arXiv subjects

AmirEhsan Khorashadizadeh

Publications and source records attributed to AmirEhsan Khorashadizadeh.

12 recordsLinked to original sources

arXiv2026

TomoTransformer: Towards a Foundation Model for CT Reconstruction

Supervised deep learning has advanced sparse-view tomographic reconstruction. However, conventional models, which typically map filtered back-projection (FBP) images or sinograms to clean reconstructions, are brittle under distribution shifts. Because they require retraining whenever projection counts and angles, detector resolutions, or data distributions change, their deployment in real-world applications remains limited. To address this, we introduce TomoTransformer, a transformer-based architecture that treats each \textit{local} filtered projection as an individual token and predicts missing views via self-attention. Crucially, TomoTransformer operates in a \emph{back-projection space} that separates projections across spatial locations, making view interpolation geometrically well-posed and invariant to detector size. This design yields a single foundation model that can process any number of input projections, at arbitrary angular locations and detector dimensions, and query any number of target angles without retraining. Trained on a large-scale dataset spanning diverse medical CT anatomies and natural images, TomoTransformer generalizes effectively across anatomies, materials, and resolutions. Extensive evaluations on several benchmark sparse-view datasets show that TomoTransformer significantly outperforms concurrent multi-purpose models like ViewTrans and matches or exceeds strong protocol-specific baselines, while remaining fully agnostic to the number of input and target projections. Furthermore, the model demonstrates robust zero-shot generalization on real experimental nanoscale brain data collected from an X-ray synchrotron, showcasing its practical utility for real-world applications.

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arXiv2026

CryoLithe: Rapid Cryo-ET Reconstruction via Transform-Localized Deep Learning

Cryo-electron tomography (cryo-ET) enables 3D visualization of cellular structures. Accurate reconstruction of high-resolution volumes is complicated by the very low signal-to-noise ratio and a restricted range of sample tilts. Recent self-supervised deep learning approaches, which post-process initial reconstructions by filtered backprojection (FBP), have significantly improved reconstruction quality with respect to signal processing iterative algorithms, but they are slow, taking dozens of hours for an expert to reconstruct a tomogram and demand large memory. We present CryoLithe, an end-to-end network that directly estimates the volume from an aligned tilt series. CryoLithe achieves denoising and missing wedge correction comparable or better than state-of-the-art self-supervised deep learning approaches such as Icecream, Cryo-CARE, IsoNet or DeepDeWedge, while being two orders of magnitude faster. To achieve this, we implement a local, memory-efficient reconstruction network. We demonstrate that leveraging transform-domain locality makes our network robust to distribution shifts, enabling effective supervised training and giving excellent results on real data$\unicode{x2013}$without retraining or fine-tuning. CryoLithe reconstructions facilitate downstream cryo-ET analysis, including segmentation and subtomogram averaging and is openly available: https://github.com/swing-research/CryoLithe.

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arXiv2025

Marginal Flow: a flexible and efficient framework for density estimation

Current density modeling approaches suffer from at least one of the following shortcomings: expensive training, slow inference, approximate likelihood, mode collapse or architectural constraints like bijective mappings. We propose a simple yet powerful framework that overcomes these limitations altogether. We define our model $q_θ(x)$ through a parametric distribution $q(x|w)$ with latent parameters $w$. Instead of directly optimizing the latent variables $w$, our idea is to marginalize them out by sampling $w$ from a learnable distribution $q_θ(w)$, hence the name Marginal Flow. In order to evaluate the learned density $q_θ(x)$ or to sample from it, we only need to draw samples from $q_θ(w)$, which makes both operations efficient. The proposed model allows for exact density evaluation and is orders of magnitude faster than competing models both at training and inference. Furthermore, Marginal Flow is a flexible framework: it does not impose any restrictions on the neural network architecture, it enables learning distributions on lower-dimensional manifolds (either known or to be learned), it can be trained efficiently with any objective (e.g. forward and reverse KL divergence), and it easily handles multi-modal targets. We evaluate Marginal Flow extensively on various tasks including synthetic datasets, simulation-based inference, distributions on positive definite matrices and manifold learning in latent spaces of images.

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arXiv2025

Localized Supervised Learning for Cryo-ET Reconstruction

Cryo-electron tomography (Cryo-ET) is a powerful tool in structural biology for 3D visualization of cells and biological systems at resolutions sufficient to identify individual proteins in situ. The measurements are collected by tilting the frozen specimen and exposing it to an electron beam of known dosage. As the biological samples are prone to electron damage, the samples can be exposed to only a limited dosage of electrons, leading to noisy and incomplete measurements. Thus, the reconstructions are noisy and incomplete, leading to the missing wedge problem. Currently, self-supervised learning is used to compensate for this issue. This typically involves, for each volume to recover, training a large 3D UNet on the initial noisy reconstruction, leading to large training time and memory requirements. In this work, we exploit the local nature of the forward model to train a lightweight network using only localized data from the measurements. This design provides flexibility in balancing computational and time requirements while reconstructing the volumes with high accuracy. We observe experimentally that this network can work well on unseen datasets, despite using a network trained on a few measurements.

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arXiv2025

Glimpse: Generalized Locality for Scalable and Robust CT

Deep learning has become the state-of-the-art approach to medical tomographic imaging. A common approach is to feed the result of a simple inversion, for example the backprojection, to a multiscale convolutional neural network (CNN) which computes the final reconstruction. Despite good results on in-distribution test data, this often results in overfitting certain large-scale structures and poor generalization on out-of-distribution (OOD) samples. Moreover, the memory and computational complexity of multiscale CNNs scale unfavorably with image resolution, making them impractical for application at realistic clinical resolutions. In this paper, we introduce Glimpse, a local coordinate-based neural network for computed tomography which reconstructs a pixel value by processing only the measurements associated with the neighborhood of the pixel. Glimpse significantly outperforms successful CNNs on OOD samples, while achieving comparable or better performance on in-distribution test data and maintaining a memory footprint almost independent of image resolution; 5GB memory suffices to train on 1024x1024 images which is orders of magnitude less than CNNs. Glimpse is fully differentiable and can be used plug-and-play in arbitrary deep learning architectures, enabling feats such as correcting miscalibrated projection orientations. Our implementation and Google Colab demo can be accessed at https://github.com/swing-research/Glimpse.

cs.CV↗

arXiv2024

LoFi: Neural Local Fields for Scalable Image Reconstruction

Neural fields or implicit neural representations (INRs) have attracted significant attention in computer vision and imaging due to their efficient coordinate-based representation of images and 3D volumes. In this work, we introduce a coordinate-based framework for solving imaging inverse problems, termed LoFi (Local Field). Unlike conventional methods for image reconstruction, LoFi processes local information at each coordinate separately by multi-layer perceptrons (MLPs), recovering the object at that specific coordinate. Similar to INRs, LoFi can recover images at any continuous coordinate, enabling image reconstruction at multiple resolutions. With comparable or better performance than standard deep learning models like convolutional neural networks (CNNs) and vision transformers (ViTs), LoFi achieves excellent generalization to out-of-distribution data with memory usage almost independent of image resolution. Remarkably, training on 1024x1024 images requires less than 200MB of memory -- much below standard CNNs and ViTs. Additionally, LoFi's local design allows it to train on extremely small datasets with 10 samples or fewer, without overfitting and without the need for explicit regularization or early stopping.

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arXiv2023

Deep Injective Prior for Inverse Scattering

In electromagnetic inverse scattering, the goal is to reconstruct object permittivity using scattered waves. While deep learning has shown promise as an alternative to iterative solvers, it is primarily used in supervised frameworks which are sensitive to distribution drift of the scattered fields, common in practice. Moreover, these methods typically provide a single estimate of the permittivity pattern, which may be inadequate or misleading due to noise and the ill-posedness of the problem. In this paper, we propose a data-driven framework for inverse scattering based on deep generative models. Our approach learns a low-dimensional manifold as a regularizer for recovering target permittivities. Unlike supervised methods that necessitate both scattered fields and target permittivities, our method only requires the target permittivities for training; it can then be used with any experimental setup. We also introduce a Bayesian framework for approximating the posterior distribution of the target permittivity, enabling multiple estimates and uncertainty quantification. Extensive experiments with synthetic and experimental data demonstrate that our framework outperforms traditional iterative solvers, particularly for strong scatterers, while achieving comparable reconstruction quality to state-of-the-art supervised learning methods like the U-Net.

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arXiv2023

FunkNN: Neural Interpolation for Functional Generation

Can we build continuous generative models which generalize across scales, can be evaluated at any coordinate, admit calculation of exact derivatives, and are conceptually simple? Existing MLP-based architectures generate worse samples than the grid-based generators with favorable convolutional inductive biases. Models that focus on generating images at different scales do better, but employ complex architectures not designed for continuous evaluation of images and derivatives. We take a signal-processing perspective and treat continuous image generation as interpolation from samples. Indeed, correctly sampled discrete images contain all information about the low spatial frequencies. The question is then how to extrapolate the spectrum in a data-driven way while meeting the above design criteria. Our answer is FunkNN -- a new convolutional network which learns how to reconstruct continuous images at arbitrary coordinates and can be applied to any image dataset. Combined with a discrete generative model it becomes a functional generator which can act as a prior in continuous ill-posed inverse problems. We show that FunkNN generates high-quality continuous images and exhibits strong out-of-distribution performance thanks to its patch-based design. We further showcase its performance in several stylized inverse problems with exact spatial derivatives.

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arXiv2023

Conditional Injective Flows for Bayesian Imaging

Most deep learning models for computational imaging regress a single reconstructed image. In practice, however, ill-posedness, nonlinearity, model mismatch, and noise often conspire to make such point estimates misleading or insufficient. The Bayesian approach models images and (noisy) measurements as jointly distributed random vectors and aims to approximate the posterior distribution of unknowns. Recent variational inference methods based on conditional normalizing flows are a promising alternative to traditional MCMC methods, but they come with drawbacks: excessive memory and compute demands for moderate to high resolution images and underwhelming performance on hard nonlinear problems. In this work, we propose C-Trumpets -- conditional injective flows specifically designed for imaging problems, which greatly diminish these challenges. Injectivity reduces memory footprint and training time while low-dimensional latent space together with architectural innovations like fixed-volume-change layers and skip-connection revnet layers, C-Trumpets outperform regular conditional flow models on a variety of imaging and image restoration tasks, including limited-view CT and nonlinear inverse scattering, with a lower compute and memory budget. C-Trumpets enable fast approximation of point estimates like MMSE or MAP as well as physically-meaningful uncertainty quantification.

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arXiv2022

Deep Variational Inverse Scattering

Inverse medium scattering solvers generally reconstruct a single solution without an associated measure of uncertainty. This is true both for the classical iterative solvers and for the emerging deep learning methods. But ill-posedness and noise can make this single estimate inaccurate or misleading. While deep networks such as conditional normalizing flows can be used to sample posteriors in inverse problems, they often yield low-quality samples and uncertainty estimates. In this paper, we propose U-Flow, a Bayesian U-Net based on conditional normalizing flows, which generates high-quality posterior samples and estimates physically-meaningful uncertainty. We show that the proposed model significantly outperforms the recent normalizing flows in terms of posterior sample quality while having comparable performance with the U-Net in point estimation.

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arXiv2022

Implicit Neural Representation for Mesh-Free Inverse Obstacle Scattering

Implicit representation of shapes as level sets of multilayer perceptrons has recently flourished in different shape analysis, compression, and reconstruction tasks. In this paper, we introduce an implicit neural representation-based framework for solving the inverse obstacle scattering problem in a mesh-free fashion. We express the obstacle shape as the zero-level set of a signed distance function which is implicitly determined by network parameters. To solve the direct scattering problem, we implement the implicit boundary integral method. It uses projections of the grid points in the tubular neighborhood onto the boundary to compute the PDE solution directly in the level-set framework. The proposed implicit representation conveniently handles the shape perturbation in the optimization process. To update the shape, we use PyTorch's automatic differentiation to backpropagate the loss function w.r.t. the network parameters, allowing us to avoid complex and error-prone manual derivation of the shape derivative. Additionally, we propose a deep generative model of implicit neural shape representations that can fit into the framework. The deep generative model effectively regularizes the inverse obstacle scattering problem, making it more tractable and robust, while yielding high-quality reconstruction results even in noise-corrupted setups.

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arXiv2021

Trumpets: Injective Flows for Inference and Inverse Problems

We propose injective generative models called Trumpets that generalize invertible normalizing flows. The proposed generators progressively increase dimension from a low-dimensional latent space. We demonstrate that Trumpets can be trained orders of magnitudes faster than standard flows while yielding samples of comparable or better quality. They retain many of the advantages of the standard flows such as training based on maximum likelihood and a fast, exact inverse of the generator. Since Trumpets are injective and have fast inverses, they can be effectively used for downstream Bayesian inference. To wit, we use Trumpet priors for maximum a posteriori estimation in the context of image reconstruction from compressive measurements, outperforming competitive baselines in terms of reconstruction quality and speed. We then propose an efficient method for posterior characterization and uncertainty quantification with Trumpets by taking advantage of the low-dimensional latent space.

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