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Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to…
Automated cell detection and localization from microscopy images are significant tasks in biomedical research and clinical practice. In this paper, we design a new cell detection and localization algorithm that combines deep convolutional…
Four-dimensional scanning transmission electron microscopy (4D-STEM) of local atomic diffraction patterns is emerging as a powerful technique for probing intricate details of atomic structure and atomic electric fields. However, efficient…
Sparse autoencoders (SAEs) have been applied to large language models and protein language models, but not systematically to electronic health record (EHR) foundation models. We train TopK SAEs on FlatASCEND, a 14.5-million-parameter…
In recent years, layered image compression is demonstrated to be a promising direction, which encodes a compact representation of the input image and apply an up-sampling network to reconstruct the image. To further improve the quality of…
Automated and semi-automated techniques in biomedical electron microscopy (EM) enable the acquisition of large datasets at a high rate. Segmentation methods are therefore essential to analyze and interpret these large volumes of data, which…
In this paper we introduce the deep kernelized autoencoder, a neural network model that allows an explicit approximation of (i) the mapping from an input space to an arbitrary, user-specified kernel space and (ii) the back-projection from…
Modern electron tomography has progressed to higher resolution at lower doses by leveraging compressed sensing methods that minimize total variation (TV). However, these sparsity-emphasized reconstruction algorithms introduce tunable…
Learned image compression research has achieved state-of-the-art compression performance with auto-encoder based neural network architectures, where the image is mapped via convolutional neural networks (CNN) into a latent representation…
Mesh autoencoders are commonly used for dimensionality reduction, sampling and mesh modeling. We propose a general-purpose DEep MEsh Autoencoder (DEMEA) which adds a novel embedded deformation layer to a graph-convolutional mesh…
The application of convolutional autoencoder deep learning to imaging data for planetary science and astrobiological use is briefly reviewed and explored with a focus on the need to understand algorithmic rationale, process, and results…
The underlying dynamics and patterns of 3D surface meshes deforming over time can be discovered by unsupervised learning, especially autoencoders, which calculate low-dimensional embeddings of the surfaces. To study the deformation patterns…
Half of wavefunction information is undetected by conventional transmission electron microscopy (CTEM) as only the intensity, and not the phase, of an image is recorded. Following successful applications of deep learning to optical hologram…
Petascale electron microscopy (EM) datasets push storage, transfer, and downstream analysis toward their current limits. We present a vector-quantized variational autoencoder-based (VQ-VAE) compression framework for EM that spans 16x to…
Modern neural networks have revolutionized the fields of computer vision (CV) and Natural Language Processing (NLP). They are widely used for solving complex CV tasks and NLP tasks such as image classification, image generation, and machine…
This work investigates three methods for calculating loss for autoencoder-based pretraining of image encoders: The commonly used reconstruction loss, the more recently introduced deep perceptual similarity loss, and a feature prediction…
Linear encoding of sparse vectors is widely popular, but is commonly data-independent -- missing any possible extra (but a priori unknown) structure beyond sparsity. In this paper we present a new method to learn linear encoders that adapt…
Instance segmentation in electron microscopy (EM) volumes is tough due to complex shapes and sparse annotations. Self-supervised learning helps but still struggles with intricate visual patterns in EM. To address this, we propose a…
Autoencoders are a type of unsupervised neural networks, which can be used to solve various tasks, e.g., dimensionality reduction, image compression, and image denoising. An AE has two goals: (i) compress the original input to a…
Deep convolutional neural networks contain tens of millions of parameters, making them impossible to work efficiently on embedded devices. We propose iterative approach of applying low-rank approximation to compress deep convolutional…