Yongjie Xu

Tengfei Wang, Xin Wang, Yongmao Hou et al.

3D Gaussian Splatting (3DGS) has emerged as a transformative method in the field of real-time novel synthesis. Based on 3DGS, recent advancements cope with large-scale scenes via spatial-based partition strategy to reduce video memory and optimization time costs. In this work, we introduce a parallel Gaussian splatting method, termed PG-SAG, which fully exploits semantic cues for both partitioning and Gaussian kernel optimization, enabling fine-grained building surface reconstruction of large-scale urban areas without downsampling the original image resolution. First, the Cross-modal model - Language Segment Anything is leveraged to segment building masks. Then, the segmented building regions is grouped into sub-regions according to the visibility check across registered images. The Gaussian kernels for these sub-regions are optimized in parallel with masked pixels. In addition, the normal loss is re-formulated for the detected edges of masks to alleviate the ambiguities in normal vectors on edges. Finally, to improve the optimization of 3D Gaussians, we introduce a gradient-constrained balance-load loss that accounts for the complexity of the corresponding scenes, effectively minimizing the thread waiting time in the pixel-parallel rendering stage as well as the reconstruction lost. Extensive experiments are tested on various urban datasets, the results demonstrated the superior performance of our PG-SAG on building surface reconstruction, compared to several state-of-the-art 3DGS-based methods. Project Web:https://github.com/TFWang-9527/PG-SAG.

Yichu Xu, Xin-Chun Li, Le Gan et al.

Merging models becomes a fundamental procedure in some applications that consider model efficiency and robustness. The training randomness or Non-I.I.D. data poses a huge challenge for averaging-based model fusion. Previous research efforts focus on element-wise regularization or neural permutations to enhance model averaging while overlooking weight scope variations among models, which can significantly affect merging effectiveness. In this paper, we reveal variations in weight scope under different training conditions, shedding light on its influence on model merging. Fortunately, the parameters in each layer basically follow the Gaussian distribution, which inspires a novel and simple regularization approach named Weight Scope Alignment (WSA). It contains two key components: 1) leveraging a target weight scope to guide the model training process for ensuring weight scope matching in the subsequent model merging. 2) fusing the weight scope of two or more models into a unified one for multi-stage model fusion. We extend the WSA regularization to two different scenarios, including Mode Connectivity and Federated Learning. Abundant experimental studies validate the effectiveness of our approach.

Xiang Zhang, Juntai Cao, Jiaqi Wei et al.

Tokenization is the first - and often underappreciated - layer of computation in language models. While Chain-of-Thought (CoT) prompting enables transformer models to approximate recurrent computation by externalizing intermediate steps, we show that the success of such reasoning is fundamentally bounded by the structure of tokenized inputs. This work presents a theoretical and empirical investigation into how tokenization schemes, particularly subword-based methods like byte-pair encoding (BPE), impede symbolic computation by merging or obscuring atomic reasoning units. We introduce the notion of Token Awareness to formalize how poor token granularity disrupts logical alignment and prevents models from generalizing symbolic procedures. Through systematic evaluation on arithmetic and symbolic tasks, we demonstrate that token structure dramatically affect reasoning performance, causing failure even with CoT, while atomically-aligned formats unlock strong generalization, allowing small models (e.g., GPT-4o-mini) to outperform larger systems (e.g., o1) in structured reasoning. Our findings reveal that symbolic reasoning ability in LLMs is not purely architectural, but deeply conditioned on token-level representations.

ChenRui Duan, Zelin Zang, Siyuan Li et al.

Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov Chain Monte Carlo methods face slow convergence and computational burdens. Existing Variational Inference methods, which require pre-generated topologies and typically treat tree structures and branch lengths independently, may overlook critical sequence features, limiting their accuracy and flexibility. We propose PhyloGen, a novel method leveraging a pre-trained genomic language model to generate and optimize phylogenetic trees without dependence on evolutionary models or aligned sequence constraints. PhyloGen views phylogenetic inference as a conditionally constrained tree structure generation problem, jointly optimizing tree topology and branch lengths through three core modules: (i) Feature Extraction, (ii) PhyloTree Construction, and (iii) PhyloTree Structure Modeling. Meanwhile, we introduce a Scoring Function to guide the model towards a more stable gradient descent. We demonstrate the effectiveness and robustness of PhyloGen on eight real-world benchmark datasets. Visualization results confirm PhyloGen provides deeper insights into phylogenetic relationships.

ChenRui Duan, Zelin Zang, Yongjie Xu et al.

Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the capture of structurally and functionally relevant gene contexts. Moreover, these approaches struggle with encoding biologically meaningful genes and fail to address the One-to-Many and Many-to-One relationships inherent in metagenomic data. To overcome these challenges, we introduce FGBERT, a novel metagenomic pre-trained model that employs a protein-based gene representation as a context-aware and structure-relevant tokenizer. FGBERT incorporates Masked Gene Modeling (MGM) to enhance the understanding of inter-gene contextual relationships and Triplet Enhanced Metagenomic Contrastive Learning (TMC) to elucidate gene sequence-function relationships. Pre-trained on over 100 million metagenomic sequences, FGBERT demonstrates superior performance on metagenomic datasets at four levels, spanning gene, functional, bacterial, and environmental levels and ranging from 1k to 213k input sequences. Case studies of ATP Synthase and Gene Operons highlight FGBERT's capability for functional recognition and its biological relevance in metagenomic research.

Zelin Zang, Liangyu Li, Yongjie Xu et al.

Spatial transcriptomics (ST) technologies have revolutionized the study of gene expression patterns in tissues by providing multimodality data in transcriptomic, spatial, and morphological, offering opportunities for understanding tissue biology beyond transcriptomics. However, we identify the modality bias phenomenon in ST data species, i.e., the inconsistent contribution of different modalities to the labels leads to a tendency for the analysis methods to retain the information of the dominant modality. How to mitigate the adverse effects of modality bias to satisfy various downstream tasks remains a fundamental challenge. This paper introduces Multiple-modality Structure Transformation, named MuST, a novel methodology to tackle the challenge. MuST integrates the multi-modality information contained in the ST data effectively into a uniform latent space to provide a foundation for all the downstream tasks. It learns intrinsic local structures by topology discovery strategy and topology fusion loss function to solve the inconsistencies among different modalities. Thus, these topology-based and deep learning techniques provide a solid foundation for a variety of analytical tasks while coordinating different modalities. The effectiveness of MuST is assessed by performance metrics and biological significance. The results show that it outperforms existing state-of-the-art methods with clear advantages in the precision of identifying and preserving structures of tissues and biomarkers. MuST offers a versatile toolkit for the intricate analysis of complex biological systems.

Zelin Zang, WenZhe Li, Fei Chen et al.

In single-cell research, tracing and analyzing high-throughput single-cell differentiation trajectories is crucial for understanding complex biological processes. Key to this is the modeling and generation of hierarchical data that represents the intrinsic structure within datasets. Traditional methods face limitations in terms of computational cost, performance, generative capacity, and stability. Recent VAEs based approaches have made strides in addressing these challenges but still require specialized network modules for each tree branch, limiting their stability and ability to capture deep hierarchical relationships. To overcome these challenges, we introduce diffusion-based approach called HDTree. HDTree captures tree relationships within a hierarchical latent space using a unified hierarchical codebook and quantized diffusion processes to model tree node transitions. This method improves stability by eliminating branch-specific modules and enhancing generative capacity through gradual hierarchical changes simulated by the diffusion process. HDTree's effectiveness is demonstrated through comparisons on both general-purpose and single-cell datasets, where it outperforms existing methods in terms of accuracy and performance. These contributions provide a new tool for hierarchical lineage analysis, enabling more accurate and efficient modeling of cellular differentiation paths and offering insights for downstream biological tasks. The code of HDTree is available at anonymous link https://anonymous.4open.science/r/code_HDTree_review-A8DB.

Zelin Zang, Siyuan Li, Di Wu et al.

Unsupervised attributed graph representation learning is challenging since both structural and feature information are required to be represented in the latent space. Existing methods concentrate on learning latent representation via reconstruction tasks, but cannot directly optimize representation and are prone to oversmoothing, thus limiting the applications on downstream tasks. To alleviate these issues, we propose a novel graph embedding framework named Deep Manifold Attributed Graph Embedding (DMAGE). A node-to-node geodesic similarity is proposed to compute the inter-node similarity between the data space and the latent space and then use Bergman divergence as loss function to minimize the difference between them. We then design a new network structure with fewer aggregation to alleviate the oversmoothing problem and incorporate graph structure augmentation to improve the representation's stability. Our proposed DMAGE surpasses state-of-the-art methods by a significant margin on three downstream tasks: unsupervised visualization, node clustering, and link prediction across four popular datasets.