Understanding the structural dynamics of biomolecules is crucial for uncovering biological functions. As molecular dynamics (MD) simulation data becomes more available, deep generative models have been developed to synthesize realistic MD trajectories. However, existing methods produce fixed-length trajectories by jointly denoising high-dimensional spatiotemporal representations, which conflicts with MD’s frame-by-frame integration process and fails to capture time-dependent conformational diversity. Inspired by MD's sequential nature, we introduce a new probabilistic autoregressive (ProAR) framework for trajectory generation. ProAR uses a dual-network system that models each frame as a multivariate Gaussian distribution and employs an anti-drifting sampling strategy to reduce cumulative errors. This approach captures conformational uncertainty and time-coupled structural changes while allowing flexible generation of trajectories of arbitrary length. Experiments on ATLAS, a large-scale protein MD dataset, demonstrate that for long trajectory generation, our model achieves a 7.5% reduction in reconstruction RMSE and an average 25.8% improvement in conformation change accuracy compared to previous state-of-the-art methods. For conformation sampling task, it performs comparably to specialized time-independent models, providing a flexible and dependable alternative to standard MD simulations.

Three-dimensional atomic arrangements of biomolecules are key to demystifying biological functions. The rapid expansion of accessible structural data, driven by advances in AI for science, highlights the critical challenge of efficiently modeling large-scale biomolecular structures, which are high-dimensional systems shaped by biological assembly principles. To address this, we introduce BiHiTo, a multi-level Biomolecular Hierarchy-inspired Tokenizer that intrinsically mimics natural biological assembly hierarchies. Specifically, we design a multi-codebook quantizer that mirrors the natural hierarchy of biomolecular structure, enabling simultaneous capture of representations spanning atomic motifs to global conformational variations. This hierarchical alignment markedly improves the biological interpretability and reconstruction fidelity of biomolecular structure.Extensive experiments demonstrate that BiHiTo delivers state-of-the-art performance and robust generalization across molecular dynamics trajectories and macromolecular complexes, facilitating advances in structure generation and dynamic conformation exploration. In the reconstruction of the CASP14 and OOD test set FastFolding protein multi-conformation data, our method achieves a 17% and 51% reduction in RMSD compared to Bio2Token, respectively.

Predicting the mutation prevalence trends of emerging viruses in the real world is an efficient means to update vaccines or drugs in advance. It is crucial to develop a computational method for the prediction of real-world prevalent SARS-CoV-2 mutations considering the impact of multiple selective pressures within and between hosts. Here, a deep-learning generative framework for real-world prevalent SARS-CoV-2 mutation prediction, named ViralForesight, is developed on top of protein language models and in silico virus evolution. Through the paradigm of host-to-herd in silico virus evolution, ViralForesight reproduced previous real-world prevalent SARS-CoV-2 mutations for multiple lineages with superior performance. More importantly, ViralForesight correctly predicted the future prevalent mutations that dominated the COVID-19 pandemic in the real world more than half a year in advance with in vitro experimental validation. Overall, ViralForesight demonstrates a proactive approach to the prevention of emerging viral infections, accelerating the process of discovering future prevalent mutations with the power of generative deep learning.

Predicting the protein stability changes upon mutations is one of the effective ways to improve the efficiency of protein engineering. Here, we propose a dual-view ensemble learning-based framework, DVE-stability, for mutation-induced protein stability change prediction from single sequence. DVE-stability integrates the global and local dependencies of mutations to capture the intramolecular interactions from two views through ensemble learning, in which a structural microenvironment simulation module is designed to indirectly introduce the information of structural microenvironment at the sequence level. DVE-stability achieved state-of-the-art prediction performance on seven single-point mutation benchmark datasets, and comprehensively surpassed other methods on five of them. Furthermore, DVE-stability outperformed other methods comprehensively through zero-shot inference on multiple-point mutation prediction task, demonstrating superior model generalizability to capture the epistasis of multiple-point mutations. More importantly, DVE-stability exhibited superior generalization performance in predicting rare beneficial mutations that are crucial for practical protein directed evolution scenarios. In addition, DVE-stability identified important intramolecular interactions via attention scores, demonstrating interpretable. Overall, DVE-stability provides a flexible and efficient tool for mutation-induced protein stability change prediction in an interpretable ensemble learning manner.

Face identity editing (FIE) shows great value in AI content creation. Low-resolution FIE approaches have achieved tremendous progress, but high-quality FIE struggles. Two major challenges hinder higher-resolution and higher-performance development of FIE: lack of high-resolution dataset and unacceptable complexity forbidding for mobile platforms. To address both issues, we establish a novel large-scale, high-quality dataset tailored for FIE. Based on our SimSwap (Chen et al. 2020), we propose an upgraded version named SimSwap++ with significantly boosted model efficiency. SimSwap++ features two major innovations for high-performance model compression. First, a novel computational primitive named Conditional Dynamic Convolution (CD-Conv) is proposed to address the inefficiency of conditional schemes (e.g., AdaIN) in tiny models. CD-Conv achieves anisotropic processing and injection with significantly lower complexity compared to standard conditional operators, e.g., modulated convolution. Second, a Morphable Knowledge Distillation (MKD) is presented to further trim the overall model. Unlike conventional homogeneous teacher-student structures, MKD is designed to be heterogeneous and mutually compensable, endowing the student with the multi-path morphable property; thus, our student maximally inherits the teacher's knowledge after distillation while further reducing its complexity through structure re-parameterization. Extensive experiments demonstrate that our SimSwap++ achieves state-of-the-art performance (97.55% ID accuracy on FaceForensics++) with extremely low complexity (2.5 GFLOPs).

The ability of scale-equivariance processing blocks plays a central role in arbitrary-scale image super-resolution tasks. Inspired by this crucial observation, this work proposes two novel scale-equivariant modules within a transformer-style framework to enhance arbitrary-scale image super-resolution (ASISR) performance, especially in high upsampling rate image extrapolation. In the feature extraction phase, we design a plug-in module called Adaptive Feature Extractor, which injects explicit scale information in frequency-expanded encoding, thus achieving scale-adaption in representation learning. In the upsampling phase, a learnable Neural Kriging upsampling operator is introduced, which simultaneously encodes both relative distance (i.e., scale-aware) information as well as feature similarity (i.e., with priori learned from training data) in a bilateral manner, providing scale-encoded spatial feature fusion. The above operators are easily plugged into multiple stages of a SR network, and a recent emerging pretraining strategy is also adopted to impulse the model's performance further. Extensive experimental results have demonstrated the outstanding scale-equivariance capability offered by the proposed operators and our learning framework, with much better results than previous SOTA methods at arbitrary scales for SR. Our code is available at https://github.com/neura1chen/EQSR

We develop a generalized 3D shape generation prior model, tailored for multiple 3D tasks including unconditional shape generation, point cloud completion, and cross-modality shape generation, etc. On one hand, to precisely capture local fine detailed shape information, a vector quantized variational autoencoder (VQ-VAE) is utilized to index local geometry from a compactly learned code-book based on a broad set of task training data. On the other hand, a discrete diffusion generator is introduced to model the inherent structural dependencies among different tokens. In the meantime, a multi-frequency fusion module (MFM) is developed to suppress high-frequency shape feature fluctuations, guided by multi-frequency contextual information. The above designs jointly equip our proposed 3D shape prior model with high-fidelity, diverse features as well as the capability of cross-modality alignment, and extensive experiments have demonstrated superior performances on various 3D shape generation tasks.

While lightweight ViT framework has made tremendous progress in image super-resolution, its uni-dimensional self-attention modeling, as well as homogeneous aggregation scheme, limit its effective receptive field (ERF) to include more comprehensive interactions from both spatial and channel dimensions. To tackle these drawbacks, this work proposes two enhanced components under a new Omni-SR architecture. First, an Omni Self-Attention (OSA) block is proposed based on dense interaction principle, which can simultaneously model pixel-interaction from both spatial and channel dimensions, mining the potential correlations across omni-axis (i.e., spatial and channel). Coupling with mainstream window partitioning strategies, OSA can achieve superior performance with compelling computational budgets. Second, a multi-scale interaction scheme is proposed to mitigate sub-optimal ERF (i.e., premature saturation) in shallow models, which facilitates local propagation and meso-/global-scale interactions, rendering an omni-scale aggregation building block. Extensive experiments demonstrate that Omni-SR achieves recordhigh performance on lightweight super-resolution benchmarks (e.g., 26.95dB@Urban100 x4 with only 792K parameters). Our code is available at https://github.com/Francis0625/Omni-SR.

Dynamic convolution has achieved significant gain in performance and computational complexity, thanks to its powerful representation capability given limited filter number/layers. However, SOTA dynamic convolution operators are sensitive to input noises (e.g., Gaussian noise, shot noise, e.t.c.) and lack sufficient spatial contextual information in filter generation. To alleviate this inherent weakness, we propose a lightweight and heterogeneous-structure (i.e., static and dynamic) operator, named Bi-volution. On the one hand, Bi-volution is designed as a dual-branch structure to fully leverage complementary properties of static/dynamic convolution, which endows Bi-volution more robust properties and higher performance. On the other hand, the Spatial Augmented Kernel Generation module is proposed to improve the dynamic convolution, realizing the learning of spatial context information with negligible additional computational complexity. Extensive experiments illustrate that the ResNet-50 equipped with Bi-volution achieves a highly competitive boost in performance (+2.8% top-1 accuracy on ImageNet classification, +2.4% box AP and +2.2% mask AP on COCO detection and instance segmentation) while maintaining extremely low FLOPs (i.e., [email protected] GFLOPs). Furthermore, our Bi-volution shows better robustness than dynamic convolution against various noise and input corruptions. Our code is available at https://github.com/neuralchen/Bivolution.