More Like this

1. Differentiating ischemic stroke patients from healthy subjects using a large-scale, retrospective EEG database and machine learning methods

   https://doi.org/10.1016/j.jstrokecerebrovasdis.2024.107714  

   Peterson, William; Ramakrishnan, Nithya; Browder, Krag; Sanossian, Nerses; Nguyen, Peggy; Fink, Ezekiel (June 2024, Journal of Stroke and Cerebrovascular Diseases)

   Objectives: We set out to develop a machine learning model capable of distinguishing patients presenting with ischemic stroke from a healthy cohort of subjects. The model relies on a 3-min resting electroencephalogram (EEG) recording from which features can be computed. Materials and methods: Using a large-scale, retrospective database of EEG recordings and matching clinical reports, we were able to construct a dataset of 1385 healthy subjects and 374 stroke patients. With subjects often producing more than one recording per session, the final dataset consisted of 2401 EEG recordings (63% healthy, 37% stroke). Results: Using a rich set of features encompassing both the spectral and temporal domains, our model yielded an AUC of 0.95, with a sensitivity and specificity of 93% and 86%, respectively. Allowing for multiple recordings per subject in the training set boosted sensitivity by 7%, attributable to a more balanced dataset. Conclusions: Our work demonstrates strong potential for the use of EEG in conjunction with machine learning methods to distinguish stroke patients from healthy subjects. Our approach provides a solution that is not only timely (3-minutes recording time) but also highly precise and accurate (AUC: 0.95). Keywords: Electroencephalogram (EEG); Feature engineering; Ischemic stroke; Large vessel occlusion; Machine learning; Prehospital stroke scale. 

   more » « less
2. CREIMBO: Cross-Regional Ensemble Interactions in Multi-view Brain Observations

   Mudrik, Noga; Ly, Ryan; Ruebel, Oliver; Charles, Adam S (January 2025, The International Conference on Learning Representations)

   Modern recordings of neural activity provide diverse observations of neurons across brain areas, behavioral conditions, and subjects; presenting an exciting opportunity to reveal the fundamentals of brain-wide dynamics. Current analysis methods, however, often fail to fully harness the richness of such data, as they provide either uninterpretable representations (e.g., via deep networks) or oversimplify models (e.g., by assuming stationary dynamics or analyzing each session independently). Here, instead of regarding asynchronous neural recordings that lack alignment in neural identity or brain areas as a limitation, we leverage these diverse views into the brain to learn a unified model of neural dynamics. Specifically, we assume that brain activity is driven by multiple hidden global sub-circuits. These sub-circuits represent global basis interactions between neural ensembles—functional groups of neurons—such that the time-varying decomposition of these sub-circuits defines how the ensembles’ interactions evolve over time non-stationarily and non-linearly. We discover the neural ensembles underlying non-simultaneous observations, along with their non-stationary evolving interactions, with our new model, CREIMBO (Cross-Regional Ensemble Interactions in Multi-view Brain Observations). CREIMBO identifies the hidden composition of per-session neural ensembles through novel graph-driven dictionary learning and models the ensemble dynamics on a low-dimensional manifold spanned by a sparse time-varying composition of the global sub-circuits. Thus, CREIMBO disentangles overlapping temporal neural processes while preserving interpretability due to the use of a shared underlying sub-circuit basis. Moreover, CREIMBO distinguishes session-specific computations from global (session-invariant) ones by identifying session covariates and variations in sub-circuit activations. We demonstrate CREIMBO’s ability to recover true components in synthetic data, and uncover meaningful brain dynamics in human high-density electrode recordings, including cross-subject neural mechanisms as well as inter- vs. intra-region dynamical motifs. Furthermore, using mouse whole-brain recordings, we show CREIMBO’s ability to discover dynamical interactions that capture task and behavioral variables and meaningfully align with the biological importance of the brain areas they represent 

   more » « less
3. CORAAL QA: A Dataset and Framework for Open Domain Spontaneous Speech Question Answering from Long Audio Files

   https://doi.org/10.1109/ICASSP48485.2024.10447109  

   Shankar, Natarajan Balaji; Johnson, Alexander; Chance, Christina; Veeramani, Hariram; Alwan, Abeer (April 2024, Proceedings of the IEEE International Conference on Acoustics Speech and Signal Processing)

   This paper presents a novel dataset (CORAAL QA) and framework for audio question-answering from long audio recordings contain- ing spontaneous speech. The dataset introduced here provides sets of questions that can be factually answered from short spans of a long audio files (typically 30min to 1hr) from the Corpus of Re- gional African American Language. Using this dataset, we divide the audio recordings into 60 second segments, automatically tran- scribe each segment, and use PLDA scoring of BERT-based seman- tic embeddings to rank the relevance of ASR transcript segments in answering the target question. In order to improve this framework through data augmentation, we use large language models including ChatGPT and Llama 2 to automatically generate further training ex- amples and show how prompt engineering can be optimized for this process. By creatively leveraging knowledge from large-language models, we achieve state-of-the-art question-answering performance in this information retrieval task. 

   more » « less
4. Region-based conversion of neural activity across sessions

   https://doi.org/10.1109/NER52421.2023.10123786  

   Eum, Woohyun; Smith, Carlton; Saxena, Shreya (April 2023, IEEE)

   A common way to advance our understanding of brain processing is to decode behavior from recorded neural signals. In order to study the neural correlates of learning a task, we would like to decode behavior across the entire timespan of learning, which can take multiple recording sessions across many days. However, decoding across sessions is hindered due to a high amount of session-to-session variability in neural recordings. Here, we propose utilizing multidimensional neural signals from Localized semi-non negative matrix factorization processing (LocaNMF) with high behavioral correlations across sessions, as well as a novel data augmentation method and region-based converter, to optimally align neural recordings. We apply our method to widefield calcium activity across many sessions while a mouse learns a decision-making task. We first decompose each session's neural activity into region-based spatial and temporal components that can reconstruct the data with high variance. Next, we perform data augmentation of the neural data to smooth the variability across trials. Finally, we design a region-based neural converter across sessions that transforms one session's neural signals into another while preserving its dimensionality. We test our approach by decoding the mouse's behavior in the decision-making task, and find that our method outperforms approaches that use purely anatomical information while analyzing neural activity across sessions. By preserving the high dimensionality in the neural data while converting neural activity across sessions, our method can be used towards further analyses of neural data across sessions and the neural correlates of learning. 

   more » « less
5. SONYC URBAN SOUND TAGGING (SONYC-UST): A MULTILABEL DATASET FROM AN URBAN ACOUSTIC SENSOR NETWORK

   Cartwright, M.; Mendez, A.; Cramer, J.; Lostanlen, V.; Dove, G.; Wu, H.; Salamon, J.; Nov, O.; Bello, J. P. (October 2019, Detection and Classification of Acoustic Scenes and Events 2019)

   SONYC Urban Sound Tagging (SONYC-UST) is a dataset for the development and evaluation of machine listening systems for realworld urban noise monitoring. It consists of 3068 audio recordings from the “Sounds of New York City” (SONYC) acoustic sensor network. Via the Zooniverse citizen science platform, volunteers tagged the presence of 23 fine-grained classes that were chosen in consultation with the New York City Department of Environmental Protection. These 23 fine-grained classes can be grouped into eight coarse-grained classes. In this work, we describe the collection of this dataset, metrics used to evaluate tagging systems, and the results of a simple baseline model. 

   more » « less