Abstract In the field of 3D content generation, single image scene reconstruction methods still struggle to simultaneously ensure the quality of individual assets and the coherence of the overall scene in complex environments, while texture editing techniques often fail to maintain both local continuity and multi‐view consistency. In this paper, we propose a novel system ZeroScene, which leverages the prior knowledge of large vision models to accomplish both single image‐to‐3D scene reconstruction and texture editing in a zero‐shot manner. ZeroScene extracts object‐level 2D segmentation and depth information from input images to infer spatial relationships within the scene. It then jointly optimizes 3D and 2D projection losses of the point cloud to update object poses for precise scene alignment, ultimately constructing a coherent and complete 3D scene that encompasses both foreground and background. Moreover, ZeroScene supports texture editing of objects in the scene. By imposing constraints on the diffusion model and introducing a mask‐guided progressive image generation strategy, we effectively maintain texture consistency across multiple viewpoints and further enhance the realism of rendered results through Physically Based Rendering (PBR) material estimation. Experimental results demonstrate that our framework not only ensures the geometric and appearance accuracy of generated assets, but also faithfully reconstructs scene layouts and produces highly detailed textures that closely align with text prompts. Leveraging generative artificial intelligence, ZeroScene can transform 2D images into diversified 3D worlds with various styles, showing broad application potential in virtual content creation, such as digital twins and immersive game production, while also effectively supports “real‐to‐sim” transfer in robotics through the generation of highly realistic and trainable simulation environments. Project page: https://xdlbw.github.io/ZeroScene .

MOTIVATION: Accurately identifying and predicting molecular properties is a crucial task in molecular machine learning, and the key lies in how to extract effective molecular representations. Contrastive learning opens new avenues for representation learning, and a large amount of unlabeled data enables the model to generalize to the huge chemical space. However, existing contrastive learning-based models face two challenges: (i) existing methods destroy the original molecular environment and ignore chemical prior information, and (ii) there is a lack of a prior knowledge to guide the prediction of molecular properties. RESULTS: In this work, we propose a molecular property prediction framework called MolFCL, which consists of fragment-based contrastive learning and functional group-based prompt learning. Specifically, we introduced fragment-fragment interactions for the first time in the contrastive learning framework and designed a fragment-based augmented molecular graph that integrates the original chemical environment and fragment reactions. Furthermore, we proposed a novel functional group-based prompt learning during fine-tuning, which first incorporates functional group knowledge and the corresponding atomic signals, to improve molecular representation and provide interpretable analyses. The results show that MolFCL outperforms state-of-the-art baseline models on 23 molecular property prediction datasets. Moreover, visualizations show that MolFCL can learn to embed molecules into representations that can distinguish chemical properties. MolFCL can give higher weight to functional groups consistent with chemical knowledge during the prediction of molecular properties, which offers an interpretable ability of the model. Overall, MolFCL is a practically useful tool for molecular property prediction and assists drug scientists in designing drugs more effectively. AVAILABILITY AND IMPLEMENTATION: MolFCL is available at https://github.com/tangxiangcsu/MolFCLSupplementary.

MOTIVATION: Antiviral peptides (AVPs) are short chains of amino acids, showing great potential as antiviral drugs. The traditional wisdom (e.g. wet experiments) for identifying the AVPs is time-consuming and laborious, while cutting-edge computational methods are less accurate to predict them. RESULTS: In this article, we propose an AVPs prediction model via biological words representation, dubbed AVPpred-BWR. Based on the fact that the secondary structures of AVPs mainly consist of α-helix and loop, we explore the biological words of 1mer (corresponding to loops) and 4mer (4 continuous residues, corresponding to α-helix). That is, the peptides sequences are decomposed into biological words, and then the concealed sequential information is represented by training the Word2Vec models. Moreover, in order to extract multi-scale features, we leverage a CNN-Transformer framework to process the embeddings of 1mer and 4mer generated by Word2Vec models. To the best of our knowledge, this is the first time to realize the word segmentation of protein primary structure sequences based on the regularity of protein secondary structure. AVPpred-BWR illustrates clear improvements over its competitors on the independent test set (e.g. improvements of 4.6% and 11.0% for AUROC and MCC, respectively, compared to UniDL4BioPep). AVAILABILITY AND IMPLEMENTATION: AVPpred-BWR is publicly available at: https://github.com/zyweizm/AVPpred-BWR or https://zenodo.org/records/14880447 (doi: 10.5281/zenodo.14880447).

Construction and analysis of functional brain networks (FBNs) with resting-state functional magnetic resonance imaging (rs-fMRI) is a promising method to diagnose functional brain diseases. Nevertheless, the existing methods suffer from several limitations. First, the functional connectivities (FCs) of the FBN are usually measured by the temporal co-activation level between rs-fMRI time series from regions of interest (ROIs). While enjoying simplicity, the existing approach implicitly assumes simultaneous co-activation of all the ROIs, and models only their synchronous dependencies. However, the FCs are not necessarily always synchronous due to the time lag of information flow and cross-time interactions between ROIs. Therefore, it is desirable to model asynchronous FCs. Second, the traditional methods usually construct FBNs at individual level, leading to large variability and degraded diagnosis accuracy when modeling asynchronous FBN. Third, the FBN construction and analysis are conducted in two independent steps without joint alignment for the target diagnosis task. To address the first limitation, this paper proposes an effective sliding-window-based method to model spatiotemporal FCs in Transformer. Regarding the second limitation, we propose to learn common and individual FBNs adaptively with the common FBN as prior knowledge, thus alleviating the variability and enabling the network to focus on the individual disease-specific asynchronous FCs. To address the third limitation, the common and individual asynchronous FBNs are built and analyzed by an integrated network, enabling end-to-end training and improving the flexibility and discriminability. The effectiveness of the proposed method is consistently demonstrated on three data sets for mild cognitive impairment (MCI) diagnosis.