Fluorescence microscopy is ubiquitously used in cell biology research to characterize the cellular role of a protein. To help elucidate the relationship between the amino acid sequence of a protein and its cellular function, we introduce CELL-Diff, a unified diffusion model facilitating bidirectional transformations between protein sequences and their corresponding microscopy images. Utilizing reference cell morphology images and a protein sequence, CELL-Diff efficiently generates corresponding protein images. Conversely, given a protein image, the model outputs protein sequences. CELL-Diff integrates continuous and diffusion models within a unified framework and is implemented using a transformer-based network. We train CELL-Diff on the Human Protein Atlas (HPA) dataset and fine-tune it on the OpenCell dataset. Experimental results demonstrate that CELL-Diff outperforms existing methods in generating high-fidelity protein images, making it a practical tool for investigating subcellular protein localization and interactions.

The data bottleneck has emerged as a fundamental challenge in learning based image restoration methods. Researchers have attempted to generate synthesized training data using paired or unpaired samples to address this challenge. This study proposes SeNM-VAE, a semi-supervised noise modeling method that leverages both paired and un-paired datasets to generate realistic degraded data. Our approach is based on modeling the conditional distribution of degraded and clean images with a specially designed graphical model. Under the variational inference framework, we develop an objective function for handling both paired and unpaired data. We employ our method to generate paired training samples for real-world image denoising and super-resolution tasks. Our approach excels in the quality of synthetic degraded images compared to other unpaired and paired noise modeling methods. Furthermore, our approach demonstrates remarkable performance in downstream image restoration tasks, even with limited paired data. With more paired data, our method achieves the best performance on the SIDD dataset.

In recent years, machine learning has demonstrated impressive capability in handling molecular science tasks. To support various molecular properties at scale, machine learning models are trained in the multi-task learning paradigm. Nevertheless, data of different molecular properties are often not aligned: some quantities, e.g. equilibrium structure, demand more cost to compute than others, e.g. energy, so their data are often generated by cheaper computational methods at the cost of lower accuracy, which cannot be directly overcome through multi-task learning. Moreover, it is not straightforward to leverage abundant data of other tasks to benefit a particular task. To handle such data heterogeneity challenges, we exploit the specialty of molecular tasks that there are physical laws connecting them, and design consistency training approaches that allow different tasks to exchange information directly so as to improve one another. Particularly, we demonstrate that the more accurate energy data can improve the accuracy of structure prediction. We also find that consistency training can directly leverage force and off-equilibrium structure data to improve structure prediction, demonstrating a broad capability for integrating heterogeneous data.

Abstract. Ground-based astronomy utilizes modern telescopes to obtain information on the universe by analyzing recorded signals. Due to atmospheric turbulence, the reconstruction process requires solving a deconvolution problem with an unknown point spread function (PSF). The crucial step in PSF estimation is to obtain a high-resolution phase from low-resolution phase gradients, which is a challenging problem. In this paper, when multiple frames of low-resolution phase gradients are available, we introduce PhaseNet, a deep learning approach based on the Taylor frozen flow hypothesis. Our approach incorporates a data-driven residual regularization term, of which the gradient is parameterized by a network, into the Laplacian regularization based model. To solve the model, we unroll the Nesterov accelerated gradient algorithm so that the network can be efficiently and effectively trained. Finally, we evaluate the performance of PhaseNet under various atmospheric conditions and demonstrate its superiority over TV and Laplacian regularization based methods.

Collecting paired training data is difficult in practice, but the unpaired samples broadly exist. Current approaches aim at generating synthesized training data from unpaired samples by exploring the relationship between the corrupted and clean data. This work proposes LUD-VAE, a deep generative method to learn the joint probability density function from data sampled from marginal distributions. Our approach is based on a carefully designed probabilistic graphical model in which the clean and corrupted data domains are conditionally independent. Using variational inference, we maximize the evidence lower bound (ELBO) to estimate the joint probability density function. Furthermore, we show that the ELBO is computable without paired samples under the inference invariant assumption. This property provides the mathematical rationale of our approach in the unpaired setting. Finally, we apply our method to real-world image denoising, super-resolution, and low-light image enhancement tasks and train the models using the synthetic data generated by the LUD-VAE. Experimental results validate the advantages of our method over other approaches.