arXiv subjects

Alon Zabatani

Publications and source records attributed to Alon Zabatani.

3 recordsLinked to original sources

arXiv2026

Structure from Noise: Confirmation Bias in Particle Picking in Structural Biology

The computational pipelines of single-particle cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) include an early particle-picking stage, in which a micrograph or tomogram is scanned to extract candidate particles, typically via template matching or deep-learning-based techniques. The extracted particles are then passed to downstream tasks such as classification and 3D reconstruction. Although it is well understood empirically that particle picking can be sensitive to the choice of templates or learned priors, a quantitative theory of the bias introduced by this stage has been lacking. Here, we develop a mathematical framework for analyzing bias in template matching-based detection with concrete applications to cryo-EM and cryo-ET. We study this bias through two downstream tasks: (i) maximum-likelihood estimation of class means in a Gaussian mixture model (GMM) and (ii) 3D volume reconstruction from the extracted particle stack. We show that when template matching is applied to pure noise, then under broad noise models, the resulting maximum-likelihood estimates converge asymptotically to deterministic, noise-dependent transforms of the user-specified templates, yielding a structure from noise effect. We further characterize how the resulting bias depends on the noise statistics, sample size, dimension, and detection threshold. Finally, controlled experiments using standard cryo-EM software corroborate the theory, demonstrating reproducible structure from noise artifacts in low-SNR data.

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arXiv2025

Solving ill-conditioned polynomial equations using score-based priors with application to multi-target detection

Recovering signals from low-order moments is a fundamental yet notoriously difficult task in inverse problems. This recovery process often reduces to solving ill-conditioned systems of polynomial equations. In this work, we propose a new framework that integrates score-based diffusion priors with moment-based estimators to regularize and solve these nonlinear inverse problems. This introduces a new role for generative models: stabilizing polynomial recovery from noisy statistical features. As a concrete application, we study the multi-target detection (MTD) model in the high-noise regime. We demonstrate two main results: (i) diffusion priors substantially improve recovery from third-order moments, and (ii) they make the super-resolution MTD problem, otherwise ill-posed, feasible. Numerical experiments on MNIST data confirm consistent gains in reconstruction accuracy across SNR levels. Our results suggest a promising new direction for combining generative priors with nonlinear polynomial inverse problems.

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arXiv2023

Score-based diffusion priors for multi-target detection

Multi-target detection (MTD) is the problem of estimating an image from a large, noisy measurement that contains randomly translated and rotated copies of the image. Motivated by the single-particle cryo-electron microscopy technology, we design data-driven diffusion priors for the MTD problem, derived from score-based stochastic differential equations models. We then integrate the prior into the approximate expectation-maximization algorithm. In particular, our method alternates between an expectation step that approximates the expected log-likelihood and a maximization step that balances the approximated log-likelihood with the learned log-prior. We show on two datasets that adding the data-driven prior substantially reduces the estimation error, in particular in high noise regimes.

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