Neural sequence detection plays a vital role in neuroscience research. Recent impressive works utilize convolutive nonnegative matrix factorization and Neyman-Scott process to solve this problem. However, they still face two limitations. Firstly, they accommodate the entire dataset into memory and perform iterative updates of multiple passes, which can be inefficient when the dataset is large or grows frequently. Secondly, they rely on the prior knowledge of the number of sequence types, which can be impractical with data when the future situation is unknown. To tackle these limitations, we propose a hierarchical Dirichlet point process model for efficient neural sequence detection. Instead of computing the entire data, our model can sequentially detect sequences in an online unsupervised manner with Particle filters. Besides, the Dirichlet prior enables our model to automatically introduce new sequence types on the fly as needed, thus avoiding specifying the number of types in advance.

Identifying interpretable patterns in multi-electrode recordings is a longstanding and increasingly pressing challenge in neuroscience.

The widespread use of Magnetic Resonance Imaging (MRI) in combination with deep learning shows promise for many high-impact automated diagnostic and prognostic tools. However, training new models requires large amounts of labeled data, a challenge due to high cost of precise annotations and data privacy. To address this issue, we introduce the MRI-CORE, a vision foundation model trained using more than 6 million slices from over 110 thousand MRI volumes across 18 body locations. Our experiments show notable improvements in performance over state-of-the-art methods in 13 data-restricted segmentation tasks, as well as in image classification, and zero-shot segmentation, showing the strong potential of MRI-CORE to enable data-efficient development of artificial intelligence models. We also present data on which strategies yield most useful foundation models and a novel analysis relating similarity between pre-training and downstream task data with transfer learning performance. Our model is publicly available with a permissive license. Magnetic Resonance Imaging (MRI) is one of the most widely used imaging modalities in medical diagnostics, with around 100-150 million scans performed annually worldwide (Papanicolas et al. 2018). MRI supports a wide range of clinical tasks, including lesion detection, tissue classification, and disease monitoring. Among these tasks, segmentation plays a particularly important role, as it enables precise delineation of anatomical structures and pathological regions, directly impacting diagnosis, treatment planning, and longitudinal studies (Mazurowski et al. 2023; Ma et al. 2024; Azad et al. 2024; Xu et al. 2024). Recent advances in deep learning have significantly improved the automation and accuracy of MRI-based analyses across a variety of tasks. However, deep learning-based methods typically require large amounts of manually annotated data and lack task transferability, making them difficult to scale across new tasks, anatomies, or patient populations.

The segmentation of multiple organs in multi-parametric MRI studies is critical for many applications in radiology, such as correlating imaging biomarkers with disease status (e.g., cirrhosis, diabetes). Recently, three publicly available tools, such as MRSegmentator (MRSeg), TotalSegmentator MRI (TS), and TotalVibeSegmentator (VIBE), have been proposed for multi-organ segmentation in MRI. However, the performance of these tools on specific MRI sequence types has not yet been quantified. In this work, a subset of 40 volumes from the public Duke Liver Dataset was curated. The curated dataset contained 10 volumes each from the pre-contrast fat saturated T1, arterial T1w, venous T1w, and delayed T1w phases, respectively. Ten abdominal structures were manually annotated in these volumes. Next, the performance of the three public tools was benchmarked on this curated dataset. The results indicated that MRSeg obtained a Dice score of 80.7 $\pm$ 18.6 and Hausdorff Distance (HD) error of 8.9 $\pm$ 10.4 mm. It fared the best ($p < .05$) across the different sequence types in contrast to TS and VIBE.

Neural sequence detection plays a vital role in neuroscience research. Recent impressive works utilize convolutive nonnegative matrix factorization and Neyman-Scott process to solve this problem. However, they still face two limitations. Firstly, they accommodate the entire dataset into memory and perform iterative updates of multiple passes, which can be inefficient when the dataset is large or grows frequently. Secondly, they rely on the prior knowledge of the number of sequence types, which can be impractical with data when the future situation is unknown.

The Magnetic Resonance Fingerprinting (MRF) approach aims to estimate multiple MR or physiological parameters simultaneously with a single fast acquisition sequence. Most of the MRF studies proposed so far have used simple MR sequence types to measure relaxation times (T1, T2). In that case, deep learning algorithms have been successfully used to speed up the reconstruction process. In theory, the MRF concept could be used with a variety of other MR sequence types and should be able to provide more information about the tissue microstructures. Yet, increasing the complexity of the numerical models often leads to prohibited simulation times, and estimating multiple parameters from one sequence implies new dictionary dimensions whose sizes become too large for standard computers and DL architectures.In this paper, we propose to analyze the MRF signal coming from a complex balance Steady-state free precession (bSSFP) type sequence to simultaneously estimate relaxometry maps (T1, T2), Field maps (B1, B0) as well as microvascular properties such as the local Cerebral Blood Volume (CBV) or the averaged vessel Radius (R).To bypass the curse of dimensionality, we propose an efficient way to simulate the MR signal coming from numerical voxels containing realistic microvascular networks as well as a Bidirectional Long Short-Term Memory network used for the matching process.On top of standard MRF maps, our results on 3 human volunteers suggest that our approach can quickly produce high-quality quantitative maps of microvascular parameters that are otherwise obtained using longer dedicated sequences and intravenous injection of a contrast agent. This approach could be used for the management of multiple pathologies and could be tuned to provide other types of microstructural information.

Sparse sequences of neural spikes are posited to underlie aspects of working memory, motor production, and learning. Discovering these sequences in an unsupervised manner is a longstanding problem in statistical neuroscience. Promising recent work utilized a convolutive nonnegative matrix factorization model to tackle this challenge. However, this model requires spike times to be discretized, utilizes a sub-optimal least-squares criterion, and does not provide uncertainty estimates for model predictions or estimated parameters. We address each of these shortcomings by developing a point process model that characterizes fine-scale sequences at the level of individual spikes and represents sequence occurrences as a small number of marked events in continuous time. This ultra-sparse representation of sequence events opens new possibilities for spike train modeling. For example, we introduce learnable time warping parameters to model sequences of varying duration, which have been experimentally observed in neural circuits. We demonstrate these advantages on experimental recordings from songbird higher vocal center and rodent hippocampus.