Minkyu Jeon

Minkyu Jeon, Hyeonjin Park, Hyunwoo J. Kim et al.

The application of modern machine learning to retinal image analyses offers valuable insights into a broad range of human health conditions beyond ophthalmic diseases. Additionally, data sharing is key to fully realizing the potential of machine learning models by providing a rich and diverse collection of training data. However, the personally-identifying nature of retinal images, encompassing the unique vascular structure of each individual, often prevents this data from being shared openly. While prior works have explored image de-identification strategies based on synthetic averaging of images in other domains (e.g. facial images), existing techniques face difficulty in preserving both privacy and clinical utility in retinal images, as we demonstrate in our work. We therefore introduce k-SALSA, a generative adversarial network (GAN)-based framework for synthesizing retinal fundus images that summarize a given private dataset while satisfying the privacy notion of k-anonymity. k-SALSA brings together state-of-the-art techniques for training and inverting GANs to achieve practical performance on retinal images. Furthermore, k-SALSA leverages a new technique, called local style alignment, to generate a synthetic average that maximizes the retention of fine-grain visual patterns in the source images, thus improving the clinical utility of the generated images. On two benchmark datasets of diabetic retinopathy (EyePACS and APTOS), we demonstrate our improvement upon existing methods with respect to image fidelity, classification performance, and mitigation of membership inference attacks. Our work represents a step toward broader sharing of retinal images for scientific collaboration. Code is available at https://github.com/hcholab/k-salsa.

Sanghyeok Lee, Minkyu Jeon, Injae Kim et al.

Data augmentation is key to improving the generalization ability of deep learning models. Mixup is a simple and widely-used data augmentation technique that has proven effective in alleviating the problems of overfitting and data scarcity. Also, recent studies of saliency-aware Mixup in the image domain show that preserving discriminative parts is beneficial to improving the generalization performance. However, these Mixup-based data augmentations are underexplored in 3D vision, especially in point clouds. In this paper, we propose SageMix, a saliency-guided Mixup for point clouds to preserve salient local structures. Specifically, we extract salient regions from two point clouds and smoothly combine them into one continuous shape. With a simple sequential sampling by re-weighted saliency scores, SageMix preserves the local structure of salient regions. Extensive experiments demonstrate that the proposed method consistently outperforms existing Mixup methods in various benchmark point cloud datasets. With PointNet++, our method achieves an accuracy gain of 2.6% and 4.0% over standard training in 3D Warehouse dataset (MN40) and ScanObjectNN, respectively. In addition to generalization performance, SageMix improves robustness and uncertainty calibration. Moreover, when adopting our method to various tasks including part segmentation and standard 2D image classification, our method achieves competitive performance.

Minkyu Jeon, Rishwanth Raghu, Miro Astore et al.

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. Its unique ability to capture structural variability has spurred the development of heterogeneous reconstruction algorithms that can infer distributions of 3D structures from noisy, unlabeled imaging data. Despite the growing number of advanced methods, progress in the field is hindered by the lack of standardized benchmarks with ground truth information and reliable validation metrics. Here, we introduce CryoBench, a suite of datasets, metrics, and benchmarks for heterogeneous reconstruction in cryo-EM. CryoBench includes five datasets representing different sources of heterogeneity and degrees of difficulty. These include conformational heterogeneity generated from designed motions of antibody complexes or sampled from a molecular dynamics simulation, as well as compositional heterogeneity from mixtures of ribosome assembly states or 100 common complexes present in cells. We then analyze state-of-the-art heterogeneous reconstruction tools, including neural and non-neural methods, assess their sensitivity to noise, and propose new metrics for quantitative evaluation. We hope that CryoBench will be a foundational resource for accelerating algorithmic development and evaluation in the cryo-EM and machine learning communities. Project page: https://cryobench.cs.princeton.edu.

Jeffrey Gu, Minkyu Jeon, Ambri Ma et al.

Cryo-electron microscopy (cryo-EM) is an indispensable technique for determining the 3D structures of dynamic biomolecular complexes. While typically applied to image a single molecular species, cryo-EM has the potential for structure determination of many targets simultaneously in a high-throughput fashion. However, existing methods typically focus on modeling conformational heterogeneity within a single or a few structures and are not designed to resolve compositional heterogeneity arising from mixtures of many distinct molecular species. To address this challenge, we propose CryoHype, a transformer-based hypernetwork for cryo-EM reconstruction that dynamically adjusts the weights of an implicit neural representation. Using CryoHype, we achieve state-of-the-art results on a challenging benchmark dataset containing 100 structures. We further demonstrate that CryoHype scales to the reconstruction of 1,000 distinct structures from unlabeled cryo-EM images in the fixed-pose setting.

Minji Lee, Colin Kalicki, Minkyu Jeon et al.

Models from the AlphaFold (AF) family reliably predict one dominant conformation for most well-ordered proteins but struggle to capture biologically relevant alternate states. Several efforts have focused on eliciting greater conformational variability through ad hoc inference-time perturbations of AF models or their inputs. Despite their progress, these approaches remain inefficient and fail to consistently recover major conformational modes. Here, we investigate both the optimal location and manner-of-operation for perturbing latent representations in the AF3 architecture. We distill our findings in ConforNets: channel-wise affine transforms of the pre-Pairformer pair latents. Unlike previous methods, ConforNets globally modulate AF3 representations, making them reusable across proteins. On unsupervised generation of alternate states, ConforNets achieve state-of-the-art success rates on all existing multi-state benchmarks. On the novel supervised task of conformational transfer, ConforNets trained on one source protein can induce a conserved conformational change across a protein family. Collectively, these results introduce a mechanism for conformational control in AF3-based models.

Weeyoung Kwon, Jeahun Sung, Minkyu Jeon et al.

Neural rendering methods such as Neural Radiance Fields (NeRF) and 3D Gaussian Splatting (3DGS) have achieved significant progress in photorealistic 3D scene reconstruction and novel view synthesis. However, most existing models assume clean and high-resolution (HR) multi-view inputs, which limits their robustness under real-world degradations such as noise, blur, low-resolution (LR), and weather-induced artifacts. To address these limitations, the emerging field of 3D Low-Level Vision (3D LLV) extends classical 2D Low-Level Vision tasks including super-resolution (SR), deblurring, weather degradation removal, restoration, and enhancement into the 3D spatial domain. This survey, referred to as R\textsuperscript{3}eVision, provides a comprehensive overview of robust rendering, restoration, and enhancement for 3D LLV by formalizing the degradation-aware rendering problem and identifying key challenges related to spatio-temporal consistency and ill-posed optimization. Recent methods that integrate LLV into neural rendering frameworks are categorized to illustrate how they enable high-fidelity 3D reconstruction under adverse conditions. Application domains such as autonomous driving, AR/VR, and robotics are also discussed, where reliable 3D perception from degraded inputs is critical. By reviewing representative methods, datasets, and evaluation protocols, this work positions 3D LLV as a fundamental direction for robust 3D content generation and scene-level reconstruction in real-world environments.