of bias that can be traced back to the features of a trained model. Through analysis and experiments, we show that the while some bias cannot be mitigated without sacrificing accuracy, feature-wise bias amplification can be mitigated through targeted feature selection. We present two new feature selection algorithms for mitigating bias amplification in linear models, and show how they can be adapted to convolutional neural networks efficiently. Our experiments on synthetic and real data demonstrate that these algorithms consistently lead to reduced bias without harming accuracy, in some cases eliminating predictive bias altogether while providing modest gains in accuracy. 

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2. 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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3. Experimental Study of Machine Learning based Malware Detection Systems’ Practical Utility

   Li, Yuping ; Caragea, Doina ; Hall, Lawrence ; Ou, Xinming ( January 2020 , HICSS SYMPOSIUM ON CYBERSECURITY BIG DATA ANALYTICS)

   Thanks to the numerous machine learning based malware detection (MLMD) research in recent years and the readily available online malware scanning system (e.g., VirusTotal), it becomes relatively easy to build a seemingly successful MLMD system using the following standard procedure: first prepare a set of ground truth data by checking with VirusTotal, then extract features from training dataset and build a machine learning detection model, and finally evaluate the model with a disjoint testing dataset. We argue that such evaluation methods do not expose the real utility of ML based malware detection in practice since the ML model is both built and tested on malware that are known at the time of training. The user could simply run them through VirusTotal just as how the researchers obtained the ground truth, instead of using the more sophisticated ML approach. However, ML based malware detection has the potential of identifying malware that has not been known at the time of training, which is the real value ML brings to this problem. We present experimentation study on how well a machine learning based malware detection system can achieve this. Our experiments showed that MLMD can consistently generate previously unknown malware knowledge, e.g., malware that is not detectable by existing malware detection systems at MLMD’s training time. Our research illustrates an ideal usage scenario for MLMD systems and demonstrates that such systems can benefit malware detection in practice. For example, by utilizing the new signals provided by the MLMD system and the detection capability of existing malware detection systems, we can more quickly uncover new malware variants or families. 

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4. Extending a Physics-informed Machine-learning Network for Superresolution Studies of Rayleigh–Bénard Convection

   https://doi.org/10.3847/1538-4357/ad1c55  

   Salim, Diane M. ; Burkhart, Blakesley ; Sondak, David ( March 2024 , The Astrophysical Journal)

   Advancing our understanding of astrophysical turbulence is bottlenecked by the limited resolution of numerical simulations that may not fully sample scales in the inertial range. Machine-learning (ML) techniques have demonstrated promise in upscaling resolution in both image analysis and numerical simulations (i.e., superresolution). Here we employ and further develop a physics-constrained convolutional neural network ML model called “MeshFreeFlowNet” (MFFN) for superresolution studies of turbulent systems. The model is trained on both the simulation images and the evaluated partial differential equations (PDEs), making it sensitive to the underlying physics of a particular fluid system. We develop a framework for 2D turbulent Rayleigh–Bénard convection generated with theDedaluscode by modifying the MFFN architecture to include the full set of simulation PDEs and the boundary conditions. Our training set includes fully developed turbulence sampling Rayleigh numbers (Ra) ofRa= 10⁶–10¹⁰. We evaluate the success of the learned simulations by comparing the power spectra of the directDedalussimulation to the predicted model output and compare both ground-truth and predicted power spectral inertial range scalings to theoretical predictions. We find that the updated network performs well at allRastudied here in recovering large-scale information, including the inertial range slopes. The superresolution prediction is overly dissipative at smaller scales than that of the inertial range in all cases, but the smaller scales are better recovered in more turbulent than laminar regimes. This is likely because more turbulent systems have a rich variety of structures at many length scales compared to laminar flows.

    

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5. Data-driven seismic response prediction of structural components

   https://doi.org/10.1177/87552930211053345  

   Luo, Huan ; Paal, Stephanie German ( October 2021 , Earthquake Spectra)

   Lateral stiffness of structural components, such as reinforced concrete (RC) columns, plays an important role in resisting the lateral earthquake loads. The lateral stiffness relates the lateral force to the lateral deformation, having a critical effect on the accuracy of the lateral seismic response predictions. The classical methods (e.g. fiber beam–column model) to estimate the lateral stiffness require calculations from section, element, and structural levels, which is time-consuming. Moreover, the shear deformation and bond-slip effect may also need to be included to more accurately calculate the lateral stiffness, which further increases the modeling difficulties and the computational cost. To reduce the computational time and enhance the accuracy of the predictions, this article proposes a novel data-driven method to predict the laterally seismic response based on the estimated lateral stiffness. The proposed method integrates the machine learning (ML) approach with the hysteretic model, where ML is used to compute the parameters that govern the nonlinear properties of the lateral response of target structural components directly from a training set composed of experimental data (i.e. data-driven procedure) and the hysteretic model is used to directly output the lateral stiffness based on the computed parameters and then to perform the seismic analysis. We apply the proposed method to predict the lateral seismic response of various types of RC columns subjected to cyclic loading and ground motions. We present the detailed model formulation for the application, including the developments of a modified hysteretic model, a hybrid optimization algorithm, and two data-driven seismic response solvers. The results predicted by the proposed method are compared with those obtained by classical methods with the experimental data serving as the ground truth, showing that the proposed method significantly outperforms the classical methods in both generalized prediction capabilities and computational efficiency.

    

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