Ju Chen

Zhen Wang, Yiming Gao, Jieyuan Liu et al.

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}.

Yiming Gao, Zhen Wang, Jefferson Chen et al.

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

Jieyuan Liu, Jianyang Gu, Shijie Chen et al.

Knowledge-based visual question answering (KB-VQA) lets vision-language systems answer questions that exceed their parametric knowledge by conditioning a reader on passages retrieved from a Wikipedia-scale knowledge base. In pure-text long-context LLMs, retrieved-context use follows the U-shaped "lost-in-the-middle" effect of Liu et al. (2024): information at the start and end of context is used, the middle is lost. Whether this transfers to deployed multimodal KB-VQA is open. To close this gap, we design the first controlled probe of reader-side position dependence in multimodal KB-VQA: a gold-position protocol in which only the gold passage's prompt slot varies within question. We run it on three open-source 7B/8B VLM readers and two KB-VQA benchmarks at k up to 20. The shape flips from U to primacy: gold-at-first beats gold-at-last by 16 to 26 points on every reader-by-benchmark cell, an effect we call "Lost at the End". Three targeted ablations narrow the cause: a text-only control shows the multimodal setting amplifies an already-present text-mode primacy 2.2 to 4.5 times, and image-position and distractor-shuffle ablations together pin the locus to prompt slot 0 of the instruction-tuned reader. On a frozen reader, three retrieval-side fixes (MMR, oracle reranking, rank-based reordering) all leave the gap intact (no separable improvement). Our findings indicate that recall@k is the wrong metric for deployed KB-VQA and that closing the gap requires reader-side intervention; we release our protocol as a controlled instrument for evaluating such interventions.

Haicheng Wang, Zhemeng Yu, Gabriele Spadaro et al.

Recently, Multi-modal Large Language Models (MLLMs) have shown remarkable effectiveness for multi-modal tasks due to their abilities to generate and understand cross-modal data. However, processing long sequences of visual tokens extracted from visual backbones poses a challenge for deployment in real-time applications. To address this issue, we introduce FOLDER, a simple yet effective plug-and-play module designed to reduce the length of the visual token sequence, mitigating both computational and memory demands during training and inference. Through a comprehensive analysis of the token reduction process, we analyze the information loss introduced by different reduction strategies and develop FOLDER to preserve key information while removing visual redundancy. We showcase the effectiveness of FOLDER by integrating it into the visual backbone of several MLLMs, significantly accelerating the inference phase. Furthermore, we evaluate its utility as a training accelerator or even performance booster for MLLMs. In both contexts, FOLDER achieves comparable or even better performance than the original models, while dramatically reducing complexity by removing up to 70% of visual tokens.

Mengting Chen, Xi Chen, Zhonghua Zhai et al.

This paper introduces a novel framework for virtual try-on, termed Wear-Any-Way. Different from previous methods, Wear-Any-Way is a customizable solution. Besides generating high-fidelity results, our method supports users to precisely manipulate the wearing style. To achieve this goal, we first construct a strong pipeline for standard virtual try-on, supporting single/multiple garment try-on and model-to-model settings in complicated scenarios. To make it manipulable, we propose sparse correspondence alignment which involves point-based control to guide the generation for specific locations. With this design, Wear-Any-Way gets state-of-the-art performance for the standard setting and provides a novel interaction form for customizing the wearing style. For instance, it supports users to drag the sleeve to make it rolled up, drag the coat to make it open, and utilize clicks to control the style of tuck, etc. Wear-Any-Way enables more liberated and flexible expressions of the attires, holding profound implications in the fashion industry.