More Like this

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. 

   more » « less
2. Predicting Wildlife Trafficking Routes with Differentiable Shortest Paths

   Ferber, A. ( May 2023 , Part of the Lecture Notes in Computer Science book series (LNCS,volume 13884))

   Cire, A.A. (Ed.)

   Wildlife trafficking (WT), the illegal trade of wild fauna, flora, and their parts, directly threatens biodiversity and conservation of trafficked species, while also negatively impacting human health, national security, and economic development. Wildlife traffickers obfuscate their activities in plain sight, leveraging legal, large, and globally linked transportation networks. To complicate matters, defensive interdiction resources are limited, datasets are fragmented and rarely interoperable, and interventions like setting checkpoints place a burden on legal transportation. As a result, interpretable predictions of which routes wildlife traffickers are likely to take can help target defensive efforts and understand what wildlife traffickers may be considering when selecting routes. We propose a data-driven model for predicting trafficking routes on the global commercial flight network, a transportation network for which we have some historical seizure data and a specification of the possible routes that traffickers may take. While seizure data has limitations such as data bias and dependence on the deployed defensive resources, this is a first step towards predicting wildlife trafficking routes on real-world data. Our seizure data documents the planned commercial flight itinerary of trafficked and successfully interdicted wildlife. We aim to provide predictions of highly-trafficked flight paths for known origin-destination pairs with plausible explanations that illuminate how traffickers make decisions based on the presence of criminal actors, markets, and resilience systems. We propose a model that first predicts likelihoods of which commercial flights will be taken out of a given airport given input features, and then subsequently finds the highest-likelihood flight path from origin to destination using a differentiable shortest path solver, allowing us to automatically align our model’s loss with the overall goal of correctly predicting the full flight itinerary from a given source to a destination. We evaluate the proposed model’s predictions and interpretations both quantitatively and qualitatively, showing that the predicted paths are aligned with observed held-out seizures, and can be interpreted by policy-makers 

   more » « less
3. Deep neural networks for wearable sensor-based activity recognition in Parkinson’s disease: investigating generalizability and model complexity

   https://doi.org/10.1186/s12938-024-01214-2  

   Davidashvilly, Shelly ; Cardei, Maria ; Hssayeni, Murtadha ; Chi, Christopher ; Ghoraani, Behnaz ( February 2024 , BioMedical Engineering OnLine)

   The research gap addressed in this study is the applicability of deep neural network (NN) models on wearable sensor data to recognize different activities performed by patients with Parkinson’s Disease (PwPD) and the generalizability of these models to PwPD using labeled healthy data.

   The experiments were carried out utilizing three datasets containing wearable motion sensor readings on common activities of daily living. The collected readings were from two accelerometer sensors. PAMAP2 and MHEALTH are publicly available datasets collected from 10 and 9 healthy, young subjects, respectively. A private dataset of a similar nature collected from 14 PwPD patients was utilized as well. Deep NN models were implemented with varying levels of complexity to investigate the impact of data augmentation, manual axis reorientation, model complexity, and domain adaptation on activity recognition performance.

   A moderately complex model trained on the augmented PAMAP2 dataset and adapted to the Parkinson domain using domain adaptation achieved the best activity recognition performance with an accuracy of 73.02%, which was significantly higher than the accuracy of 63% reported in previous studies. The model’s F1 score of 49.79% significantly improved compared to the best cross-testing of 33.66% F1 score with only data augmentation and 2.88% F1 score without data augmentation or domain adaptation.

   These findings suggest that deep NN models originating on healthy data have the potential to recognize activities performed by PwPD accurately and that data augmentation and domain adaptation can improve the generalizability of models in the healthy-to-PwPD transfer scenario. The simple/moderately complex architectures tested in this study could generalize better to the PwPD domain when trained on a healthy dataset compared to the most complex architectures used. The findings of this study could contribute to the development of accurate wearable-based activity monitoring solutions for PwPD, improving clinical decision-making and patient outcomes based on patient activity levels.

    

   more » « less
4. Validity Assessment of Legal Will Statements as Natural Language Inference

   https://doi.org/10.18653/v1/2022.findings-emnlp.447  

   Kwak, Alice ; Israelsen, Jacob ; Morrison, Clayton T. ; Bambauer, Derek ; Surdeanu, Mihai ( December 2022 , Findings of the Association for Computational Linguistics: EMNLP 2022)

   This work introduces a natural language inference (NLI) dataset that focuses on the validity of statements in legal wills. This dataset is unique because: (a) each entailment decision requires three inputs: the statement from the will, the law, and the conditions that hold at the time of the testator’s death; and (b) the included texts are longer than the ones in current NLI datasets. We trained eight neural NLI models in this dataset. All the models achieve more than 80% macro F1 and accuracy, which indicates that neural approaches can handle this task reasonably well. However, group accuracy, a stricter evaluation measure that is calculated with a group of positive and negative examples generated from the same statement as a unit, is in mid 80s at best, which suggests that the models’ understanding of the task remains superficial. Further ablative analyses and explanation experiments indicate that all three text segments are used for prediction, but some decisions rely on semantically irrelevant tokens. This indicates that overfitting on these longer texts likely happens, and that additional research is required for this task to be solved. 

   more » « less
5. Explaining Text Matching on Neural Natural Language Inference

   https://doi.org/10.1145/3418052  

   Kim, Youngwoo ; Jang, Myungha ; Allan, James ( October 2020 , ACM Transactions on Information Systems)

   null (Ed.)

   Natural language inference (NLI) is the task of detecting the existence of entailment or contradiction in a given sentence pair. Although NLI techniques could help numerous information retrieval tasks, most solutions for NLI are neural approaches whose lack of interpretability prohibits both straightforward integration and diagnosis for further improvement. We target the task of generating token-level explanations for NLI from a neural model. Many existing approaches for token-level explanation are either computationally costly or require additional annotations for training. In this article, we first introduce a novel method for training an explanation generator that does not require additional human labels. Instead, the explanation generator is trained with the objective of predicting how the model’s classification output will change when parts of the inputs are modified. Second, we propose to build an explanation generator in a multi-task learning setting along with the original NLI task so the explanation generator can utilize the model’s internal behavior. The experiment results suggest that the proposed explanation generator outperforms numerous strong baselines. In addition, our method does not require excessive additional computation at prediction time, which renders it an order of magnitude faster than the best-performing baseline. 

   more » « less