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1. Towards Automated Ethogramming: Cognitively-Inspired Event Segmentation for Streaming Wildlife Video Monitoring

   https://doi.org/10.1007/s11263-023-01781-2  

   Mounir, Ramy ; Shahabaz, Ahmed ; Gula, Roman ; Theuerkauf, Jörn ; Sarkar, Sudeep ( April 2023 , International Journal of Computer Vision)

   Advances in visual perceptual tasks have been mainly driven by the amount, and types, of annotations of large-scale datasets. Researchers have focused on fully-supervised settings to train models using offline epoch-based schemes. Despite the evident advancements, limitations and cost of manually annotated datasets have hindered further development for event perceptual tasks, such as detection and localization of objects and events in videos. The problem is more apparent in zoological applications due to the scarcity of annotations and length of videos-most videos are at most ten minutes long. Inspired by cognitive theories, we present a self-supervised perceptual prediction framework to tackle the problem of temporal event segmentation by building a stable representation of event-related objects. The approach is simple but effective. We rely on LSTM predictions of high-level features computed by a standard deep learning backbone. For spatial segmentation, the stable representation of the object is used by an attention mechanism to filter the input features before the prediction step. The self-learned attention maps effectively localize the object as a side effect of perceptual prediction. We demonstrate our approach on long videos from continuous wildlife video monitoring, spanning multiple days at 25 FPS. We aim to facilitate automated ethogramming by detecting and localizing events without the need for labels. Our approach is trained in an online manner on streaming input and requires only a single pass through the video, with no separate training set. Given the lack of long and realistic (includes real-world challenges) datasets, we introduce a new wildlife video dataset–nest monitoring of the Kagu (a flightless bird from New Caledonia)–to benchmark our approach. Our dataset features a video from 10 days (over 23 million frames) of continuous monitoring of the Kagu in its natural habitat. We annotate every frame with bounding boxes and event labels. Additionally, each frame is annotated with time-of-day and illumination conditions. We will make the dataset, which is the first of its kind, and the code available to the research community. We find that the approach significantly outperforms other self-supervised, traditional (e.g., Optical Flow, Background Subtraction) and NN-based (e.g., PA-DPC, DINO, iBOT), baselines and performs on par with supervised boundary detection approaches (i.e., PC). At a recall rate of 80%, our best performing model detects one false positive activity every 50 min of training. On average, we at least double the performance of self-supervised approaches for spatial segmentation. Additionally, we show that our approach is robust to various environmental conditions (e.g., moving shadows). We also benchmark the framework on other datasets (i.e., Kinetics-GEBD, TAPOS) from different domains to demonstrate its generalizability. The data and code are available on our project page:https://aix.eng.usf.edu/research_automated_ethogramming.html

    

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2. Physics-based Scene-level Reasoning for Object Pose Estimation in Clutter

   Mitash, Chaitanya ; Boularias, Abdeslam ; Bekris, Kostas ( May 2019 , The international journal of robotics research)

   This paper focuses on vision-based pose estimation for multiple rigid objects placed in clutter, especially in cases involving occlusions and objects resting on each other. Progress has been achieved recently in object recognition given advancements in deep learning. Nevertheless, such tools typically require a large amount of training data and significant manual effort to label objects. This limits their applicability in robotics, where solutions must scale to a large number of objects and variety of conditions. Moreover, the combinatorial nature of the scenes that could arise from the placement of multiple objects is hard to capture in the training dataset. Thus, the learned models might not produce the desired level of precision required for tasks, such as robotic manipulation. This work proposes an autonomous process for pose estimation that spans from data generation to scene-level reasoning and self-learning. In particular, the proposed framework first generates a labeled dataset for training a Convolutional Neural Network (CNN) for object detection in clutter. These detections are used to guide a scene-level optimization process, which considers the interactions between the different objects present in the clutter to output pose estimates of high precision. Furthermore, confident estimates are used to label online real images from multiple views and re-train the process in a self-learning pipeline. Experimental results indicate that this process is quickly able to identify in cluttered scenes physically-consistent object poses that are more precise than the ones found by reasoning over individual instances of objects. Furthermore, the quality of pose estimates increases over time given the self-learning process. 

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3. Spatio-Temporal Event Segmentation for Wildlife Extended Videos

   https://doi.org/10.1007/978-3-031-11349-9  

   Mounir, R. ; Gula, R. ; J., Sarkar ( July 2022 , International Conference on Computer Vision and Image Processing)

   Raman, B. ; Murala, S. ; Chowdhury, A. ; Dhall, A. ; Goyal, P. (Ed.)

   Using offline training schemes, researchers have tackled the event segmentation problem by providing full or weak-supervision through manually annotated labels or self-supervised epoch-based training. Most works consider videos that are at most 10’s of minutes long. We present a self-supervised perceptual prediction framework capable of temporal event segmentation by building stable representations of objects over time and demonstrate it on long videos, spanning several days at 25 FPS. The approach is deceptively simple but quite effective. We rely on predictions of high-level features computed by a standard deep learning backbone. For prediction, we use an LSTM, augmented with an attention mechanism, trained in a self-supervised manner using the prediction error. The self-learned attention maps effectively localize and track the event-related objects in each frame. The proposed approach does not require labels. It requires only a single pass through the video, with no separate training set. Given the lack of datasets of very long videos, we demonstrate our method on video from 10 d (254 h) of continuous wildlife monitoring data that we had collected with required permissions. We find that the approach is robust to various environmental conditions such as day/night conditions, rain, sharp shadows, and windy conditions. For the task of temporally locating events at the activity level, we had an 80% activity recall rate for one false activity detection every 50 min. We will make the dataset, which is the first of its kind, and the code available to the research community. Project page is available at https://ramymounir.com/publications/EventSegmentation/. 

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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. 

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5. Turbulence strength C n 2 estimation from video using physics-based deep learning

   https://doi.org/10.1364/OE.469976  

   Saha, Ripon Kumar ; Salcin, Esen ; Kim, Jihoo ; Smith, Joseph ; Jayasuriya, Suren ( October 2022 , Optics Express)

   Images captured from a long distance suffer from dynamic image distortion due to turbulent flow of air cells with random temperatures, and thus refractive indices. This phenomenon, known as image dancing, is commonly characterized by its refractive-index structure constant$C_n^2$as a measure of the turbulence strength. For many applications such as atmospheric forecast model, long-range/astronomy imaging, and aviation safety, optical communication technology,$C_n^2$estimation is critical for accurately sensing the turbulent environment. Previous methods for$C_n^2$estimation include estimation from meteorological data (temperature, relative humidity, wind shear, etc.) for single-point measurements, two-ended pathlength measurements from optical scintillometer for path-averaged$C_n^2$, and more recently estimating$C_n^2$from passive video cameras for low cost and hardware complexity. In this paper, we present a comparative analysis of classical image gradient methods for$C_n^2$estimation and modern deep learning-based methods leveraging convolutional neural networks. To enable this, we collect a dataset of video capture along with reference scintillometer measurements for ground truth, and we release this unique dataset to the scientific community. We observe that deep learning methods can achieve higher accuracy when trained on similar data, but suffer from generalization errors to other, unseen imagery as compared to classical methods. To overcome this trade-off, we present a novel physics-based network architecture that combines learned convolutional layers with a differentiable image gradient method that maintains high accuracy while being generalizable across image datasets.

    

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