Multi-Hypothesis Test-Time Adaptation to Mitigate Underspecification

Test-Time Adaptation (TTA) seeks to improve model robustness under distribution shifts by adapting parameters using unlabeled target data. However, in the absence of supervision, entropy-based adaptation is fundamentally underconstrained: multiple distinct parameter updates can achieve similarly low entropy while inducing drastically different decision boundaries. This phenomenon, known as underspecification, renders standard TTA brittle and prone to collapse into spurious modes. In this work, we reinterpret TTA through a posterior-inspired lens induced by entropy minimization, where low-entropy solutions define a pseudo-likelihood over parameters. Instead of committing to a single point estimate, we introduce a particle-based diversification framework that explores multiple plausible adaptation trajectories simultaneously. Our method can be viewed as a structured exploration of multiple plausible adaptation solutions, implemented through multi-level diversification at the output, parameter, optimizer, and input levels. Crucially, the framework acts as a plug-and-play wrapper compatible with existing TTA methods. Extensive experiments on challenging benchmarks demonstrate consistent gains in stability and robustness, achieving improvements of 3-4% under mixed shifts, 2-3% with batch size one, and 1-2.5% under label shifts, outperforming state-of-the-art baselines. Our results suggest that treating TTA as a multi-hypothesis inference problem, rather than a single-point optimization task, is key to mitigating underspecification and enabling reliable real-world deployment.

SrDetection: A Self-Referential Framework for Data Leakage Detection in Code Large Language Models

Evaluating code large language models (Code LLMs) requires reliable detection of data leakage, where benchmark performance is artificially inflated by exposure to benchmark data during pre-training. Existing approaches either assume access to proprietary training corpora, rely on brittle heuristics such as timestamp filtering, or use external reference sets with manually tuned, non-generalizable thresholds. To address these limitations, we introduce \textbf{SrDetection}, a unified \textbf{s}elf-\textbf{r}eferential leakage detection framework for both gray-box (access to model logits) and black-box (access to model outputs) settings. SrDetection generates semantically equivalent variants of a benchmark sample and detects leakage by contrasting the model's behavior on the original versus its variants, flagging cases where the original is disproportionately easier for the model. We further design a controlled leakage detection testbed and evaluate SrDetection in this environment. Across different models and training stages, SrDetection improves average F1 by 21.52 points in the gray-box setting and 14.46 points in the black-box setting over strong baselines, demonstrating robust, threshold-independent leakage detection. Finally, a gray-box study of 15 widely used Code LLMs on four popular benchmarks reveals benchmark-specific leakage patterns beyond prior overlap-based analyses\footnote{\footnotesize Source code and data are available at https://github.com/SMinL/SrDetectionCode

MS-DKC: A Dataset Knowledge Card Framework for Designing and Adapting Medical Image Segmentation Models

Medical image segmentation is often framed as a search for stronger architectures, but this can obscure a more fundamental question: what does the dataset require from the model? In medical imaging, this requirement is shaped by foreground occupancy, morphology, boundary ambiguity, topology sensitivity, annotation quality, acquisition variation, and operating point. This paper introduces the Medical Segmentation Dataset Knowledge Card (MS-DKC), a framework for making these factors explicit. MS-DKC records dataset evidence through image/acquisition, morphology, supervision, context-dependence, and deployment-risk descriptors. These descriptors are mapped to failure modes, design priors, and risk-aligned criteria, making segmentation design more traceable than architecture-first comparison. We evaluate MS-DKC on DRIVE, ISIC2018, and ACDC, representing distinct regimes. DRIVE contains sparse, thin, branching vessels, favoring detail-preserving models, sensitivity-aware optimization, threshold analysis, and topology-aware metrics. DKC-TNet-v2 achieved Dice 0.8044 and IoU 0.6730 with 35103 parameters, while SA-UNetv2-DKC-AmbRef reached Dice 0.8141, IoU 0.6865, sensitivity 0.8265, specificity 0.9804, and AUC 0.9853. ISIC2018 involves compact but appearance-variable lesions; validation-constrained score-function selection on Att-Next-Topo/ATTNext produced MS-DKC-AttNextTopo-VCSF-NoAug with Dice 0.8872, IoU 0.8214, precision 0.9173, Boundary F1 0.4878, and ASSD 4.13, while plausible additions failed to improve the risk-aligned profile. ACDC provides a multi-class cardiac case, where MS-DKC recommends four-class softmax segmentation, class-balanced Dice/CE supervision, and class-wise surface evaluation. Overall, the results support dataset-conditioned design: different datasets require different priors, operating points, and evidence before a model can be judged appropriate.

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.