Xinwang Liu
Famous AuthorPublications
SpaCellAgent: A Self-Evolving LLM-Based Multi-Agent Framework for Trajectory Analysis
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.
ImgCoT: Compressing Long Chain of Thought into Compact Visual Tokens for Efficient Reasoning of Large Language Model
Compressing long chains of thought (CoT) into compact latent tokens is crucial for efficient reasoning with large language models (LLMs). Recent studies employ autoencoders to achieve this by reconstructing textual CoT from latent tokens, thus encoding CoT semantics. However, treating textual CoT as the reconstruction target forces latent tokens to preserve surface-level linguistic features (e.g., word choice and syntax), introducing a strong linguistic inductive bias that prioritizes linguistic form over reasoning structure and limits logical abstraction. Thus, we propose ImgCoT that replaces the reconstruction target from textual CoT to the visual CoT obtained by rendering CoT into images. This substitutes linguistic bias with spatial inductive bias, i.e., a tendency to model spatial layouts of the reasoning steps in visual CoT, enabling latent tokens to better capture global reasoning structure. Moreover, although visual latent tokens encode abstract reasoning structure, they may blur reasoning details. We thus propose a loose ImgCoT, a hybrid reasoning that augments visual latent tokens with a few key textual reasoning steps, selected based on low token log-likelihood. This design allows LLMs to retain both global reasoning structure and fine-grained reasoning details with fewer tokens than the complete CoT. Extensive experiments across multiple datasets and LLMs demonstrate the effectiveness of the two versions of ImgCoT.
Beyond Parameter Finetuning: Test-Time Representation Refinement for Node Classification
Graph Neural Networks frequently exhibit significant performance degradation in the out-of-distribution test scenario. While test-time training (TTT) offers a promising solution, existing Parameter Finetuning (PaFT) paradigm suffer from catastrophic forgetting, hindering their real-world applicability. We propose TTReFT, a novel Test-Time Representation FineTuning framework that transitions the adaptation target from model parameters to latent representations. Specifically, TTReFT achieves this through three key innovations: (1) uncertainty-guided node selection for specific interventions, (2) low-rank representation interventions that preserve pre-trained knowledge, and (3) an intervention-aware masked autoencoder that dynamically adjust masking strategy to accommodate the node selection scheme. Theoretically, we establish guarantees for TTReFT in OOD settings. Empirically, extensive experiments across five benchmark datasets demonstrate that TTReFT achieves consistent and superior performance. Our work establishes representation finetuning as a new paradigm for graph TTT, offering both theoretical grounding and immediate practical utility for real-world deployment.