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  1. Abstract

    We study the effects of absorption in the medium on synthetic aperture imaging. We model absorption using the loss tangent, which is the imaginary part of the relative dielectric permittivity, and study two cases: (i) the loss tangent is known and (ii) the loss tangent is unknown. When the loss tangent is known and used in Kirchhoff migration (KM), we find that images of targets are range-shifted by approximately a central wavelength so that their predicted locations are closer to the synthetic aperture than they actually are. In contrast, we find that when the medium is unknown, the KM image does not exhibit this range-shift. Hence, we determine that it is better to not make use of any knowledge of the absorption when imaging. Using a recently developed transformation of KM images, which we call reciprocal-KM (rKM), we achieve tunably high-resolution images of targets through adjusting the value of a user-defined parameterε. When rKM is applied to an imaging region containing two targets, we find that their predicted locations shift, especially in range, but within a fraction of central wavelength of their true locations.

     
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  2. Abstract

    In response to the COVID-19 pandemic, many higher educational institutions moved their courses on-line in hopes of slowing disease spread. The advent of multiple highly-effective vaccines offers the promise of a return to “normal” in-person operations, but it is not clear if—or for how long—campuses should employ non-pharmaceutical interventions such as requiring masks or capping the size of in-person courses. In this study, we develop and fine-tune a model of COVID-19 spread to UC Merced’s student and faculty population. We perform a global sensitivity analysis to consider how both pharmaceutical and non-pharmaceutical interventions impact disease spread. Our work reveals that vaccines alone may not be sufficient to eradicate disease dynamics and that significant contact with an infectious surrounding community will maintain infections on-campus. Our work provides a foundation for higher-education planning allowing campuses to balance the benefits of in-person instruction with the ability to quarantine/isolate infectious individuals.

     
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  3. Abstract Motivation

    Single-cell RNA sequencing (scRNAseq) technologies allow for measurements of gene expression at a single-cell resolution. This provides researchers with a tremendous advantage for detecting heterogeneity, delineating cellular maps or identifying rare subpopulations. However, a critical complication remains: the low number of single-cell observations due to limitations by rarity of subpopulation, tissue degradation or cost. This absence of sufficient data may cause inaccuracy or irreproducibility of downstream analysis. In this work, we present Automated Cell-Type-informed Introspective Variational Autoencoder (ACTIVA): a novel framework for generating realistic synthetic data using a single-stream adversarial variational autoencoder conditioned with cell-type information. Within a single framework, ACTIVA can enlarge existing datasets and generate specific subpopulations on demand, as opposed to two separate models [such as single-cell GAN (scGAN) and conditional scGAN (cscGAN)]. Data generation and augmentation with ACTIVA can enhance scRNAseq pipelines and analysis, such as benchmarking new algorithms, studying the accuracy of classifiers and detecting marker genes. ACTIVA will facilitate analysis of smaller datasets, potentially reducing the number of patients and animals necessary in initial studies.

    Results

    We train and evaluate models on multiple public scRNAseq datasets. In comparison to GAN-based models (scGAN and cscGAN), we demonstrate that ACTIVA generates cells that are more realistic and harder for classifiers to identify as synthetic which also have better pair-wise correlation between genes. Data augmentation with ACTIVA significantly improves classification of rare subtypes (more than 45% improvement compared with not augmenting and 4% better than cscGAN) all while reducing run-time by an order of magnitude in comparison to both models.

    Availability and implementation

    The codes and datasets are hosted on Zenodo (https://doi.org/10.5281/zenodo.5879639). Tutorials are available at https://github.com/SindiLab/ACTIVA.

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
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  4. Abstract

    We have recently introduced a modification of the multiple signal classification method for synthetic aperture radar. This method incorporates a user‐defined parameter,ϵ, that allows for tunable quantitative high‐resolution imaging. However, this method requires relatively large single‐to‐noise ratios (SNR) to work effectively. Here, we first identify the fundamental mechanism in that method that produces high‐resolution images. Then we introduce a modification to Kirchhoff Migration (KM) that uses the same mechanism to produce tunable, high‐resolution images. This modified KM method can be applied to low SNR measurements. We show simulation results that demonstrate the features of this method.

     
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  5. Abstract

    We develop and analyze a quantitative signal subspace imaging method for single-frequency array imaging. This method is an extension to multiple signal classification which uses (i) the noise subspace to determine the location and support of targets, and (ii) the signal subspace to recover quantitative information about the targets. For point targets, we are able to recover the complex reflectivity and for an extended target under the Born approximation, we are able to recover a scalar quantity that is related to the product of the volume and relative dielectric permittivity of the target. Our resolution analysis for a point target demonstrates this method is capable of achieving exact recovery of the complex reflectivity at subwavelength resolution. Additionally, this resolution analysis shows that noise in the data effectively acts as a regularization to the imaging functional resulting in a method that is surprisingly more robust and effective with noise than without noise.

     
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  6. Spatial transcriptomics (ST) technologies are rapidly becoming the extension of single-cell RNA sequencing (scRNAseq), holding the potential of profiling gene expression at a single-cell resolution while maintaining cellular compositions within a tissue. Having both expression profiles and tissue organization enables researchers to better understand cellular interactions and heterogeneity, providing insight into complex biological processes that would not be possible with traditional sequencing technologies. Data generated by ST technologies are inherently noisy, high-dimensional, sparse, and multi-modal (including histological images, count matrices, etc.), thus requiring specialized computational tools for accurate and robust analysis. However, many ST studies currently utilize traditional scRNAseq tools, which are inadequate for analyzing complex ST datasets. On the other hand, many of the existing ST-specific methods are built upon traditional statistical or machine learning frameworks, which have shown to be sub-optimal in many applications due to the scale, multi-modality, and limitations of spatially resolved data (such as spatial resolution, sensitivity, and gene coverage). Given these intricacies, researchers have developed deep learning (DL)-based models to alleviate ST-specific challenges. These methods include new state-of-the-art models in alignment, spatial reconstruction, and spatial clustering, among others. However, DL models for ST analysis are nascent and remain largely underexplored. In this review, we provide an overview of existing state-of-the-art tools for analyzing spatially resolved transcriptomics while delving deeper into the DL-based approaches. We discuss the new frontiers and the open questions in this field and highlight domains in which we anticipate transformational DL applications. 
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  7. Zelinski, Michael E. ; Taha, Tarek M. ; Howe, Jonathan (Ed.)
    Image classification forms an important class of problems in machine learning and is widely used in many realworld applications, such as medicine, ecology, astronomy, and defense. Convolutional neural networks (CNNs) are machine learning techniques designed for inputs with grid structures, e.g., images, whose features are spatially correlated. As such, CNNs have been demonstrated to be highly effective approaches for many image classification problems and have consistently outperformed other approaches in many image classification and object detection competitions. A particular challenge involved in using machine learning for classifying images is measurement data loss in the form of missing pixels, which occurs in settings where scene occlusions are present or where the photodetectors in the imaging system are partially damaged. In such cases, the performance of CNN models tends to deteriorate or becomes unreliable even when the perturbations to the input image are small. In this work, we investigate techniques for improving the performance of CNN models for image classification with missing data. In particular, we explore training on a variety of data alterations that mimic data loss for producing more robust classifiers. By optimizing the categorical cross-entropy loss function, we demonstrate through numerical experiments on the MNIST dataset that training with these synthetic alterations can enhance the classification accuracy of our CNN models. 
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