Jieyuan Liu

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}.

Jiasong Wu, Jieyuan Liu, Youyong Kong et al.

In this paper, we present a new algorithm, called MagnitudeCut, for recovering a signal from the phase of its Fourier transform. We casted our recovering problem into a new convex optimization problem, and then solved it by the block coordinate descent algorithm and the interior point algorithm, in which the iteration process consists of matrix vector product and inner product. We used the new method for reconstruction of a set of signal/image. The simulation results reveal that the proposed MagnitudeCut method can reconstruct the original signal with fewer sampling number of the phase information than that of the Greedy algorithm and iterative method under the same reconstruction error. Moreover, our algorithm can also reconstruct the symmetric image from its Fourier phase.

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

Chenyang Li, Jieyuan Liu, Bin Li et al.

Vision-Language Action (VLA) models have shown remarkable progress in robotic manipulation by leveraging the powerful perception abilities of Vision-Language Models (VLMs) to understand environments and directly output actions. However, by default, VLA models may overly attend to image tokens in the task-irrelevant region, which we describe as 'distracting tokens'. This behavior can disturb the model from the generation of the desired action tokens in each step, affecting the success rate of tasks. In this paper, we introduce a simple yet effective plug-and-play Distracting Token Pruning (DTP) framework, which dynamically detects and prunes these distracting image tokens. By correcting the model's visual attention patterns, we aim to improve the task success rate, as well as exploring the performance upper boundaries of the model without altering its original architecture or adding additional inputs. Experiments on the SIMPLER Benchmark (Li et al., 2024) show that our method consistently achieving relative improvements in task success rates across different types of novel VLA models, demonstrating generalizability to transformer-based VLAs. Further analysis reveals a negative correlation between the task success rate and the amount of attentions in the task-irrelevant region for all models tested, highlighting a common phenomenon of VLA models that could guide future research. We also publish our code at: https://anonymous.4open.science/r/CBD3.

Yanbin Yin, Kun Zhou, Zhen Wang et al.

The recent explosion of large language models (LLMs), each with its own general or specialized strengths, makes scalable, reliable benchmarking more urgent than ever. Standard practices nowadays face fundamental trade-offs: closed-ended question-based benchmarks (eg MMLU) struggle with saturation as newer models emerge, while crowd-sourced leaderboards (eg Chatbot Arena) rely on costly and slow human judges. Recently, automated methods (eg LLM-as-a-judge) shed light on the scalability, but risk bias by relying on one or a few "authority" models. To tackle these issues, we propose Decentralized Arena (dearena), a fully automated framework leveraging collective intelligence from all LLMs to evaluate each other. It mitigates single-model judge bias by democratic, pairwise evaluation, and remains efficient at scale through two key components: (1) a coarse-to-fine ranking algorithm for fast incremental insertion of new models with sub-quadratic complexity, and (2) an automatic question selection strategy for the construction of new evaluation dimensions. Across extensive experiments across 66 LLMs, dearena attains up to 97% correlation with human judgements, while significantly reducing the cost. Our code and data will be publicly released on https://github.com/maitrix-org/de-arena.

Zhen Wang, Fan Bai, Zhongyan Luo et al.

Autonomous agents powered by large language models (LLMs) promise to accelerate scientific discovery end-to-end, but rigorously evaluating their capacity for verifiable discovery remains a central challenge. Existing benchmarks face a trade-off: they either heavily rely on LLM-as-judge evaluations of automatically generated research outputs or optimize convenient yet isolated performance metrics that provide coarse proxies for scientific insight. To address this gap, we introduce FIRE-Bench (Full-cycle Insight Rediscovery Evaluation), a benchmark that evaluates agents through the rediscovery of established findings from recent, high-impact machine learning research. Agents are given only a high-level research question extracted from a published, verified study and must autonomously explore ideas, design experiments, implement code, execute their plans, and derive conclusions supported by empirical evidence. We evaluate a range of state-of-the-art agents with frontier LLMs backbones like gpt-5 on FIRE-Bench. Our results show that full-cycle scientific research remains challenging for current agent systems: even the strongest agents achieve limited rediscovery success (<50 F1), exhibit high variance across runs, and display recurring failure modes in experimental design, execution, and evidence-based reasoning. FIRE-Bench provides a rigorous and diagnostic framework for measuring progress toward reliable agent-driven scientific discovery.