Xiang Xiao

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.

Andras Huebner, Wei Ji, Xiang Xiao

Automatic meeting summarization is becoming increasingly popular these days. The ability to automatically summarize meetings and to extract key information could greatly increase the efficiency of our work and life. In this paper, we experiment with different approaches to improve the performance of query-based meeting summarization. We started with HMNet\cite{hmnet}, a hierarchical network that employs both a word-level transformer and a turn-level transformer, as the baseline. We explore the effectiveness of pre-training the model with a large news-summarization dataset. We investigate adding the embeddings of queries as a part of the input vectors for query-based summarization. Furthermore, we experiment with extending the locate-then-summarize approach of QMSum\cite{qmsum} with an intermediate clustering step. Lastly, we compare the performance of our baseline models with BART, a state-of-the-art language model that is effective for summarization. We achieved improved performance by adding query embeddings to the input of the model, by using BART as an alternative language model, and by using clustering methods to extract key information at utterance level before feeding the text into summarization models.