RNA molecules often function through multiple experimentally observed conformational states. A central challenge is to capture ensemble diversity without sacrificing structural fidelity: samples may collapse toward averaged representative structures or drift into unsupported conformational regions. We introduce REFLEX (RNA Ensemble generation calibrated by FLEXibility), a sequence-conditioned generator for RNA backbone-frame ensembles based on a heteroscedastic stochastic bridge on SE(3). During training, experimental B-factors calibrate residue-wise bridge widths, exposing each observed conformer through local perturbation neighborhoods with residue-specific scales while keeping constrained regions sharper. A learned flexibility condition guides the bridge-field network to recover target conformer-specific frames from these calibrated noisy states. At inference, REFLEX uses only the input sequence, requiring no MSA-subsampling heuristics. On a multi-conformer RNA benchmark, REFLEX achieves the best precision-recall trade-off for ensemble coverage across evaluation thresholds, while recovery-stress ablations indicate gains in target-frame recovery under stronger perturbations.
Web services built on large language models (LLMs) receive many paraphrases of earlier queries, which a semantic cache answers from stored responses. A reused answer can be wrong, so wrong answers must stay below a share $δ$ of the queries. Existing caches reuse above a fixed similarity threshold or, like vCache, learn a per-entry rule that bounds each query's error by $δ$. However, fixed thresholds break the budget on new streams, and per-entry rules need labels on every entry before reusing it. We find an unspent error budget, as vCache realizes only 12-55% of $δ$ on three public query streams. Surplus spends this budget where reuse is most likely correct. It ranks queries by a risk score shared across paraphrase clusters and opens risk bins as far as an audited error estimate allows. Free labels from every LLM call and a ledger of realized errors keep this threshold safe under drift. On five streams, including ORCAS search queries, Surplus holds $δ$ in every test cell, which no baseline does. On the shuffled streams it serves 40% more hits than vCache, and its pooled hit rate beats the best baseline holding $δ$ in each cell by 4.10 points. In a vLLM testbed it cuts the mean latency by 31.59% at the highest load, against 23.67% for vCache.
Farbod Tavakkoli, Gregory Diamos, Kenneth Church, Roderic Paulk, Ashish Vaswani, David Kanter, Jorden Terrazas, Mark Austin 等 13 位作者
We present Open Telco (OTel), an open telecom AI resource that releases derived telecom datasets for retrieval, reranking, instruction tuning, and safety/abstention, together with 30 full-parameter post-trained baselines spanning 10 embedding models, 3 rerankers, and 17 language models. The community has already engaged substantially with the resource: as of May 3, 2026, the released models have been downloaded over 16 million times and the project has received 157+ pieces of media coverage worldwide. Building on prior open telecom datasets and benchmarks, OTel provides documented telecom data sources, held-out evaluation partitions, trained embedding models, rerankers, context-grounded LLMs, and safety/abstention data in one unified resource. Each baseline starts from an open-weight model and is post-trained on OTel-derived data using an open training recipe, then evaluated on held-out OTel evaluation partitions. OTel post-training improves performance across all three model families: embedding retrieval reaches 93.1% NDCG@10, reranking reaches 0.947 MRR@10, and language-model correctness reaches 87.8%. We release OTel as a reproducible starting point and invite the community to expand the data, improve embedding and reranking models, and build stronger context-grounded telecom LLMs.
Software development sessions often involve several unfinished tasks rather than one issue carried through to completion. As coding agents take on repository-level development, they need to recover an earlier task's requirements and partial progress after intervening work. Existing repository-level benchmarks typically score one issue-to-patch episode and do not directly measure whether an agent can resume a task after advancing other unfinished work in the same repository. We introduce \textbf{\ourmethod}, a benchmark for focus-task resumption in sessions that interleave unfinished tasks drawn from the same source repository, with a persistent checkout for each task. Each focus task is evaluated in matched uninterrupted and switched sessions with identical focus requirements and executable verifiers. The switched session interleaves ordered stages from other unfinished tasks in the same repository, while only the final focus patch is scored. \ourmethod~contains 200 focus tasks from 19 Python repositories, reconstructed from issue, pull-request, and review histories and rendered as 400 matched session specifications. Across 7 coding agents, interleaved unfinished work produces an average focus-task resolution gap of 11.5 percentage points, ranging from 6.0 to 15.0 percentage points. Trajectory analysis identifies cross-task requirement confusion and loss of task state as recurrent resumption behaviors. We introduce a plug-in context-management module that selects task-relevant history and maintains concise task-state summaries. On OpenCode, the module improves focus-task completion under same-repository task switching by 5.5 to 15.5 percentage points across the evaluated models. Code is available at github.com/Miraclecsc/Switch-SWE.
Hongxuan Liu, Roman Bushuiev, Ivy Lightheart, Mrunali Manjrekar, Anton Bushuiev, Magdalena Lederbauer, Filip Jozefov, Yinkai Wang 等 15 位作者
Reliable benchmarking is critical for developing machine learning models for tandem mass spectrometry (MS/MS) based molecule discovery. Subtle issues in experimental design and model evaluation procedures can degrade the trustworthiness of such benchmarks and lead to erroneous conclusions. We conduct a thorough review of model evaluation issues in the recent MS/MS machine learning literature, using the standard MassSpecGym benchmark suite as a case study to illustrate the impact of these issues. We find evaluation issues in at least 17 of 26 papers reporting MassSpecGym benchmark results in the first year of its adoption. We isolate three classes of failures: (i) data leakage, (ii) shortcut learning, and (iii) implementation bugs and metric divergence. Through extensive experimentation and code replication, we quantify the impact of these issues and show how they corrupt the evaluation standards MassSpecGym was designed to enforce. We distill our findings into recommendations generalizable to MS/MS challenges, benchmarks, and custom evaluation setups. We also release MassSpecGym v1.5, an implementation of our recommendations in the MassSpecGym benchmarking suite which addresses the failure modes identified in this audit. MassSpecGym v1.5 is publicly available at https://github.com/pluskal-lab/MassSpecGym.
Visual foundation models learn rich pathological morphology but lack explicit concept-level supervision. Vision--language pretraining can provide this supervision but requires costly image--text pairs. Here, we introduce GloSAGE, a semantic self-distillation framework that uses lesion profiles predicted by a pretrained visual teacher to construct structured pathology descriptions. Reliability-guided selection identifies image--text anchors, while Knowledge-Structured Pathology Text Synthesis and Evidence-Guided Negative-pair Construction account for partially observed lesions. Image--text alignment trains projection layers while retaining the frozen visual encoder; an intermediate Semantic Transfer Layer supplies features for downstream tasks. Developed on GloMillion and evaluated across seven glomerulus- and case-level cohorts, GloSAGE supported zero-shot lesion recognition, image--text retrieval, hard-negative discrimination and concept-intervention analyses. It outperformed its source visual model in most lesion-recognition tasks and improved lesion grading, while supporting competitive case-level disease classification, injury grading and baseline renal function estimation. Ablations supported the combined contributions of knowledge-structured text and evidence-guided negatives, and the intermediate transfer layer improved mean lesion-recognition ROC-AUC relative to the complete projection output. A frozen language model conditioned on GloSAGE features generated glomerular descriptions. These findings suggest that teacher-derived lesion profiles can provide annotation-efficient semantic supervision for extending a glomerular visual foundation model.
The ratio of two densities provides a direct characterization of their differences. We consider the two-sample comparison problem by estimating this ratio given i.i.d. observations from two distributions. To this end, we propose additive tree models for density ratio estimation along with efficient algorithms using a new loss function, the balancing loss. The loss allows tree-based models to be trained using several algorithms originally designed for supervised learning, such as forward-stagewise optimization and gradient boosting. Moreover, the balancing loss resembles an exponential family kernel, and it can serve as a pseudo-likelihood with conjugate priors. This property enables generalized Bayesian inference on the density ratio using backfitting samplers designed for Bayesian additive regression trees (BART). Our Bayesian strategy provides uncertainty quantification for the inferred density ratio, which is critical for applications involving high-dimensional and data-limited distributions with potentially substantial uncertainty. We further show connections of the balancing loss to the exponential loss in binary classification and to the variational form of f-divergence, particularly the squared Hellinger distance. Numerical experiments demonstrate that the proposed boosting algorithms achieve high accuracy at low computational cost, and that the Bayesian additive tree is competitive in accuracy while additionally providing uncertainty quantification, which the compared estimators do not offer. Finally, we demonstrate its application to assessing the quality of generative models for microbiome compositional data.
Nearly incompressible materials arise in soft tissues, elastomers, gels, and other soft solids. Yet, numerical modeling remains challenging because displacement-based formulations can exhibit volumetric locking near incompressibility. Mixed displacement-pressure formulations address this difficulty but require compatible approximation spaces satisfying the inf-sup condition. In mixed formulations, discontinuous pressure spaces are attractive since pressure degrees of freedom can be condensed locally. In high-order isogeometric analysis, however, their Galerkin stability requires pressure-grid coarsening that increases with polynomial degree. Here, we develop a variational multiscale (VMS) stabilized mixed isogeometric formulation that retains this locality while substantially relaxing the restriction. The key observation is that VMS stabilization controls nonconstant elementwise pressure modes and is unconditionally stable with respect to its parameter, provided the elementwise constant pressure component satisfies the inf-sup condition. Consequently, for maximally continuous displacement splines, a pressure grid coarsened by a factor of two satisfies the constant-mode inf-sup criterion independently of polynomial degree. Local condensation then yields a displacement-only system, facilitating use in existing displacement solvers. The formulation is further extended to immersed isogeometric analysis with extended B-splines, pressure-cell aggregation, subdivision-based cut-cell quadrature, and weak enforcement of essential boundary conditions. Discrete inf-sup studies and convergence analyses in the Kirsch and Cook's membrane benchmarks demonstrate stability and show that the immersed treatment preserves mixed stability properties. The proposed framework therefore provides a local, high-order, and robust approach for nearly incompressible problems in mesh-conforming and immersed settings.
We study the algebraic compatibility between quantum homomorphic encryption and stabilizer quantum error correction in an honest-but-curious model, restricting the encryption to the transversal block-Pauli mask $(X^aZ^b)^{\otimes n}$ controlled by two secret key bits $a$ and $b$. We prove a necessary and sufficient criterion for an $[[n,1,d]]$ stabilizer code to remain compatible with this mask, namely that the transversal $X$ and $Z$ operators commute with every stabilizer generator, and we specialize it to a classical-code criterion for Calderbank--Shor--Steane codes. Combining code-space preservation with the logical action of the mask, every stabilizer code falls, with respect to each of the two transversal mask operators, into exactly one of three classes: incompatible, compatible but trivially acting, or compatible with a nontrivial logical Pauli action; the two operators need not fall into the same class. We verify this classification by exact symplectic computation for rotated and planar surface codes, toric codes, triangular and toric color codes, the $[[15,1,3]]$ code and several small codes, and find that the class is fixed by the lattice size and the boundary presentation rather than by the topological phase: the surface-code family realizes all three classes, whereas color codes realize only the two compatible ones. For encrypted computation we show that the Shor code does not implement the logical $T$ gate by a transversal $T^{\otimes 9}$, whereas suitable triorthogonal codes do so up to a Clifford correction. We formulate logical-Pauli masking as a code-independent algebraic template. Syndrome extraction and recovery are key-independent whenever the mask preserves the code space, so that the client only needs the block size and the class of the code to decrypt.
Montgomery Bohde, Hongxuan Liu, Mrunali Manjrekar, Magdalena Lederbauer, Shuiwang Ji, Runzhong Wang, Connor W. Coley
Tandem mass spectrometry is prominent in scientific discovery workflows for identifying unknown small molecules, yet high-throughput structural elucidation remains challenging. While recent autoregressive and graph diffusion models have shown promise in de novo elucidation, performance remains limited by poor scalability during both training and inference time. In this work, we present FRIGID, a framework with a novel diffusion language model that generates molecular structures conditioned on mass spectra via intermediate fingerprint representations and determined chemical formulae, training at the scale of hundreds of millions of unlabeled structures. We then demonstrate how forward fragmentation models enable inference-time scaling by identifying spectrum-inconsistent fragments and refining them through targeted remasking and denoising. While FRIGID already achieves strong performance with its diffusion base, inference-time scaling significantly improves its accuracy, surpassing 18% Top-1 accuracy on the challenging MassSpecGym benchmark and tripling the Top-1 accuracy of the leading methods on NPLIB1. Further empirical analyses show that FRIGID exhibits log-linear performance scaling with increasing inference-time compute, opening a promising new direction for continued improvements in de novo structural elucidation. FRIGID code is publicly available at https://github.com/coleygroup/FRIGID.
Ge Chang, Jinbo Su Renmin University of China, Jiacheng Liu, Pengfei Yang, Yuhao Shang, Huiwen Zheng, Hongli Ma GDS, Yan Liang 等 10 位作者
Integrating textual graphs into Large Language Models (LLMs) is promising for complex graph-based QA. However, a key bottleneck is retrieving informative yet compact subgraphs that fit the LLM context. Existing retrievers often struggle, relying either on shallow embedding similarity or costly interactive policies that require excessive supervision.To address these challenges, we introduce Graph-S^3, an agentic textual graph reasoning framework featuring an LLM-based retriever trained with synthetic stepwise supervision. Rather than relying on final answer rewards—which often yield sparse and unstable signals—we optimize the retriever by evaluating each step against offline-extracted golden subgraphs.Our approach distills golden subgraphs via a specialized data synthesis pipeline to formulate dense rewards, facilitating a two-stage training scheme that effectively learns the interactive graph exploration policy.Based on extensive experiments on three common datasets in comparison with seven strong baselines, our approach achieves an average improvement of 15.6% in accuracy and 17.2% in F_1 score. The advantage is even higher in more complicated multi-hop reasoning tasks.
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cs.CL · cs.AI
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Shuochen Chang Shanghai Jiaotong University and ByteDance Inc., Tong Bai, Xiaofeng Zhang, Qianli Ma Shanghai Jiao Tong University, Qingyang Liu, Zhaohe Liao Alibaba Group and Shanghai Jiao Tong University, Yibo Miao Moonshot AI, Li Niu Shanghai Jiao Tong University
Latent reasoning enables Large Language Models (LLMs) to perform multi-step inference within continuous hidden states, offering efficiency gains over explicit Chain-of-Thought (CoT). However, the opacity of these continuous thought vectors hinders their reliability and controllability. This paper bridges the gap between mechanistic interpretability and actionable control. We first present a systematic analysis using structural, causal, and geometric probes, revealing that latent vectors encode compressed, faithful representations of reasoning steps, with early vectors acting as critical causal hubs. Building on this, we operationalize these interpretability insights into a suite of training-free, decode-time interventions that refine the latent reasoning process by imposing the identified geometric and semantic priors. Extensive experiments across multiple model scales and diverse task domains demonstrate that our approaches consistently improve reasoning accuracy. Our interpretability-guided interventions consistently unlock latent capabilities and improve reasoning accuracy without any parameter updates.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Michael Ginn University of Colorado at Boulder, Lindia Tjuatja CMU, Carnegie Mellon University, Enora Rice University of Colorado at Boulder, Ali Marashian University of Colorado at Boulder, Maria Valentini University of Colorado at Boulder, Jasmine Xu CMU, Carnegie Mellon University, Graham Neubig Carnegie Mellon University, Alexis Palmer University of Colorado at Boulder
Automated interlinear gloss prediction with neural networks is a promising approach to accelerate language documentation efforts. However, while state-of-the-art models like GlossLM (Ginn et al., 2024) achieve high scores on glossing benchmarks, user studies with linguists have found critical barriers to the usefulness of such models in real-world scenarios (Rice et al., 2025). In particular, existing models typically generate morpheme-level glosses but assign them to whole words without predicting the actual morpheme boundaries, making the predictions less interpretable and thus untrustworthy to human annotators.We conduct the first study on neural models that jointly predict interlinear glosses and the corresponding morphological segmentation from raw text. We run experiments to determine the optimal way to train models that balance segmentation and glossing accuracy, as well as the alignment between the two tasks. We extend the training corpus of GlossLM and pretrain PolyGloss, a family of seq2seq multilingual models for joint segmentation and glossing that outperforms GlossLM on glossing and beats various open-source LLMs on segmentation, glossing, and alignment. In addition, we demonstrate that PolyGloss can be quickly adapted to a new dataset via low-rank adaptation.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Qianli Ma Shanghai Jiao Tong University, Chang Guo, Zhiheng Tian, Siyu Wang, Jipeng Xiao, Yuanhao Yue Alibaba Group, Zhipeng Zhang Shanghai Jiaotong University and Didi Research
Writing effective rebuttals is a high-stakes task that demands more than linguistic fluency, as it requires precise alignment between reviewer intent and manuscript details. Current solutions typically treat this as a direct-to-text generation problem, suffering from hallucination, overlooked critiques, and a lack of verifiable grounding. To address these limitations, we introduce RebuttalAgent, the first multi-agents framework that reframes rebuttal generation as an evidence-centric planning task. Our system decomposes complex feedback into atomic concerns and dynamically constructs hybrid contexts by synthesizing compressed summaries with high-fidelity text while integrating an autonomous and on-demand external search module to resolve concerns requiring outside literature. By generating an inspectable response plan before drafting, RebuttalAgent ensures that every argument is explicitly anchored in internal or external evidence. We validate our approach on the proposed RebuttalBench and demonstrate that our pipeline outperforms strong baselines in coverage, faithfulness, and strategic coherence, offering a transparent and controllable assistant for the peer review process. Code will be released.
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cs.CL · cs.MA
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
This paper presents the first end-to-end pipeline for Handwritten Text Recognition (HTR) for Old Nepali, a historically significant but low-resource language. We adopt a line-level transcription approach and systematically explore encoder-decoder architectures and data-centric techniques to improve recognition accuracy. Our best model achieves a Character Error Rate (CER) of 4.9%. In addition, we implement and evaluate decoding strategies and analyze token-level confusions to better understand model behavior and error patterns. Although the evaluation dataset is confidential, we release our training code, model configurations, and evaluation scripts to support further research on HTR for low-resource historical scripts.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Weakly Supervised Video Anomaly Detection (WSVAD) aims to localize abnormal segments using only video-level labels during training.Although the paradigm significantly reduces annotation costs, the coarse-grained labels fail to precisely describe the full videos, resulting in the introduction of substantial Weakly Labeled Information (WLI) during training. The presence of WLI makes it difficult for the model to accurately learn the boundary between normal and abnormal behaviors, leading to misclassifications and compromising the precision of anomaly localization.To tackle the challenges posed by WLI, we propose a triplet learning strategy that selects hard segments from normal videos as anchors. By combining contrastive learning with Multiple Instance Learning (MIL) strategy, we increase the projection distance between abnormal segments and anchor samples, to reduce the interference of WLI in anomaly detection.Moreover, considering that anomalies typically occur in dynamic foreground regions, we further design a motion-aware feature enhancement module that extracts dynamic areas within each video segment to emphasize the representation of critical features.This not only improves the accuracy of anchors in triplets, but also enhances the discriminative power of instance features in MIL. Extensive experiments on UCF-Crime, XD-Violence, and MSAD datasets demonstrate the effectiveness of our approach.
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cs.CV
Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition · 2026 · 正式发表
We present Artiverse, a diverse and physically grounded dataset of high-quality articulated 3D objects designed for realistic functional modeling and simulation. Artiverse contains 5.4K human-authored objects across a broad range of 88 categories, aggregated from multiple 3D static repositories. Objects are annotated with functional parts, interior structures, realistic kinematic relationships including multi-DoF joints, and physical attributes such as metric scale, material, and mass. We develop a semi-automated annotation pipeline that combines few-shot segmentation, geometric reasoning, and multi-stage human verification to achieve high-quality and efficient annotation, reducing manual annotation time by over 30%. We demonstrate the value of Artiverse on tasks of part mobility analysis, articulated object generation, and physics-based interaction. Artiverse provides a data resource to advance functional understanding for articulated objects.
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cs.CV
Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition · 2026 · 正式发表