PatRe: A Full-Stage Office Action and Rebuttal Generation Benchmark for Patent Examination

Patent examination is a complex, multi-stage process requiring both technical expertise and legal reasoning, increasingly challenged by rising application volumes. Prior benchmarks predominantly view patent examination as discriminative classification or static extraction, failing to capture its inherently interactive and iterative nature, similar to the peer review and rebuttal process in academic publishing. In this paper, we introduce PatRe, the first benchmark that models the full patent examination lifecycle, including Office Action generation and applicant rebuttal. PatRe comprises 480 real-world cases and supports both oracle and retrieval-simulated evaluation settings. Our benchmark reframes patent examination as a dynamic, multi-turn process of justification and response. Extensive experiments across various LLMs reveal critical insights into model performance, including differences between proprietary and open-source models, as well as task asymmetries between examiner analysis and applicant-side rebuttal. These findings highlight both the potential and current limitations of LLMs in modeling complex, real-world legal reasoning and technical novelty judgment in patent examination. We release our code and dataset to facilitate future research on patent examination modeling.

Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability

Immune checkpoint inhibitors (ICIs) have transformed cancer therapy; yet substantial proportion of patients exhibit intrinsic or acquired resistance, making accurate pre-treatment response prediction a critical unmet need. Transcriptomics-based biomarkers derived from bulk and single-cell RNA sequencing (scRNA-seq) offer a promising avenue for capturing tumour-immune interactions, yet the cross-cohort generalisability of existing prediction models remains unclear.We systematically benchmark nine state-of-the-art transcriptomic ICI response predictors, five bulk RNA-seq-based models (COMPASS, IRNet, NetBio, IKCScore, and TNBC-ICI) and four scRNA-seq-based models (PRECISE, DeepGeneX, Tres and scCURE), using publicly available independent datasets unseen during model development. Overall, predictive performance was modest: bulk RNA-seq models performed at or near chance level across most cohorts, while scRNA-seq models showed only marginal improvements. Pathway-level analyses revealed sparse and inconsistent biomarker signals across models. Although scRNA-seq-based predictors converged on immune-related programs such as allograft rejection, bulk RNA-seq-based models exhibited little reproducible overlap. PRECISE and NetBio identified the most coherent immune-related themes, whereas IRNet predominantly captured metabolic pathways weakly aligned with ICI biology. Together, these findings demonstrate the limited cross-cohort robustness and biological consistency of current transcriptomic ICI prediction models, underscoring the need for improved domain adaptation, standardised preprocessing, and biologically grounded model design.

PLOT: Enhancing Preference Learning via Optimal Transport

Preference learning in Large Language Models (LLMs) has advanced significantly, yet existing methods remain limited by modest performance gains, high computational costs, hyperparameter sensitivity, and insufficient modeling of global token-level relationships. We introduce PLOT, which enhances Preference Learning in fine-tuning-based alignment through a token-level loss derived from Optimal Transport. By formulating preference learning as an Optimal Transport Problem, PLOT aligns model outputs with human preferences while preserving the original distribution of LLMs, ensuring stability and robustness. Furthermore, PLOT leverages token embeddings to capture semantic relationships, enabling globally informed optimization. Experiments across two preference categories - Human Values and Logic & Problem Solving - spanning seven subpreferences demonstrate that PLOT consistently improves alignment performance while maintaining fluency and coherence. These results substantiate optimal transport as a principled methodology for preference learning, establishing a theoretically grounded framework that provides new insights for preference learning of LLMs.

FlowPIE: Test-Time Scientific Idea Evolution with Flow-Guided Literature Exploration

Scientific idea generation (SIG) is critical to AI-driven autonomous research, yet existing approaches are often constrained by a static retrieval-then-generation paradigm, leading to homogeneous and insufficiently divergent ideas. In this work, we propose FlowPIE, a tightly coupled retrieval-generation framework that treats literature exploration and idea generation as a co-evolving process. FlowPIE expands literature trajectories via a flow-guided Monte Carlo Tree Search (MCTS) inspired by GFlowNets, using the quality of current ideas assessed by an LLM-based generative reward model (GRM) as a supervised signal to guide adaptive retrieval and construct a diverse, high-quality initial population. Based on this population, FlowPIE models idea generation as a test-time idea evolution process, applying selection, crossover, and mutation with the isolation island paradigm and GRM-based fitness computation to incorporate cross-domain knowledge. It effectively mitigates the information cocoons arising from over-reliance on parametric knowledge and static literature. Extensive evaluations demonstrate that FlowPIE consistently produces ideas with higher novelty, feasibility and diversity compared to strong LLM-based and agent-based frameworks, while enabling reward scaling during test time.

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.