Weishu Zhao

Outongyi Lv, Bingxin Zhou, Jing Wang et al.

Social networks represent a common form of interconnected data frequently depicted as graphs within the domain of deep learning-based inference. These communities inherently form dynamic systems, achieving stability through continuous internal communications and opinion exchanges among social actors along their social ties. In contrast, neural message passing in deep learning provides a clear and intuitive mathematical framework for understanding information propagation and aggregation among connected nodes in graphs. Node representations are dynamically updated by considering both the connectivity and status of neighboring nodes. This research harmonizes concepts from sociometry and neural message passing to analyze and infer the behavior of dynamic systems. Drawing inspiration from opinion dynamics in sociology, we propose ODNet, a novel message passing scheme incorporating bounded confidence, to refine the influence weight of local nodes for message propagation. We adjust the similarity cutoffs of bounded confidence and influence weights of ODNet and define opinion exchange rules that align with the characteristics of social network graphs. We show that ODNet enhances prediction performance across various graph types and alleviates oversmoothing issues. Furthermore, our approach surpasses conventional baselines in graph representation learning and proves its practical significance in analyzing real-world co-occurrence networks of metabolic genes. Remarkably, our method simplifies complex social network graphs solely by leveraging knowledge of interaction frequencies among entities within the system. It accurately identifies internal communities and the roles of genes in different metabolic pathways, including opinion leaders, bridge communicators, and isolators.

Hanbo Huang, Xuan Gong, Jing Wang et al.

Characterizing the physiological life boundaries of microbial strains, including viable temperature, pH, salinity, substrate utilization, and morphology, is central to biotechnology and ecology, yet traditionally requires exhaustive in vitro screening. Existing computational approaches either treat physiological traits as isolated supervised targets or repurpose biological foundation models as static encoders, leaving the genotype-to-physiology gap largely unbridged. We formulate microbial life-boundary prediction as a unified genome-to-physiology task and address it with a genome-conditioned, tool-augmented LLM agent. To support this task, we curate a strain-centric benchmark from IJSEM, NCBI, and BacDive covering 1,525 strains and 6,448 instances across viability intervals, environmental optima, substrate utilization, categorical traits, and morphology. Architecturally, the agent injects frozen LucaOne genome embeddings into a Qwen backbone via lightweight token fusion, and reasons over a similarity-based RAG module and a Genome-scale Metabolic Model (GEM) perturbation tool. We optimize the agent through a three-stage pipeline of gene-text alignment, agentic SFT on distilled trajectories, and GRPO with a novel counterfactual gene-grounding reward that reinforces the policy only when the authentic genome embedding causally improves correct-token generation relative to a zero-gene ablation. The resulting 4B-parameter agent matches or surpasses substantially larger frontier LLMs, with ablations confirming that genome-token fusion, dynamic tool use, and the counterfactual reward each yield distinct, significant gains.

Xuan Gong, Hanbo Huang, Hao Zheng et al.

Long chain-of-thought (CoT) reasoning improves large vision--language models, but visual information often fades during generation, limiting long-horizon multimodal reasoning. Existing methods either re-inject vision at inference or train policies for stronger grounding, but where to intervene relies on perception heuristics rather than principled gain analysis, and how local visual influence propagates remains implicit. We study this problem from an information-theoretic standpoint and derive a lower bound on the downstream visual gain of a one-step intervention, which suggests two factors: local branching room (token entropy) and downstream visual propagation potential (suffix divergence from a vision-marginalized reference). Guided by this analysis, we propose reflection-anchor policy optimization (RAPO), a GRPO-based policy optimization method that selects high-entropy reflection anchors and optimizes a chain-masked finite-window KL surrogate for downstream visual dependence. Experiments on reasoning-intensive and general-domain benchmarks show that RAPO delivers substantial gains over strong baselines across multiple LVLM backbones. Mechanism analyses further indicate that reflection anchors are enriched for visually sensitive decision points and that RAPO increases contrastive visual-dependence signals along generated trajectories.

Zhiyu Wang, Bingxin Zhou, Jing Wang et al.

Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLASMA, the first deep learning framework for efficient and interpretable residue-level protein substructure alignment. We reformulate the problem as a regularized optimal transport task and leverage differentiable Sinkhorn iterations. For a pair of input protein structures, PLASMA outputs a clear alignment matrix with an interpretable overall similarity score. Through extensive quantitative evaluations and three biological case studies, we demonstrate that PLASMA achieves accurate, lightweight, and interpretable residue-level alignment. Additionally, we introduce PLASMA-PF, a training-free variant that provides a practical alternative when training data are unavailable. Our method addresses a critical gap in protein structure analysis tools and offers new opportunities for functional annotation, evolutionary studies, and structure-based drug design. Reproducibility is ensured via our official implementation at https://github.com/ZW471/PLASMA-Protein-Local-Alignment.git.

Zelin Liu, Bocheng Li, Yuling Zhou et al.

The Mariana Trench and the Qinghai-Tibet Plateau exhibit significant similarities in geological origins and microbial metabolic functions. Given that deep-sea biological sampling faces prohibitive costs, recognizing structurally homologous terrestrial analogs of the Mariana Trench on the Qinghai-Tibet Plateau is of great significance. Yet, no existing model adequately addresses cross-domain topographic similarity retrieval, either neglecting geographical knowledge or sacrificing computational efficiency. To address these challenges, we present \underline{\textbf{G}}eography-knowledge \underline{\textbf{E}}nhanced \underline{\textbf{A}}nalog \underline{\textbf{R}}ecognition (\textbf{GEAR}) Framework, a three-stage pipeline designed to efficiently retrieve analogs from 2.5 million square kilometers of the Qinghai-Tibet Plateau: (1) Skeleton guided Screening and Clipping: Recognition of candidate valleys and initial screening based on size and linear morphological criteria. (2) Physics aware Filtering: The Topographic Waveform Comparator (TWC) and Morphological Texture Module (MTM) evaluate the waveform and texture and filter out inconsistent candidate valleys. (3) Graph based Fine Recognition: We design a \underline{\textbf{M}}orphology-integrated \underline{\textbf{S}}iamese \underline{\textbf{G}}raph \underline{\textbf{N}}etwork (\textbf{MSG-Net}) based on geomorphological metrics. Correspondingly, we release an expert-annotated topographic similarity dataset targeting tectonic collision zones. Experiments demonstrate the effectiveness of every stage. Besides, MSG-Net achieved an F1-Score 1.38 percentage points higher than the SOTA baseline. Using features extracted by MSG-Net, we discovered a significant correlation with biological data, providing evidence for future biological analysis.

Chenxu Zhou, Zelin Liu, Rui Cai et al.

Deep-sea cold seep stage assessment has traditionally relied on costly, high-risk manned submersible operations and visual surveys of macrofauna. Although microbial communities provide a promising and more cost-effective alternative, reliable inference remains challenging because the available deep-sea dataset is extremely small ($n = 13$) relative to the microbial feature dimension ($p = 26$), making purely data-driven models highly prone to overfitting. To address this, we propose a knowledge-enhanced classification framework that incorporates an ecological knowledge graph as a structural prior. By fusing macro-microbe coupling and microbial co-occurrence patterns, the framework internalizes established ecological logic into a \underline{\textbf{G}}raph-\underline{\textbf{R}}egularized \underline{\textbf{M}}ultinomial \underline{\textbf{L}}ogistic \underline{\textbf{R}}egression (GRMLR) model, effectively constraining the feature space through a manifold penalty to ensure biologically consistent classification. Importantly, the framework removes the need for macrofauna observations at inference time: macro-microbe associations are used only to guide training, whereas prediction relies solely on microbial abundance profiles. Experimental results demonstrate that our approach significantly outperforms standard baselines, highlighting its potential as a robust and scalable framework for deep-sea ecological assessment.