Spatial and Single-cell transcriptomics are transformative in deciphering cellular dynamics. As the fundamental paradigm for reconstructing cell developmental paths, trajectory inference (TI) is critical. However, existing methods require extensive manual intervention and proficiency in heterogeneous tools, posing a significant barrier to efficient TI analysis. To bridge this gap, we propose SpaCellAgent, an autonomous large language model (LLM) multi-agent framework that automates end-to-end spatiotemporal analysis and narrative generation. SpaCellAgent utilizes a multi-agent architecture for strategic workflow planning, a dynamic tool-orchestration engine for adaptive algorithm selection, and a self-evolution module that iteratively refines performance through feedback. We evaluate SpaCellAgent on six heterogeneous datasets encompassing complex temporal developmental trajectories, diverse sequencing platforms, and spatially-resolved tissue architectures. SpaCellAgent consistently demonstrates over 40% improvement in analytical efficiency while maintaining expert-aligned performance. By converting natural language specifications into optimized analytical workflows and fully automating the pipeline, SpaCellAgent democratizes advanced spatiotemporal modeling and establishes a scalable, agent-driven paradigm for computational biology. The code and materials are available at https://github.com/LittleXH-shw/SpaCellAgent.
Songhan Wang, Haoang Chi, He Li et al.· Proceedings of the 32nd ACM...· 1 citation
LLM-based Multi-agent systems (MAS) have shown strong capabilities across a wide range of domains. Their success largely hinges on the collaboration topology design, which has emerged as a central research focus in the automated MAS design. However, existing approaches are fundamentally constrained by their reliance on homogeneous LLMs, which significantly limits overall system intelligence. In response to this limitation, we for the first time propose the concept of Automated Design of Heterogeneous-LLMs-based MAS (ADHM) . ADHM sheds light on a promising avenue for advancing collective intelligence, which focuses on the automated design of cost-effective MAS composed of diverse LLMs and roles to suit various queries. Toward this challenging goal, we propose Hetero-Designer , a novel pipeline that efficiently encodes intricate dependencies among queries, LLMs and roles through a novel Binary-Star Transformer and constructs Hetero-MAS in an autoregressive graph generation process. Extensive experiments demonstrate that Hetero-Designer is:
Zhiheng Zhang, Yuanzhe Zhang, Bohan Yu et al.· Annual Meeting of the Associ...· 0 citations
Large language models (LLMs) excel at text understanding and generation, yet still struggle to reliably understand and apply externally provided procedural rules at scale. To evaluate this capability, we introduce RuleWorld, a large-scale benchmark that reformulates rules as globally reusable abstract units rather than instance-specific facts. In RuleWorld, several scenarios, including single-rule, parallel multi-rule, and multi-hop reasoning, are settled for comprehensive evaluation. We further propose DynaRule, an end-to-end framework that injects the given rules into the KV cache and turns retrieval into an internal, learnable, step-wise process. Specifically, DynaRule employs Stacked Step-Level Attention Training with a specialtoken to enable dynamic rule re-attention and updating during inference. In this way, the model can re-attend to the most relevant rules at each step, dynamically replacing outdated ones to support more stable multi-step reasoning. Experiments on RuleWorld show that existing LLMs face challenges under large rule pools, while DynaRule improves average QA accuracy by up to 19 points and achieves over 85% Recall@1 at 10K rules, outperforming strong baselines by large margins. We make our code and dataset available here: https://github.com/SharkSpicy-NLP/Beyond-Factual-Knowledge.
Bohan Yu, Pengfei Cao, Chen Han et al.· 0 citations