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.

Many self-supervised representation learning methods have achieved high performance in image classification tasks. However, these methods have limited performance on localization tasks such as object detection or semantic segmentation. Most self-supervised representation learning methods are optimized with only one global representation, which does not pay much attention to the spatial information in an image. We propose a simple and effective method that uses the positional relationships between the entities in an image by shuffling the convolution kernels. Our method extends current self-supervised learning and calculates the pixel-wise (dis) similarities between the output of the standard convolution kernels and that of the randomly shuffled convolution kernels. Our proposed method achieves higher performance on object detection, instance segmentation, and semantic segmentation when attached to recent self-supervised learning methods.

-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.

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 ModelNet40 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 image classification, our method achieves competitive performance. Code is available at https://github.com/mlvlab/SageMix.