Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and the expanded availability of experimental 3D protein structures have accelerated structure prediction, the dynamic nature of protein structures has received limited attention. This study introduces an innovative 4D diffusion model incorporating molecular dynamics (MD) simulation data to learn dynamic protein structures. Our approach is distinguished by the following components: (1) a unified diffusion model capable of generating dynamic protein structures, including both the backbone and side chains, utilizing atomic grouping and side-chain dihedral angle predictions; (2) a reference network that enhances structural consistency by integrating the latent embeddings of the initial 3D protein structures; and (3) a motion alignment module aimed at improving temporal structural coherence across multiple time steps. To our knowledge, this is the first diffusion-based model aimed at predicting protein trajectories across multiple time steps simultaneously. Validation on benchmark datasets demonstrates that our model exhibits high accuracy in predicting dynamic 3D structures of proteins containing up to 256 amino acids over 32 time steps, effectively capturing both local flexibility in stable states and significant conformational changes.

We introduce Stereo Risk, a new deep-learning approach to solve the classical stereo-matching problem in computer vision. As it is well-known that stereo matching boils down to a per-pixel disparity estimation problem, the popular state-of-the-art stereo-matching approaches widely rely on regressing the scene disparity values, yet via discretization of scene disparity values. Such discretization often fails to capture the nuanced, continuous nature of scene depth. Stereo Risk departs from the conventional discretization approach by formulating the scene disparity as an optimal solution to a continuous risk minimization problem, hence the name "stereo risk". We demonstrate that $L^1$ minimization of the proposed continuous risk function enhances stereo-matching performance for deep networks, particularly for disparities with multi-modal probability distributions. Furthermore, to enable the end-to-end network training of the non-differentiable $L^1$ risk optimization, we exploited the implicit function theorem, ensuring a fully differentiable network. A comprehensive analysis demonstrates our method's theoretical soundness and superior performance over the state-of-the-art methods across various benchmark datasets, including KITTI 2012, KITTI 2015, ETH3D, SceneFlow, and Middlebury 2014.

Neural-network-based single image depth prediction (SIDP) is a challenging task where the goal is to predict the scene's per-pixel depth at test time. Since the problem, by definition, is illposed, the fundamental goal is to come up with an approach that can reliably model the scene depth from a set of training examples. In the pursuit of perfect depth estimation, most existing state-of-the-art learning techniques predict a single scalar depth value per-pixel. Yet, it is well-known that the trained model has accuracy limits and can predict imprecise depth. Therefore, an SIDP approach must be mindful of the expected depth variations in the model's prediction at test time. Accordingly, we introduce an approach that performs continuous modeling of per-pixel depth, where we can predict and reason about the per-pixel depth and its distribution. To this end, we model per-pixel scene depth using a multivariate Gaussian distribution. Moreover, contrary to the existing uncertainty modeling methods—in the same spirit, where per-pixel depth is assumed to be independent, we introduce per-pixel covariance modeling that encodes its depth dependency w.r.t. all the scene points. Unfortunately, per-pixel depth covariance modeling leads to a computationally expensive continuous loss function, which we solve efficiently using the learned low-rank approximation of the overall covariance matrix. Notably, when tested on benchmark datasets such as KITTI, NYU, and SUN-RGB-D, the SIDP model obtained by optimizing our loss function shows state-of-the-art results. Our method's accuracy (named MG) is among the top on the KITTI depth-prediction benchmark leaderboard11http://www.cvlibs.net/datasets/kitti/eval–depth.php?benchmark=depth–prediction.

Recently, indiscernible scene understanding has attracted a lot of attention in the vision community. We further advance the frontier of this field by systematically studying a new challenge named indiscernible object counting (IOC), the goal of which is to count objects that are blended with respect to their surroundings. Due to a lack of appropriate IOC datasets, we present a large-scale dataset IOCfish5K which contains a total of 5,637 high-resolution images and 659,024 annotated center points. Our dataset consists of a large number of indiscernible objects (mainly fish) in underwater scenes, making the annotation process all the more challenging. IOCfish5K is superior to existing datasets with indiscernible scenes because of its larger scale, higher image resolutions, more annotations, and denser scenes. All these aspects make it the most challenging dataset for IOC so far, supporting progress in this area. For benchmarking purposes, we select 14 mainstream methods for object counting and carefully evaluate them on IOCfish5K. Furthermore, we propose IOCFormer, a new strong baseline that combines density and regression branches in a unified framework and can effectively tackle object counting under concealed scenes. Experiments show that IOCFormer achieves state-of-the-art scores on IOCfish5K. The resources are available at github.com/GuoleiSun/Indiscernible-Object-Counting.