More Like this

1. Flood Inundation Mapping with Limited Observations Based on Physics-Aware Topography Constraint

   https://doi.org/10.3389/fdata.2021.707951  

   Sainju, Arpan Man ; He, Wenchong ; Jiang, Zhe ; Yan, Da ; Chen, Haiquan ( July 2021 , Frontiers in Big Data)

   null (Ed.)

   Spatial classification with limited observations is important in geographical applications where only a subset of sensors are deployed at certain spots or partial responses are collected in field surveys. For example, in observation-based flood inundation mapping, there is a need to map the full flood extent on geographic terrains based on earth imagery that partially covers a region. Existing research mostly focuses on addressing incomplete or missing data through data cleaning and imputation or modeling missing values as hidden variables in the EM algorithm. These methods, however, assume that missing feature observations are rare and thus are ineffective in problems whereby the vast majority of feature observations are missing. To address this issue, we recently proposed a new approach that incorporates physics-aware structural constraint into the model representation. We design efficient learning and inference algorithms. This paper extends our recent approach by allowing feature values of samples in each class to follow a multi-modal distribution. Evaluations on real-world flood mapping applications show that our approach significantly outperforms baseline methods in classification accuracy, and the multi-modal extension is more robust than our early single-modal version. Computational experiments show that the proposed solution is computationally efficient on large datasets. 

   more » « less
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. 

   more » « less
3. CTRL: Closed-Loop Transcription to an LDR via Minimaxing Rate Reduction

   https://doi.org/10.3390/e24040456  

   Dai, Xili ; Tong, Shengbang ; Li, Mingyang ; Wu, Ziyang ; Psenka, Michael ; Chan, Kwan Ho ; Zhai, Pengyuan ; Yu, Yaodong ; Yuan, Xiaojun ; Shum, Heung-Yeung ; et al ( April 2022 , Entropy)

   This work proposes a new computational framework for learning a structured generative model for real-world datasets. In particular, we propose to learn a Closed-loop Transcriptionbetween a multi-class, multi-dimensional data distribution and a Linear discriminative representation (CTRL) in the feature space that consists of multiple independent multi-dimensional linear subspaces. In particular, we argue that the optimal encoding and decoding mappings sought can be formulated as a two-player minimax game between the encoder and decoderfor the learned representation. A natural utility function for this game is the so-called rate reduction, a simple information-theoretic measure for distances between mixtures of subspace-like Gaussians in the feature space. Our formulation draws inspiration from closed-loop error feedback from control systems and avoids expensive evaluating and minimizing of approximated distances between arbitrary distributions in either the data space or the feature space. To a large extent, this new formulation unifies the concepts and benefits of Auto-Encoding and GAN and naturally extends them to the settings of learning a both discriminative and generative representation for multi-class and multi-dimensional real-world data. Our extensive experiments on many benchmark imagery datasets demonstrate tremendous potential of this new closed-loop formulation: under fair comparison, visual quality of the learned decoder and classification performance of the encoder is competitive and arguably better than existing methods based on GAN, VAE, or a combination of both. Unlike existing generative models, the so-learned features of the multiple classes are structured instead of hidden: different classes are explicitly mapped onto corresponding independent principal subspaces in the feature space, and diverse visual attributes within each class are modeled by the independent principal components within each subspace. 

   more » « less
4. Activity recognition in wearables using adversarial multi-source domain adaptation

   https://doi.org/https://doi.org/10.1016/j.smhl.2020.100174  

   Chakma, A ; Faridee, A ; Khan, H ; Roy, N ( March 2021 , Smart health)

   null (Ed.)

   Human activity recognition (HAR) from wearable sensors data has become ubiquitous due to the widespread proliferation of IoT and wearable devices. However, recognizing human activity in heterogeneous environments, for example, with sensors of different models and make, across different persons and their on-body sensor placements introduces wide range discrepancies in the data distributions, and therefore, leads to an increased error margin. Transductive transfer learning techniques such as domain adaptation have been quite successful in mitigating the domain discrepancies between the source and target domain distributions without the costly target domain data annotations. However, little exploration has been done when multiple distinct source domains are present, and the optimum mapping to the target domain from each source is not apparent. In this paper, we propose a deep Multi-Source Adversarial Domain Adaptation (MSADA) framework that opportunistically helps select the most relevant feature representations from multiple source domains and establish such mappings to the target domain by learning the perplexity scores. We showcase that the learned mappings can actually reflect our prior knowledge on the semantic relationships between the domains, indicating that MSADA can be employed as a powerful tool for exploratory activity data analysis. We empirically demonstrate that our proposed multi-source domain adaptation approach achieves 2% improvement with OPPORTUNITY dataset (cross-person heterogeneity, 4 ADLs), whereas 13% improvement on DSADS dataset (cross-position heterogeneity, 10 ADLs and sports activities). 

   more » « less
5. EMIXER: End-to-end Multimodal X-ray Generation via Self-supervision

   Biswal, Siddharth ; Zhuang, Peiye ; Pyrros, Ayis ; Siddiqui ; Nasir ; Koyejo, Sanmi ; Sun, Jimeng ( January 2022 , Proceedings of Machine Learning Research)

   Deep generative models have enabled the automated synthesis of high-quality data for diverse applications. However, the most effective generative models are specialized to data from a single domain (e.g., images or text). Real-world applications such as healthcare require multi-modal data from multiple domains (e.g., both images and corresponding text), which are difficult to acquire due to limited availability and privacy concerns and are much harder to synthesize. To tackle this joint synthesis challenge, we propose an End-to-end MultImodal X-ray genERative model (EMIXER) for jointly synthesizing x-ray images and corresponding free-text reports, all conditional on diagnosis labels. EMIXER is an conditional generative adversarial model by 1) generating an image based on a label, 2) encoding the image to a hidden embedding, 3) producing the corresponding text via a hierarchical decoder from the image embedding, and 4) a joint discriminator for assessing both the image and the corresponding text. EMIXER also enables self-supervision to leverage vast amount of unlabeled data. Extensive experiments with real X-ray reports data illustrate how data augmentation using synthesized multimodal samples can improve the performance of a variety of supervised tasks including COVID-19 X-ray classification with very limited samples. The quality of generated images and reports are also confirmed by radiologists. We quantitatively show that EMIXER generated synthetic datasets can augment X-ray image classification, report generation models to achieve 5.94% and 6.9% improvement on models trained only on real data samples. Taken together, our results highlight the promise of state of generative models to advance clinical machine learning. 

   more » « less