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1. Can Graph Neural Networks Count Substructures?

   Zhengdao, Chen ; Lei, Chen ; Soledad, Villar ; Bruna, Joan ( December 2020 , Advances in neural information processing systems)

   null (Ed.)

   The ability to detect and count certain substructures in graphs is important for solving many tasks on graph-structured data, especially in the contexts of computa- tional chemistry and biology as well as social network analysis. Inspired by this, we propose to study the expressive power of graph neural networks (GNNs) via their ability to count attributed graph substructures, extending recent works that examine their power in graph isomorphism testing and function approximation. We distinguish between two types of substructure counting: induced-subgraph-count and subgraph-count, and establish both positive and negative answers for popular GNN architectures. Specifically, we prove that Message Passing Neural Networks (MPNNs), 2-Weisfeiler-Lehman (2-WL) and 2-Invariant Graph Networks (2-IGNs) cannot perform induced-subgraph-count of any connected substructure consisting of 3 or more nodes, while they can perform subgraph-count of star-shaped sub- structures. As an intermediary step, we prove that 2-WL and 2-IGNs are equivalent in distinguishing non-isomorphic graphs, partly answering an open problem raised in [38]. We also prove positive results for k-WL and k-IGNs as well as negative results for k-WL with a finite number of iterations. We then conduct experiments that support the theoretical results for MPNNs and 2-IGNs. Moreover, motivated by substructure counting and inspired by [45], we propose the Local Relational Pooling model and demonstrate that it is not only effective for substructure counting but also able to achieve competitive performance on molecular prediction tasks. 

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2. Explainable AI for ML jet taggers using expert variables and layerwise relevance propagation

   https://doi.org/10.1007/JHEP05(2021)208  

   Agarwal, Garvita ; Hay, Lauren ; Iashvili, Ia ; Mannix, Benjamin ; McLean, Christine ; Morris, Margaret ; Rappoccio, Salvatore ; Schubert, Ulrich ( May 2021 , Journal of High Energy Physics)

   null (Ed.)

   A bstract A framework is presented to extract and understand decision-making information from a deep neural network (DNN) classifier of jet substructure tagging techniques. The general method studied is to provide expert variables that augment inputs (“eXpert AUGmented” variables, or XAUG variables), then apply layerwise relevance propagation (LRP) to networks both with and without XAUG variables. The XAUG variables are concatenated with the intermediate layers after network-specific operations (such as convolution or recurrence), and used in the final layers of the network. The results of comparing networks with and without the addition of XAUG variables show that XAUG variables can be used to interpret classifier behavior, increase discrimination ability when combined with low-level features, and in some cases capture the behavior of the classifier completely. The LRP technique can be used to find relevant information the network is using, and when combined with the XAUG variables, can be used to rank features, allowing one to find a reduced set of features that capture part of the network performance. In the studies presented, adding XAUG variables to low-level DNNs increased the efficiency of classifiers by as much as 30-40%. In addition to performance improvements, an approach to quantify numerical uncertainties in the training of these DNNs is presented. 

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3. 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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4. Theory and model of thalamocortical processing in decision making under uncertainty. Thalamocortical Interactions Gordon Research Conference 2024, Ventura, California, February 2024. Abstract, Poster.

   Wang, Mien Brabeeba ; Lynch, Nancy ; Halassa, Michael ( February 2024 , Thalamocortical Interactions Gordon Research Conference 2024)

   Animals flexibly select actions that maximize future rewards despite facing uncertainty in sen- sory inputs, action-outcome associations or contexts. The computational and circuit mechanisms underlying this ability are poorly understood. A clue to such computations can be found in the neural systems involved in representing sensory features, sensorimotor-outcome associations and contexts. Specifically, the basal ganglia (BG) have been implicated in forming sensorimotor-outcome association [1] while the thalamocortical loop between the prefrontal cortex (PFC) and mediodorsal thalamus (MD) has been shown to engage in contextual representations [2, 3]. Interestingly, both human and non-human animal experiments indicate that the MD represents different forms of uncertainty [3, 4]. However, finding evidence for uncertainty representation gives little insight into how it is utilized to drive behavior. Normative theories have excelled at providing such computational insights. For example, de- ploying traditional machine learning algorithms to fit human decision-making behavior has clarified how associative uncertainty alters exploratory behavior [5, 6]. However, despite their computa- tional insight and ability to fit behaviors, normative models cannot be directly related to neural mechanisms. Therefore, a critical gap exists between what we know about the neural representa- tion of uncertainty on one end and the computational functions uncertainty serves in cognition. This gap can be filled with mechanistic neural models that can approximate normative models as well as generate experimentally observed neural representations. In this work, we build a mechanistic cortico-thalamo-BG loop network model that directly fills this gap. The model includes computationally-relevant mechanistic details of both BG and thalamocortical circuits such as distributional activities of dopamine [7] and thalamocortical pro- jection modulating cortical effective connectivity [3] and plasticity [8] via interneurons. We show that our network can more efficiently and flexibly explore various environments compared to com- monly used machine learning algorithms and we show that the mechanistic features we include are crucial for handling different types of uncertainty in decision-making. Furthermore, through derivation and mathematical proofs, we approximate our models to two novel normative theories. We show mathematically the first has near-optimal performance on bandit tasks. The second is a generalization on the well-known CUMSUM algorithm, which is known to be optimal on single change point detection tasks [9]. Our normative model expands on this by detecting multiple sequential contextual changes. To our knowledge, our work is the first to link computational in- sights, normative models and neural realization together in decision-making under various forms of uncertainty. 

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5. Recent Advances in the TUH EEG Corpus: Improving the Interrater Agreement for Artifacts and Epileptiform Events

   Buckwalter, Grace Chhin ( December 2021 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, Iyad Selesnick (Ed.)

   The Temple University Hospital EEG Corpus (TUEG) [1] is the largest publicly available EEG corpus of its type and currently has over 5,000 subscribers (we currently average 35 new subscribers a week). Several valuable subsets of this corpus have been developed including the Temple University Hospital EEG Seizure Corpus (TUSZ) [2] and the Temple University Hospital EEG Artifact Corpus (TUAR) [3]. TUSZ contains manually annotated seizure events and has been widely used to develop seizure detection and prediction technology [4]. TUAR contains manually annotated artifacts and has been used to improve machine learning performance on seizure detection tasks [5]. In this poster, we will discuss recent improvements made to both corpora that are creating opportunities to improve machine learning performance. Two major concerns that were raised when v1.5.2 of TUSZ was released for the Neureka 2020 Epilepsy Challenge were: (1) the subjects contained in the training, development (validation) and blind evaluation sets were not mutually exclusive, and (2) high frequency seizures were not accurately annotated in all files. Regarding (1), there were 50 subjects in dev, 50 subjects in eval, and 592 subjects in train. There was one subject common to dev and eval, five subjects common to dev and train, and 13 subjects common between eval and train. Though this does not substantially influence performance for the current generation of technology, it could be a problem down the line as technology improves. Therefore, we have rebuilt the partitions of the data so that this overlap was removed. This required augmenting the evaluation and development data sets with new subjects that had not been previously annotated so that the size of these subsets remained approximately the same. Since these annotations were done by a new group of annotators, special care was taken to make sure the new annotators followed the same practices as the previous generations of annotators. Part of our quality control process was to have the new annotators review all previous annotations. This rigorous training coupled with a strict quality control process where annotators review a significant amount of each other’s work ensured that there is high interrater agreement between the two groups (kappa statistic greater than 0.8) [6]. In the process of reviewing this data, we also decided to split long files into a series of smaller segments to facilitate processing of the data. Some subscribers found it difficult to process long files using Python code, which tends to be very memory intensive. We also found it inefficient to manipulate these long files in our annotation tool. In this release, the maximum duration of any single file is limited to 60 mins. This increased the number of edf files in the dev set from 1012 to 1832. Regarding (2), as part of discussions of several issues raised by a few subscribers, we discovered some files only had low frequency epileptiform events annotated (defined as events that ranged in frequency from 2.5 Hz to 3 Hz), while others had events annotated that contained significant frequency content above 3 Hz. Though there were not many files that had this type of activity, it was enough of a concern to necessitate reviewing the entire corpus. An example of an epileptiform seizure event with frequency content higher than 3 Hz is shown in Figure 1. Annotating these additional events slightly increased the number of seizure events. In v1.5.2, there were 673 seizures, while in v1.5.3 there are 1239 events. One of the fertile areas for technology improvements is artifact reduction. Artifacts and slowing constitute the two major error modalities in seizure detection [3]. This was a major reason we developed TUAR. It can be used to evaluate artifact detection and suppression technology as well as multimodal background models that explicitly model artifacts. An issue with TUAR was the practicality of the annotation tags used when there are multiple simultaneous events. An example of such an event is shown in Figure 2. In this section of the file, there is an overlap of eye movement, electrode artifact, and muscle artifact events. We previously annotated such events using a convention that included annotating background along with any artifact that is present. The artifacts present would either be annotated with a single tag (e.g., MUSC) or a coupled artifact tag (e.g., MUSC+ELEC). When multiple channels have background, the tags become crowded and difficult to identify. This is one reason we now support a hierarchical annotation format using XML – annotations can be arbitrarily complex and support overlaps in time. Our annotators also reviewed specific eye movement artifacts (e.g., eye flutter, eyeblinks). Eye movements are often mistaken as seizures due to their similar morphology [7][8]. We have improved our understanding of ocular events and it has allowed us to annotate artifacts in the corpus more carefully. In this poster, we will present statistics on the newest releases of these corpora and discuss the impact these improvements have had on machine learning research. We will compare TUSZ v1.5.3 and TUAR v2.0.0 with previous versions of these corpora. We will release v1.5.3 of TUSZ and v2.0.0 of TUAR in Fall 2021 prior to the symposium. ACKNOWLEDGMENTS Research reported in this publication was most recently supported by the National Science Foundation’s Industrial Innovation and Partnerships (IIP) Research Experience for Undergraduates award number 1827565. 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] I. Obeid and J. Picone, “The Temple University Hospital EEG Data Corpus,” in Augmentation of Brain Function: Facts, Fiction and Controversy. Volume I: Brain-Machine Interfaces, 1st ed., vol. 10, M. A. Lebedev, Ed. Lausanne, Switzerland: Frontiers Media S.A., 2016, pp. 394 398. https://doi.org/10.3389/fnins.2016.00196. [2] V. Shah et al., “The Temple University Hospital Seizure Detection Corpus,” Frontiers in Neuroinformatics, vol. 12, pp. 1–6, 2018. https://doi.org/10.3389/fninf.2018.00083. [3] A. Hamid et, al., “The Temple University Artifact Corpus: An Annotated Corpus of EEG Artifacts.” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2020, pp. 1-3. https://ieeexplore.ieee.org/document/9353647. [4] Y. Roy, R. Iskander, and J. Picone, “The NeurekaTM 2020 Epilepsy Challenge,” NeuroTechX, 2020. [Online]. Available: https://neureka-challenge.com/. [Accessed: 01-Dec-2021]. [5] S. Rahman, A. Hamid, D. Ochal, I. Obeid, and J. Picone, “Improving the Quality of the TUSZ Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2020, pp. 1–5. https://ieeexplore.ieee.org/document/9353635. [6] V. Shah, E. von Weltin, T. Ahsan, I. Obeid, and J. Picone, “On the Use of Non-Experts for Generation of High-Quality Annotations of Seizure Events,” Available: https://www.isip.picone press.com/publications/unpublished/journals/2019/elsevier_cn/ira. [Accessed: 01-Dec-2021]. [7] D. Ochal, S. Rahman, S. Ferrell, T. Elseify, I. Obeid, and J. Picone, “The Temple University Hospital EEG Corpus: Annotation Guidelines,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/tuh_eeg/annotations/. [8] D. Strayhorn, “The Atlas of Adult Electroencephalography,” EEG Atlas Online, 2014. [Online]. Availabl 

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