SC-Arena: A Natural Language Benchmark for Single-Cell Reasoning with Knowledge-Augmented Evaluation

Large language models (LLMs) are increasingly applied in scientific research, offering new capabilities for knowledge discovery and reasoning. In single-cell biology, however, evaluation practices for both general and specialized LLMs remain inadequate: existing benchmarks are fragmented across tasks, adopt formats such as multiple-choice classification that diverge from real-world usage, and rely on metrics lacking interpretability and biological grounding. We present SC-ARENA, a natural language evaluation framework tailored to single-cell foundation models. SC-ARENA formalizes a virtual cell abstraction that unifies evaluation targets by representing both intrinsic attributes and gene-level interactions. Within this paradigm, we define five natural language tasks (cell type annotation, captioning, generation, perturbation prediction, and scientific QA) that probe core reasoning capabilities in cellular biology. To overcome the limitations of brittle string-matching metrics, we introduce knowledge-augmented evaluation, which incorporates external ontologies, marker databases, and scientific literature to support biologically faithful and interpretable judgments. Experiments and analysis across both general-purpose and domain-specialized LLMs demonstrate that (i) under the Virtual Cell unified evaluation paradigm, current models achieve uneven performance on biologically complex tasks, particularly those demanding mechanistic or causal understanding; and (ii) our knowledge-augmented evaluation framework ensures biological correctness, provides interpretable, evidence-grounded rationales, and achieves high discriminative capacity, overcoming the brittleness and opacity of conventional metrics. SC-Arena thus provides a unified and interpretable framework for assessing LLMs in single-cell biology, pointing toward the development of biology-aligned, generalizable foundation models.

RuCL: Stratified Rubric-Based Curriculum Learning for Multimodal Large Language Model Reasoning

Reinforcement Learning with Verifiable Rewards (RLVR) has emerged as a prevailing paradigm for enhancing reasoning in Multimodal Large Language Models (MLLMs). However, relying solely on outcome supervision risks reward hacking, where models learn spurious reasoning patterns to satisfy final answer checks. While recent rubric-based approaches offer fine-grained supervision signals, they suffer from high computational costs of instance-level generation and inefficient training dynamics caused by treating all rubrics as equally learnable. In this paper, we propose Stratified Rubric-based Curriculum Learning (RuCL), a novel framework that reformulates curriculum learning by shifting the focus from data selection to reward design. RuCL generates generalized rubrics for broad applicability and stratifies them based on the model's competence. By dynamically adjusting rubric weights during training, RuCL guides the model from mastering foundational perception to tackling advanced logical reasoning. Extensive experiments on various visual reasoning benchmarks show that RuCL yields a remarkable +7.83% average improvement over the Qwen2.5-VL-7B model, achieving a state-of-the-art accuracy of 60.06%.

Beyond Quantity: Trajectory Diversity Scaling for Code Agents

As code large language models (LLMs) evolve into tool-interactive agents via the Model Context Protocol (MCP), their generalization is increasingly limited by low-quality synthetic data and the diminishing returns of quantity scaling. Moreover, quantity-centric scaling exhibits an early bottleneck that underutilizes trajectory data. We propose TDScaling, a Trajectory Diversity Scaling-based data synthesis framework for code agents that scales performance through diversity rather than raw volume. Under a fixed training budget, increasing trajectory diversity yields larger gains than adding more trajectories, improving the performance-cost trade-off for agent training. TDScaling integrates four innovations: (1) a Business Cluster mechanism that captures real-service logical dependencies; (2) a blueprint-driven multi-agent paradigm that enforces trajectory coherence; (3) an adaptive evolution mechanism that steers synthesis toward long-tail scenarios using Domain Entropy, Reasoning Mode Entropy, and Cumulative Action Complexity to prevent mode collapse; and (4) a sandboxed code tool that mitigates catastrophic forgetting of intrinsic coding capabilities. Experiments on general tool-use benchmarks (BFCL, tau^2-Bench) and code agent tasks (RebenchT, CodeCI, BIRD) demonstrate a win-win outcome: TDScaling improves both tool-use generalization and inherent coding proficiency. We plan to release the full codebase and the synthesized dataset (including 30,000+ tool clusters) upon publication.

Automatic Paper Reviewing with Heterogeneous Graph Reasoning over LLM-Simulated Reviewer-Author Debates

Existing paper review methods often rely on superficial manuscript features or directly on large language models (LLMs), which are prone to hallucinations, biased scoring, and limited reasoning capabilities. Moreover, these methods often fail to capture the complex argumentative reasoning and negotiation dynamics inherent in reviewer-author interactions. To address these limitations, we propose ReViewGraph (Reviewer-Author Debates Graph Reasoner), a novel framework that performs heterogeneous graph reasoning over LLM-simulated multi-round reviewer-author debates. In our approach, reviewer-author exchanges are simulated through LLM-based multi-agent collaboration. Diverse opinion relations (e.g., acceptance, rejection, clarification, and compromise) are then explicitly extracted and encoded as typed edges within a heterogeneous interaction graph. By applying graph neural networks to reason over these structured debate graphs, ReViewGraph captures fine-grained argumentative dynamics and enables more informed review decisions. Extensive experiments on three datasets demonstrate that ReViewGraph outperforms strong baselines with an average relative improvement of 15.73%, underscoring the value of modeling detailed reviewer-author debate structures.

RxSafeBench: Identifying Medication Safety Issues of Large Language Models in Simulated Consultation

Numerous medical systems powered by Large Language Models (LLMs) have achieved remarkable progress in diverse healthcare tasks. However, research on their medication safety remains limited due to the lack of real world datasets, constrained by privacy and accessibility issues. Moreover, evaluation of LLMs in realistic clinical consultation settings, particularly regarding medication safety, is still underexplored. To address these gaps, we propose a framework that simulates and evaluates clinical consultations to systematically assess the medication safety capabilities of LLMs. Within this framework, we generate inquiry diagnosis dialogues with embedded medication risks and construct a dedicated medication safety database, RxRisk DB, containing 6,725 contraindications, 28,781 drug interactions, and 14,906 indication-drug pairs. A two-stage filtering strategy ensures clinical realism and professional quality, resulting in the benchmark RxSafeBench with 2,443 high-quality consultation scenarios. We evaluate leading open-source and proprietary LLMs using structured multiple choice questions that test their ability to recommend safe medications under simulated patient contexts. Results show that current LLMs struggle to integrate contraindication and interaction knowledge, especially when risks are implied rather than explicit. Our findings highlight key challenges in ensuring medication safety in LLM-based systems and provide insights into improving reliability through better prompting and task-specific tuning. RxSafeBench offers the first comprehensive benchmark for evaluating medication safety in LLMs, advancing safer and more trustworthy AI-driven clinical decision support.

One Model to Critique Them All: Rewarding Agentic Tool-Use via Efficient Reasoning

Reward models (RMs) play a critical role in aligning large language models (LLMs) with human preferences. Yet in the domain of tool learning, the lack of RMs specifically designed for function-calling tasks has limited progress toward more capable agentic AI. We introduce ToolRM, a family of lightweight generative RMs tailored for general tool-use scenarios. To build these models, we propose a novel pipeline that constructs pairwise preference data using rule-based scoring and multidimensional sampling. This yields ToolPref-Pairwise-30K, a diverse, balanced, and challenging dataset of critique tasks that supports reinforcement learning with verifiable feedback. To evaluate tool-use RMs, we also introduce TRBench$_{BFCL}$, a benchmark built on the agentic evaluation suite BFCL. Trained on our constructed data, models from the Qwen3-4B/8B series achieve up to 14.28% higher accuracy, substantially outperforming frontier models such as Claude 4 and OpenAI o3 in pairwise reward judgments. Beyond training objectives, ToolRM generalizes to broader critique tasks, including Best-of-N sampling and self-correction. Experiments on ACEBench highlight its effectiveness and efficiency, enabling inference-time scaling and reducing output token usage by over 66%. We release data and model checkpoints to facilitate future research.

SemanticST: Spatially Informed Semantic Graph Learning for Clustering, Integration, and Scalable Analysis of Spatial Transcriptomics

Spatial transcriptomics (ST) technologies enable gene expression profiling with spatial resolution, offering unprecedented insights into tissue organization and disease heterogeneity. However, current analysis methods often struggle with noisy data, limited scalability, and inadequate modelling of complex cellular relationships. We present SemanticST, a biologically informed, graph-based deep learning framework that models diverse cellular contexts through multi-semantic graph construction. SemanticST builds multiple context-specific graphs capturing spatial proximity, gene expression similarity, and tissue domain structure, and learns disentangled embeddings for each. These are fused using an attention-inspired strategy to yield a unified, biologically meaningful representation. A community-aware min-cut loss improves robustness over contrastive learning, particularly in sparse ST data. SemanticST supports mini-batch training, making it the first graph neural network scalable to large-scale datasets such as Xenium (500,000 cells). Benchmarking across four platforms (Visium, Slide-seq, Stereo-seq, Xenium) and multiple human and mouse tissues shows consistent 20 percentage gains in ARI, NMI, and trajectory fidelity over DeepST, GraphST, and IRIS. In re-analysis of breast cancer Xenium data, SemanticST revealed rare and clinically significant niches, including triple receptor-positive clusters, spatially distinct DCIS-to-IDC transition zones, and FOXC2 tumour-associated myoepithelial cells, suggesting non-canonical EMT programs with stem-like features. SemanticST thus provides a scalable, interpretable, and biologically grounded framework for spatial transcriptomics analysis, enabling robust discovery across tissue types and diseases, and paving the way for spatially resolved tissue atlases and next-generation precision medicine.

Training Superior Sparse Autoencoders for Instruct Models

As large language models (LLMs) grow in scale and capability, understanding their internal mechanisms becomes increasingly critical. Sparse autoencoders (SAEs) have emerged as a key tool in mechanistic interpretability, enabling the extraction of human-interpretable features from LLMs. However, existing SAE training methods are primarily designed for base models, resulting in reduced reconstruction quality and interpretability when applied to instruct models. To bridge this gap, we propose $\underline{\textbf{F}}$inetuning-$\underline{\textbf{a}}$ligned $\underline{\textbf{S}}$equential $\underline{\textbf{T}}$raining ($\textit{FAST}$), a novel training method specifically tailored for instruct models. $\textit{FAST}$ aligns the training process with the data distribution and activation patterns characteristic of instruct models, resulting in substantial improvements in both reconstruction and feature interpretability. On Qwen2.5-7B-Instruct, $\textit{FAST}$ achieves a mean squared error of 0.6468 in token reconstruction, significantly outperforming baseline methods with errors of 5.1985 and 1.5096. In feature interpretability, $\textit{FAST}$ yields a higher proportion of high-quality features, for Llama3.2-3B-Instruct, $21.1\%$ scored in the top range, compared to $7.0\%$ and $10.2\%$ for $\textit{BT(P)}$ and $\textit{BT(F)}$. Surprisingly, we discover that intervening on the activations of special tokens via the SAEs leads to improvements in output quality, suggesting new opportunities for fine-grained control of model behavior. Code, data, and 240 trained SAEs are available at https://github.com/Geaming2002/FAST.

CLaSp: In-Context Layer Skip for Self-Speculative Decoding

Speculative decoding (SD) is a promising method for accelerating the decoding process of Large Language Models (LLMs). The efficiency of SD primarily hinges on the consistency between the draft model and the verify model. However, existing drafting approaches typically require additional modules to be trained, which can be challenging to implement and ensure compatibility across various LLMs. In this paper, we propose CLaSp, an in-context layer-skipping strategy for self-speculative decoding. Unlike prior methods, CLaSp does not require additional drafting modules or extra training. Instead, it employs a plug-and-play mechanism by skipping intermediate layers of the verify model to construct a compressed draft model. Specifically, we develop a dynamic programming algorithm that optimizes the layer-skipping process by leveraging the complete hidden states from the last verification stage as an objective. This enables CLaSp to dynamically adjust its layer-skipping strategy after each verification stage, without relying on pre-optimized sets of skipped layers. Experimental results across diverse downstream tasks demonstrate that CLaSp achieves a speedup of 1.3x ~ 1.7x on LLaMA3 series models without altering the original distribution of the generated text.

ChARM: Character-based Act-adaptive Reward Modeling for Advanced Role-Playing Language Agents

Role-Playing Language Agents (RPLAs) aim to simulate characters for realistic and engaging human-computer interactions. However, traditional reward models often struggle with scalability and adapting to subjective conversational preferences. We propose ChARM, a Character-based Act-adaptive Reward Model, addressing these challenges through two innovations: (1) an act-adaptive margin that significantly enhances learning efficiency and generalizability, and (2) a self-evolution mechanism leveraging large-scale unlabeled data to improve training coverage. Additionally, we introduce RoleplayPref, the first large-scale preference dataset specifically for RPLAs, featuring 1,108 characters, 13 subcategories, and 16,888 bilingual dialogues, alongside RoleplayEval, a dedicated evaluation benchmark. Experimental results show a 13% improvement over the conventional Bradley-Terry model in preference rankings. Furthermore, applying ChARM-generated rewards to preference learning techniques (e.g., direct preference optimization) achieves state-of-the-art results on CharacterEval and RoleplayEval. Code and dataset are available at https://github.com/calubkk/ChARM.