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  1. Abstract

    Current biotechnologies can simultaneously measure multiple high-dimensional modalities (e.g., RNA, DNA accessibility, and protein) from the same cells. A combination of different analytical tasks (e.g., multi-modal integration and cross-modal analysis) is required to comprehensively understand such data, inferring how gene regulation drives biological diversity and functions. However, current analytical methods are designed to perform a single task, only providing a partial picture of the multi-modal data. Here, we present UnitedNet, an explainable multi-task deep neural network capable of integrating different tasks to analyze single-cell multi-modality data. Applied to various multi-modality datasets (e.g., Patch-seq, multiome ATAC + gene expression, and spatial transcriptomics), UnitedNet demonstrates similar or better accuracy in multi-modal integration and cross-modal prediction compared with state-of-the-art methods. Moreover, by dissecting the trained UnitedNet with the explainable machine learning algorithm, we can directly quantify the relationship between gene expression and other modalities with cell-type specificity. UnitedNet is a comprehensive end-to-end framework that could be broadly applicable to single-cell multi-modality biology. This framework has the potential to facilitate the discovery of cell-type-specific regulation kinetics across transcriptomics and other modalities.

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    Free, publicly-accessible full text available May 3, 2024
  2. Abstract

    The rapid development of modeling techniques has brought many opportunities for data‐driven discovery and prediction. However, this also leads to the challenge of selecting the most appropriate model for any particular data task. Information criteria, such as the Akaike information criterion (AIC) and Bayesian information criterion (BIC), have been developed as a general class of model selection methods with profound connections with foundational thoughts in statistics and information theory. Many perspectives and theoretical justifications have been developed to understand when and how to use information criteria, which often depend on particular data circumstances. This review article will revisit information criteria by summarizing their key concepts, evaluation metrics, fundamental properties, interconnections, recent advancements, and common misconceptions to enrich the understanding of model selection in general.

    This article is categorized under:

    Data: Types and Structure > Traditional Statistical Data

    Statistical Learning and Exploratory Methods of the Data Sciences > Modeling Methods

    Statistical and Graphical Methods of Data Analysis > Information Theoretic Methods

    Statistical Models > Model Selection

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  3. Clinical translation of stem cell therapies for heart disease requires electrical integration of transplanted cardiomyocytes. Generation of electrically matured human induced pluripotent stem cell–derived cardiomyocytes (hiPSC-CMs) is critical for electrical integration. Here, we found that hiPSC-derived endothelial cells (hiPSC-ECs) promoted the expression of selected maturation markers in hiPSC-CMs. Using tissue-embedded stretchable mesh nanoelectronics, we achieved a long-term stable map of human three-dimensional (3D) cardiac microtissue electrical activity. The results revealed that hiPSC-ECs accelerated the electrical maturation of hiPSC-CMs in 3D cardiac microtissues. Machine learning–based pseudotime trajectory inference of cardiomyocyte electrical signals further revealed the electrical phenotypic transition path during development. Guided by the electrical recording data, single-cell RNA sequencing identified that hiPSC-ECs promoted cardiomyocyte subpopulations with a more mature phenotype, and multiple ligand-receptor interactions were up-regulated between hiPSC-ECs and hiPSC-CMs, revealing a coordinated multifactorial mechanism of hiPSC-CM electrical maturation. Collectively, these findings show that hiPSC-ECs drive hiPSC-CM electrical maturation via multiple intercellular pathways.

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  4. We study reinforcement learning (RL) in a setting with a network of agents whose states and actions interact in a local manner where the objective is to find localized policies such that the (discounted) global reward is maximized. A fundamental challenge in this setting is that the state-action space size scales exponentially in the number of agents, rendering the problem intractable for large networks. In this paper, we propose a scalable actor critic (SAC) framework that exploits the network structure and finds a localized policy that is an [Formula: see text]-approximation of a stationary point of the objective for some [Formula: see text], with complexity that scales with the local state-action space size of the largest [Formula: see text]-hop neighborhood of the network. We illustrate our model and approach using examples from wireless communication, epidemics, and traffic. 
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