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Multilevel Monte Carlo for a class of Partially Observed Processes in Neuroscience

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arXiv 2023年

作者： Maama, Mohamed Jasra, Ajay Kamatani, Kengo Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia School of Data Science The Chinese University of Hong Kong CN Shenzhen China Institute of Statistical Mathematics Tokyo190-0014 Japan

In this paper we consider Bayesian parameter inference associated to a class of partially observed stochastic differential equations (SDE) driven by jump processes. Such type of models can be routinely found in applications, of which we focus upon the case of neuroscience. The data are assumed to be observed regularly in time and driven by the SDE model with unknown parameters. In practice the SDE may not have an analytically tractable solution and this leads naturally to a time-discretization. We adapt the multilevel Markov chain Monte Carlo method of [15], which works with a hierarchy of time discretizations and show empirically and theoretically that this is preferable to using one single time discretization. The improvement is in terms of the computational cost needed to obtain a pre-specified numerical error. Our approach is illustrated on models applied to examples of Bayesian inference problems using both simulated and real observed data from neuroscience. Copyright © 2023, The Authors. All rights reserved.

关键词： Stochastic systems

CVIT: CONTINUOUS VISION TRANSFORMER FOR OPERATOR LEARNING

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arXiv 2024年

作者： Wang, Sifan Seidman, Jacob H. Sankaran, Shyam Wang, Hanwen Pappas, George J. Perdikaris, Paris Institution for Foundation of Data Science Yale University United States Graduate Program in Applied Mathematics and Computational Science University of Pennsylvania United States Department of Mechanical Engineering and Applied Mechanics University of Pennsylvania United States Department of Electrical and Systems Engineering University of Pennsylvania United States

Operator learning, which aims to approximate maps between infinite-dimensional function spaces, is an important area in scientific machine learning with applications across various physical domains. Here we introduce the Continuous Vision Transformer (CViT), a novel neural operator architecture that leverages advances in computer vision to address challenges in learning complex physical systems. CViT combines a vision transformer encoder, a novel grid-based coordinate embedding, and a query-wise cross-attention mechanism to effectively capture multi-scale dependencies. This design allows for flexible output representations and consistent evaluation at arbitrary resolutions. We demonstrate CViT’s effectiveness across a diverse range of partial differential equation (PDE) systems, including fluid dynamics, climate modeling, and reaction-diffusion processes. Our comprehensive experiments show that CViT achieves state-of-the-art performance on multiple benchmarks, often surpassing larger foundation models, even without extensive pretraining and roll-out fine-tuning. Taken together, CViT exhibits robust handling of discontinuous solutions, multi-scale features, and intricate spatio-temporal dynamics. Our contributions can be viewed as a significant step towards adapting advanced computer vision architectures for building more flexible and accurate machine learning models in the physical sciences. All data and code are publicly available at https://***/PredictiveIntelligenceLab/cvit. © 2024, CC BY-NC-SA.

关键词： computer vision

Diffusion curvature for estimating local curvature in high dimensional data 22

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Diffusion curvature for estimating local curvature in high d...

Proceedings of the 36th International Conference on Neural Information Processing Systems

作者： Dhananjay Bhaskar Kincaid MacDonald Oluwadamilola Fasina Dawson Thomas Bastian Rieck Ian Adelstein Smita Krishnaswamy Department of Genetics Yale University Department of Mathematics Yale University Applied Mathematics Program Yale University Department of Mathematics Department of Physics Yale University Institute of AI for Health Helmholtz Pioneer Campus Helmholtz Munich Department of Computer Science Department of Genetics Applied Mathematics Program Program for Computational Biology and Bioinformatics Yale University

ISBN: (纸本)9781713871088

We introduce a new intrinsic measure of local curvature on point-cloud data called diffusion curvature. Our measure uses the framework of diffusion maps, including the data diffusion operator, to structure point cloud data and define local curvature based on the laziness of a random walk starting at a point or region of the data. We show that this laziness directly relates to volume comparison results from Riemannian geometry. We then extend this scalar curvature notion to an entire quadratic form using neural network estimations based on the diffusion map of point-cloud data. We show applications of both estimations on toy data, single-cell data and on estimating local Hessian matrices of neural network loss landscapes.

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BRAINLM: A FOUNDATION MODEL FOR BRAIN ACTIVITY RECORDINGS 12

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BRAINLM: A FOUNDATION MODEL FOR BRAIN ACTIVITY RECORDINGS

12th International Conference on Learning Representations, ICLR 2024

作者： Caro, Josue Ortega de Fonseca, Antonio H. Rizvi, Syed A. Rosati, Matteo Averill, Christopher Cross, James L. Mittal, Prateek Zappala, Emanuele Dhodapkar, Rahul M. Abdallah, Chadi G. van Dijk, David Wu Tsai Institute United States Interdepartmental Neuroscience Program Yale University United States Baylor College of Medicine United States Department of Computer Science United States Yale School of Medicine United States University of Southern California United States Interdepartmental Program in Computational Biology & Bioinformatics United States Internal Medicine United States Cardiovascular Research Center Yale University United States Department of Mathematics and Statistics Idaho State University United States

We introduce the Brain Language Model (BrainLM), a foundation model for brain activity dynamics trained on 6,700 hours of fMRI recordings. Utilizing self-supervised masked-prediction training, BrainLM demonstrates proficiency in both fine-tuning and zero-shot inference tasks. Fine-tuning allows for the accurate prediction of clinical variables like age, anxiety, and PTSD as well as forecasting of future brain states. Critically, the model generalizes well to entirely new external cohorts not seen during training. In zero-shot inference mode, BrainLM can identify intrinsic functional networks directly from raw fMRI data without any network-based supervision during training. The model also generates interpretable latent representations that reveal relationships between brain activity patterns and cognitive states. Overall, BrainLM offers a versatile and interpretable framework for elucidating the complex spatiotemporal dynamics of human brain activity. It serves as a powerful "lens" through which massive repositories of fMRI data can be analyzed in new ways, enabling more effective interpretation and utilization at scale. The work demonstrates the potential of foundation models to advance computational neuroscience research. © 2024 12th International Conference on Learning Representations, ICLR 2024. All rights reserved.

关键词： Brain

Directed Scattering for Knowledge Graph-Based Cellular Signaling Analysis

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Directed Scattering for Knowledge Graph-Based Cellular Signa...

International Conference on Acoustics, Speech, and Signal Processing (ICASSP)

作者： Aarthi Venkat Joyce Chew Ferran Cardoso Rodriguez Christopher J. Tape Michael Perlmutter Smita Krishnaswamy Program for Computational Biology and Bioinformatics Yale University Department of Mathematics University of California Los Angeles Department of Oncology University College London Cancer Institute Department of Mathematics Boise State University Departments of Genetics and Computer Science Yale University

Directed graphs are a natural model for many phenomena, in particular scientific knowledge graphs such as molecular interaction or chemical reaction networks that define cellular signaling relationships. In these situations, source nodes typically have distinct biophysical properties from sinks. Due to their ordered and unidirectional relationships, many such networks also have hierarchical and multiscale structure. However, the majority of methods performing node- and edge-level tasks in machine learning do not take these properties into account, and thus have not been leveraged effectively for scientific tasks such as cellular signaling network inference. We propose a new framework called Directed Scattering Autoencoder (DSAE) which uses a directed version of a geometric scattering transform, combined with the non-linear dimensionality reduction properties of an autoencoder and the geometric properties of the hyperbolic space to learn latent hierarchies. We show this method outperforms numerous others on tasks such as embedding directed graphs and learning cellular signaling networks.

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Ground state phases of the two-dimension electron gas with a unified variational approach

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arXiv 2024年

作者： Smith, Conor Chen, Yixiao Levy, Ryan Yang, Yubo Morales, Miguel A. Zhang, Shiwei Center for Computational Quantum Physics Flatiron Institute New YorkNY10010 United States Department of Electrical and Computer Engineering University of New Mexico AlbuquerqueNM87131 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

The two-dimensional electron gas (2DEG) is a fundamental model, which is drawing increasing interest because of recent advances in experimental and theoretical studies of 2D materials. Current understanding of the ground state of the 2DEG relies on quantum Monte Carlo calculations, based on variational comparisons of different ansatze for different phases. We use a single variational ansatz, a general backflow-type wave function using a message-passing neural quantum state architecture, for a unified description across the entire density range. The variational optimization consistently leads to lower ground-state energies than previous best results. Transition into a Wigner crystal (WC) phase occurs automatically at rs = 37±1, a density lower than currently believed. Between the liquid and WC phases, the same ansatz and variational search strongly suggest the existence of intermediate states in a broad range of densities, with enhanced short-range nematic spin correlations. Copyright © 2024, The Authors. All rights reserved.

关键词： Message passing

UNRAVELING THE GEOGRAPHY OF INFECTION SPREAD: HARNESSING SUPER-AGENTS FOR PREDICTIVE MODELING

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arXiv 2023年

作者： Sikaroudi, Amir Mohammad Esmaieeli Efrat, Alon Chertkov, Michael Computer Science Department University of Arizona TucsonAZ85721 United States Program in Applied Mathematics Department of Mathematics University of Arizona TucsonAZ85721 United States

Our study presents an intermediate-level modeling approach that bridges the gap between complex Agent-Based Models (ABMs) and traditional compartmental models for infectious diseases. We introduce "super-agents" to simulate infection spread in cities, reducing computational complexity while retaining individual-level interactions. This approach leverages real-world mobility data and strategic geospatial tessellations for efficiency. Voronoi Diagram tessellations, based on specific street network locations, outperform standard Census Block Group tessellations, and a hybrid approach balances accuracy and efficiency. Benchmarking against existing ABMs highlights key optimizations. This research improves disease modeling in urban areas, aiding public health strategies in scenarios requiring geographic specificity and high computational efficiency. Copyright © 2023, The Authors. All rights reserved.

关键词： Complex networks

Exploring 3D Reconstruction with Drone Images: Advances and Challenges in Urban Environments 50

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Exploring 3D Reconstruction with Drone Images: Advances and ...

50th Annual Conference of the IEEE Industrial Electronics Society, IECON 2024

作者： Miranda Baldivieso, Thiago João da Silva Batista, Taise Grazielle Chagas, Fabio Suim Rodrigues Velho, Luiz Carlos Pacheco Ferreira Rosa, Paulo Fernando Defense Engineering Graduate Program Military Institute of Engineering Rio de Janeiro Brazil State Institute of the Environment Inea RJ Rio de Janeiro Brazil Department of Science and Industry systems University of South-Eastern Norway Kongsberg Norway Department of Computer Graphics Institute for Pure and Applied Mathematics Rio de Janeiro Brazil Electrical Engineering Graduate Program Military Institute of Engineering Rio de Janeiro Brazil

ISBN: (纸本)9781665464543

This working-in-progress paper aims to present a three-dimensional reconstruction using aerial images in different environments. The experiments were conducted with aircraft in both external and internal settings, starting with image acquisition, followed by the application of specific photogrammetry software-both commercial and open-source-and concluding with a qualitative evaluation of the results. © 2024 IEEE.

关键词： Aerial photography

Pairwise Learning for Autism Spectrum Disorder Imbalanced Classification

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Pairwise Learning for Autism Spectrum Disorder Imbalanced Cl...

IEEE Eurasia Conference on Biomedical Engineering, Healthcare and Sustainability (ECBIOS)

作者： Shu Liu Qiang Wu Xin Yang Computational and Data Science PhD Program Middle Tennessee State University Murfreesboro TN USA Department of Mathematics University of Tennessee Knoxville TN USA Department of Computer Science Middle Tennessee State University Murfreesboro TN USA

ISBN: (数字)9798350396133

ISBN: (纸本)9798350396140

This paper performs a classification task on data obtained from the Autism Brain Imaging Data Exchange (ABIDE) repository. In real-world case analysis, the number of autism spectrum disorder (ASD) patients is much smaller than typically developed people. To address this issue, this paper proposes the utilization of pairwise robust support vector machine (PRSVM) algorithms to classify autism spectrum disorder (ASD) patients. In this project's experiments, the correlation matrix derived from functional magnetic resonance imaging (fMRI) data was employed as a classification feature. A comprehensive evaluation was conducted to compare the classification performance of PRSVM with various machine learning methods. The comparative analysis encompassed various aspects, including different data dimensions, imbalanced ratios, and sample sizes, providing valuable insights into the relative performance of the algorithms under different experimental conditions. The experimental results demonstrate that PRSVM can detect autistic patients more accurately when the data is imbalanced. Moreover, the results indicate that PRSVM outperforms or achieves comparable performance to other conventional classification methods in a variety of situations. Furthermore, our approach can be further improved by augmenting the training set with either exclusively normal person samples or by incorporating patient samples and normal people samples in a proportionate manner. This augmentation strategy holds promising application value, as it contributes to improving the performance and robustness of our method.

关键词： Training Support vector machines Neuroimaging Autism Machine learning algorithms Functional magnetic resonance imaging Vectors Robustness Classification algorithms Sustainable development