CellMaster: Collaborative Cell Type Annotation in Single-Cell Analysis

Single-cell RNA-seq (scRNA-seq) enables atlas-scale profiling of complex tissues, revealing rare lineages and transient states. Yet, assigning biologically valid cell identities remains a bottleneck because markers are tissue- and state-dependent, and novel states lack references. We present CellMaster, an AI agent that mimics expert practice for zero-shot cell-type annotation. Unlike existing automated tools, CellMaster leverages LLM-encoded knowledge (e.g., GPT-4o) to perform on-the-fly annotation with interpretable rationales, without pre-training or fixed marker databases. Across 9 datasets spanning 8 tissues, CellMaster improved accuracy by 7.1% over best-performing baselines (including CellTypist and scTab) in automatic mode. With human-in-the-loop refinement, this advantage increased to 18.6%, with a 22.1% gain on subtype populations. The system demonstrates particular strength in rare and novel cell states where baselines often fail. Source code and the web application are available at \href{https://github.com/AnonymousGym/CellMaster}{https://github.com/AnonymousGym/CellMaster}.

scPilot: Large Language Model Reasoning Toward Automated Single-Cell Analysis and Discovery

We present scPilot, the first systematic framework to practice omics-native reasoning: a large language model (LLM) converses in natural language while directly inspecting single-cell RNA-seq data and on-demand bioinformatics tools. scPilot converts core single-cell analyses, i.e., cell-type annotation, developmental-trajectory reconstruction, and transcription-factor targeting, into step-by-step reasoning problems that the model must solve, justify, and, when needed, revise with new evidence. To measure progress, we release scBench, a suite of 9 expertly curated datasets and graders that faithfully evaluate the omics-native reasoning capability of scPilot w.r.t various LLMs. Experiments with o1 show that iterative omics-native reasoning lifts average accuracy by 11% for cell-type annotation and Gemini-2.5-Pro cuts trajectory graph-edit distance by 30% versus one-shot prompting, while generating transparent reasoning traces explain marker gene ambiguity and regulatory logic. By grounding LLMs in raw omics data, scPilot enables auditable, interpretable, and diagnostically informative single-cell analyses. Code, data, and package are available at https://github.com/maitrix-org/scPilot

PAN: A World Model for General, Interactable, and Long-Horizon World Simulation

A world model enables an intelligent agent to imagine, predict, and reason about how the world evolves in response to its actions, and accordingly to plan and strategize. While recent video generation models produce realistic visual sequences, they typically operate in the prompt-to-full-video manner without causal control, interactivity, or long-horizon consistency required for purposeful reasoning. Existing world modeling efforts, on the other hand, often focus on restricted domains (e.g., physical, game, or 3D-scene dynamics) with limited depth and controllability, and struggle to generalize across diverse environments and interaction formats. In this work, we introduce PAN, a general, interactable, and long-horizon world model that predicts future world states through high-quality video simulation conditioned on history and natural language actions. PAN employs the Generative Latent Prediction (GLP) architecture that combines an autoregressive latent dynamics backbone based on a large language model (LLM), which grounds simulation in extensive text-based knowledge and enables conditioning on language-specified actions, with a video diffusion decoder that reconstructs perceptually detailed and temporally coherent visual observations, to achieve a unification between latent space reasoning (imagination) and realizable world dynamics (reality). Trained on large-scale video-action pairs spanning diverse domains, PAN supports open-domain, action-conditioned simulation with coherent, long-term dynamics. Extensive experiments show that PAN achieves strong performance in action-conditioned world simulation, long-horizon forecasting, and simulative reasoning compared to other video generators and world models, taking a step towards general world models that enable predictive simulation of future world states for reasoning and acting.