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01.
arXiv (CS.LG) 2026-06-19

Agentic Symbolic Search: Characterizing PDEs Beyond Hand-crafted Expressions, Meshes, and Neural Networks

arXiv:2606.20467v1 Announce Type: new Abstract: Mathematicians understand a PDE solution through mathematical structures rather than tables of computed values. Historically, this has been the product of mathematical analysis, carried out by hand for each problem individually. Neither numerical simulation nor neural networks produce those structures directly. We propose Agentic Symbolic Search (ASYS), a prior-guided framework in which an agent translates PDE theory, public problem constraints, and accumulated search experience into testable differentiable symbolic programs. The mathematical forms are refined under evolutionary search, while their continuous parameters are fit by gradient-based optimization. This makes the search an automated form of inductive-bias injection rather than blind symbolic regression. For problems with known analytical forms, ASYS recovers these forms naturally; for other problems, ASYS constructs analytical approximations which can guide mathematicians toward further analysis. In our experiments, across five problems spanning bounded dynamics, finite-time blow-up, and free-boundary focusing, ASYS produces interpretable representations, including a geometric interface formula for Allen-Cahn 2D dynamics and a nine-parameter contraction law for Keller-Segel chemotactic blow-up, in settings where no closed-form description was previously available. ASYS shows the possibility of a new paradigm for characterizing PDE solutions, beyond handcrafted analytical solutions, mesh-based numerical solutions, and neural network approximations.

02.
arXiv (CS.CV) 2026-06-19

ReA-OVCD: Reliability-Aware Open-Vocabulary Change Detection via Semantic and Spatial Refinement

Unlike traditional remote sensing change detection that relies on predefined categories, Open-Vocabulary Change Detection (OVCD) identifies land cover changes flexibly using arbitrary text prompts. However, existing methods suffer from an inherent trade-off when modeling changes: instance-level comparison overlooks fine-grained semantic variations (e.g., partial building extensions), while direct pixel comparison proves unreliable, yielding unstable responses and boundary artifacts due to semantic ambiguity and spatial inconsistency. To this end, we propose an efficient training-free Reliability-Aware Open-Vocabulary Change Detection (ReA-OVCD) framework. It first derives candidate change regions from pixel-wise semantic discrepancies to ensure flexible and detailed localization. To ensure reliability, it subsequently introduces a collaborative refinement strategy to explicitly model change validity from both semantic and spatial perspectives. Specifically, we develop a Semantic Change Reasoning (SCR) module that reassesses changes by jointly analyzing distributional divergence and response variation, enabling the suppression of incidental inconsistencies while preserving reliable semantic shifts. In addition, a Boundary-aware Change Refinement (BCR) module is designed to mitigate artifacts stemming from boundary misalignment and uncertainty through validating whether candidate regions are supported by reliable interior pixels. Extensive experiments across multiple datasets (LEVIR-CD, WHU-CD, DSIFN, and SECOND) demonstrate that our method consistently outperforms state-of-the-art approaches, achieving $\mathrm{F}_{1}^{C}$ improvements of 2.13\% to 9.75\% with higher computational efficiency. The code is publicly available at \https://github.com/Funny0101/ReA-OVCD

03.
arXiv (CS.CL) 2026-06-19

Beyond the GUI Paradigm: Do Mobile Agents Need the Phone Screen?

Recent advances in mobile agents are dominated by the GUI paradigm, in which agents perceive UI information and emit screen interactions. However, mobile platforms also expose a command-line interface (CLI) that provides direct access to device services and data. We argue CLI deserves first-class consideration alongside GUI. We evaluate three coding agents (Claude Code, Terminus-2, mini-swe-agent) across four model APIs on AndroidWorld and MobileWorld without any mobile-specific post-training, comparing against three reproducible GUI baselines (GUI-Owl-1.5-32B, MAI-UI, Qwen3-VL-32B). Claude Code (Opus 4.7) reaches 71.8\% and 51.9\%, outperforming every reproducible GUI baseline (69.3/68.1/57.8\% on AndroidWorld; 43.2/26.3/13.3\% on MobileWorld), while every other CLI configuration remains competitive. To establish the paradigm's ceiling, we provide oracle CLI solutions that reach 88.8\% on AndroidWorld (103/116 tasks CLI-solvable) and 86.3\% on MobileWorld (101/117 tasks CLI-solvable), indicating substantial room for future improvement. To cover everyday user intents beyond the GUI scope, we introduce the CLI-Advantage Task Suite, comprising 45 templates across five categories: bulk operations, multi-condition filtering, aggregation, cross-app workflows, and hidden device state. Every CLI agent outperforms every GUI baseline in all five categories, with substantially fewer steps per task (10.7 vs.\ 18.6). To support future research on mobile CLI agents, we will open-source agent implementations, oracle solutions, the CLI-Advantage suite, and evaluation infrastructure.

04.
PLOS Medicine 2026-05-08

Climate change and non-communicable diseases: An invisible syndemic

by Gokul Parameswaran, Sadeer Al-Kindi, Sanjay Rajagopalan Climate change accelerates non-communicable diseases (NCDs) through cascading environmental disruptions and is attributed to driving increased NCD-related mortality. Yet this syndemic remains invisible and underfunded. We detail why addressing the climate-NCD intersection is critical for improving health. In this Perspective, Sanjay Rajagopalan and colleagues discusses how climate change accelerates non-communicable diseases (NCDs) and exacerbates NCD-related mortality, and calls for greater visibility and funding to address this syndemic and improve human health.

05.
arXiv (CS.LG) 2026-06-19

Evaluating deep learning models for fault diagnosis of a rotating machinery with epistemic and aleatoric uncertainty

arXiv:2412.18980v2 Announce Type: replace Abstract: Uncertainty-aware deep learning (DL) models recently gained attention in fault diagnosis as a way to promote the reliable detection of faults when out-of-distribution (OOD) data arise from unseen faults (epistemic uncertainty) or the presence of noise (aleatoric uncertainty). In this paper, we present the first comprehensive comparative study of state-of-the-art uncertainty-aware DL architectures for fault diagnosis in rotating machinery, where different scenarios affected by epistemic uncertainty and different types of aleatoric uncertainty are investigated. The selected architectures include sampling by dropout, Bayesian neural networks, and deep ensembles. Moreover, to distinguish between in-distribution and OOD data in the different scenarios two uncertainty thresholds, one of which is introduced in this paper, are alternatively applied. Our empirical findings offer guidance to practitioners and researchers who have to deploy real-world uncertainty-aware fault diagnosis systems. In particular, they reveal that, in the presence of epistemic uncertainty, all DL models are capable of effectively detecting, on average, a substantial portion of OOD data across all the scenarios. However, deep ensemble models show superior performance, independently of the uncertainty threshold used for discrimination. In the presence of aleatoric uncertainty, the noise level plays an important role. Specifically, low noise levels hinder the models' ability to effectively detect OOD data. Even in this case, however, deep ensemble models exhibit a milder degradation in performance, dominating the others. These achievements, combined with their shorter inference time, make deep ensemble architectures the preferred choice.

06.
arXiv (CS.AI) 2026-06-16

Artificial Intelligence Index Report 2026

arXiv:2606.15708v1 Announce Type: new Abstract: Welcome to the ninth edition of the AI Index report. As AI continues to advance rapidly, the question becomes whether the systems built around it can keep up. Governance frameworks, evaluation methods, education systems, and the data infrastructure needed to track AI's impact are struggling to match the pace of the technology itself. That gap between what AI can do and how prepared we are to manage it runs through every chapter of this year's report. New in this edition, the report tracks how AI is being tested more ambitiously across reasoning, safety, and real-world task execution, and why those measurements are increasingly difficult to rely on. It also features new estimates of generative AI's economic value alongside emerging evidence of its labor market effects, an analytical framework on AI sovereignty, and a science chapter developed in collaboration with Schmidt Sciences. For the first time, the report features standalone chapters on AI in science and AI in medicine, reflecting AI's growing impact across these two domains.

07.
arXiv (CS.CV) 2026-06-12

Learning Task-Aware Sampling with Shared Saliency through Density-Equalizing Mappings

In image and surface-based learning tasks, convolutional features are typically extracted using receptive fields that are sampled uniformly across the entire domain. However, informative structures are rarely distributed uniformly in practice and are often concentrated in localized regions. Such phenomena are particularly common in medical imaging, where pathological changes are spatially confined. Consequently, uniform convolution allocates equal computational effort to both informative and uninformative regions, resulting in inefficient feature extraction and suboptimal utilization of model capacity. To address this issue, we propose a framework for task-adaptive sampling that dynamically redistributes computational attention according to the spatial importance of the data. Specifically, we introduce the Density-Equalizing Convolutional Neural Network (DECNN), which employs density-equalizing mappings to guide convolution through a learned density function. The density function encodes the relative importance of different regions and induces a transformation that enlarges informative areas while compressing less relevant ones. As a result, convolutional receptive fields are redistributed non-uniformly over the domain, enabling denser sampling in task-relevant regions. By coupling this importance-driven transformation with convolution, DECNN performs adaptive feature extraction that focuses computational resources on informative structures. This leads to more efficient use of model capacity, yielding a lightweight yet expressive architecture while simultaneously producing an interpretable saliency map. Experiments on image classification and craniofacial surface analysis demonstrate that DECNN achieves competitive or superior performance with fewer parameters, accurately identifies task-relevant regions, and remains robust under complex geometric variations.

08.
arXiv (CS.CV) 2026-06-16

Landmark-free Assessment of Lower-limb Alignment with Implicit Neural Shape Functions from Knee Radiographs

Radiographic assessment of lower-limb alignment (LLA) is important for predicting joint health and surgical outcomes in total knee arthroplasty. Traditional measurement methods are manual and time-consuming, while recent machine learning approaches typically rely on locating a fixed set of anatomical landmarks. This dependence limits flexibility and may require re-annotation when clinical definitions change. To address this, we propose an automated workflow using Implicit Neural Shape Functions (INSF). Rather than relying on explicit landmark coordinates, we encode the anatomy into a compact latent space and regress clinical alignment measurements directly from these latent codes. This architecture allows for rapid extendability to new tasks without altering the backbone representation. We trained our method on an internal dataset of 566 knee radiographs, each annotated with the outline of the femur and tibia. We evaluated it on both an internal test dataset of 50 patients and a separate external set of 402 preoperative cases from the MRKR dataset. Manual clinical measurements are available for these data, and the MRKR measurements will be made publicly accessible. Performance was comparable to state-of-the-art landmark-based methods and manual agreement, while offering a flexible shape representation that can be extended to additional measurement tasks.

09.
arXiv (quant-ph) 2026-06-15

Tensor network manifolds and Riemannian fundamental theorem for tensor networks

arXiv:2606.14613v1 Announce Type: cross Abstract: Tensor networks provide a powerful framework for efficiently representing high-dimensional data and many-body quantum states. Endowing tensor networks with a Riemannian manifold structure provides a natural setting for numerical optimization and analysis. A central feature of tensor networks is their gauge freedom, whose characterisation (captured by so-called fundamental theorems) underlies both their intrinsic structure and the design of numerical algorithms. In this work, we study the interaction between the Riemannian manifold structure and the gauge freedom for several families of tensor networks. Using group actions and Riemannian submersions, we establish a Riemannian fundamental theorem for the tensor network families studied.

10.
arXiv (CS.AI) 2026-06-12

AgentRivet: an automated system for producing Rivet routines from journal publications

arXiv:2606.13535v1 Announce Type: cross Abstract: Particle physics collider experiments provide Rivet routines as part of the analysis preservation strategy for model-independent measurements. Rivet is a C++ toolkit that allow new theoretical models to be compared to the measurements, thus aiding the development and tuning of Monte Carlo event generators as well as searches for physics beyond the Standard Model. However, analysis coverage is known to be incomplete, with only 39% of measurements having documented and publicly available Rivet routines. In this article, we design and implement an automated workflow based on Large Language Models with the goal of providing the missing routines. This multi-step workflow, referred to as AgentRivet, extracts the physics analysis information from published papers and writes the missing Rivet routines, with intermediate code- and physics- reviews as part of an autonomous quality control. We report the results obtained using commercial Large Language Models, provided by OpenAI, Anthropic, and Google, for two recent measurements from the ATLAS and CMS experiments. We find that AgentRivet produces competent Rivet routines with few syntax errors. The physics fidelity of the routines is reasonable and follows the explanations given in the relevant publications. Nevertheless, physics-implementation issues do arise and are investigated using the artefacts produced by AgentRivet. The majority of physics implementation issues arise from subtle-but-ambiguous definitions in the given publication, although some models struggle to implement complex observables even when clear definitions are given.

11.
medRxiv (Medicine) 2026-06-10

Global and local genetic overlap among ME/CFS, irritable bowel syndrome and psychiatric traits: a hypothesis-generating analysis

Authors:

Background. Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and irritable bowel syndrome (IBS) frequently co-occur following infection, yet shared genetic architecture at the locus level has not been systematically characterised. Aims. To estimate global and local genetic correlations between ME/CFS (including infection-onset subgroup), IBS, major depressive disorder (MDD) and loneliness/isolation, and characterise ME/CFS cell-type heritability enrichment. Method. GWAS summary statistics: DecodeME (15,579 ME/CFS; 9,738 infection-onset), FinnGen R9 (9,296 IBS), PGC MDD Wave 2 (45,396) and UK Biobank loneliness (N=455,364). LDSC for global correlations; LAVA for local correlations across 2,495 loci; MAGMA for cell-type enrichment (Descartes Human atlas); coloc.abf for colocalisation. Results. All pairwise global correlations were significant after Bonferroni correction, including ME/CFS-all-MDD (rg=0.598, 95% CI 0.46-0.74) and ME/CFS-all-IBS (rg=0.573, 0.39-0.75). Of 4,232 local tests, 16 reached FDR

12.
arXiv (CS.CV) 2026-06-17

Spatio-Temporal Fusion Model for Standard View Classification of Echocardiographic Videos

Automated classification of standard echocardiographic views is crucial for efficient clinical workflow but faces three main challenges. First, publicly available datasets are scarce and limited in scale and view coverage. Second, the performance of some modern video-level architectures for echocardiographic view classification remains underexplored. Third, some view categories exhibit highly similar spatial appearances, making single-frame features insufficient for discrimination, while heterogeneous frame quality complicates robust temporal information fusion. To address these challenges, we release the Echocardiographic Videos of Nine Views (EV9V) dataset, comprising 5,138 videos, 910,579 frames, and 9 standard views, which is, to the best of our knowledge, the largest publicly available echocardiography video dataset. Using EV9V, we systematically benchmark representative video classification architectures, including Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), and Transformers. Furthermore, we propose a Spatio-Temporal Fusion Model (STFM), an efficient dual-stream CNN-LSTM (Long Short-Term Memory) framework that jointly captures spatial anatomical structures and temporal cardiac dynamics. The proposed framework leverages uncertainty-aware learning to preferentially sample representative video segments during training and evidence-based fusion during inference, improving robustness to variations in frame quality across echocardiographic videos. Extensive experiments demonstrate that our method achieves competitive performance across diverse video classification models, validating the effectiveness of uncertainty-aware spatio-temporal learning for echocardiographic view classification. The code is available at https://github.com/bgx666/stfm.

13.
arXiv (CS.AI) 2026-06-17

MemTrace: Probing What Final Accuracy Misses in Long-Term Memory

arXiv:2606.17328v1 Announce Type: new Abstract: LLM agents increasingly maintain long-term memory of user facts across sessions. Yet such memory is usually evaluated by aggregating accuracy over question rows or episodes. Because this approach scores question rows independently, even when several questions probe the same fact, it cannot show how that fact behaves as conditions change. We introduce MemTrace, a benchmark whose unit of measurement is the knowledge point: a single typed fact about the user, rather than an individual question. MemTrace probes each fact along three controlled dimensions: memory age, defined by how many sessions ago the fact appeared in the history; question type, covering current state, earlier state, and trajectory of change; and evidence condition, covering present, missing, and contradicted-by-false-premise settings. Evaluating 13 memory-system configurations across four paradigms, we find that similar pooled accuracy hides different failures: recovering a fact's current and earlier states does not imply tracking how it changed, and safe abstention does not imply correcting a false premise. The dominant bottleneck is evidence use, not retrieval: when systems fail, the evidence was retrievable 10 times more often than it was missing. These results suggest that improving long-term memory requires better use of reachable evidence, not simply more storage or retrieval.

14.
arXiv (CS.AI) 2026-06-16

JetParticle-JEPA: An Efficient Self-Supervised Representation Learning method for Jet Tagging in High-Energy Physics

arXiv:2606.14813v1 Announce Type: cross Abstract: Jet tagging at the Large Hadron Collider increasingly relies on deep learning models trained on massive simulated datasets, leading to high computational costs and limited robustness to detector mismodeling. We introduce JetParticle-JEPA (JP-JEPA), a self-supervised Joint-Embedding Predictive Architecture that learns physically meaningful jet representations directly from continuous particle clouds without tokenization or reconstruction of raw inputs. Built on a Particle Transformer backbone, JP-JEPA predicts latent representations of masked particles while preserving fine-grained kinematic correlations. On the JetClass benchmark, JP-JEPA achieves performance comparable to fully supervised state-of-the-art methods on the full dataset, surpasses supervised baselines in low-label regimes, and significantly outperforms existing SSL approaches. On Top Quark and Quark-Gluon Tagging benchmarks, it remains on par with supervised methods. The learned representations also exhibit strong robustness to missing detector information and improved uncertainty behavior, highlighting JP-JEPA as a promising foundation-model framework for robust and data-efficient jet physics at the LHC.

15.
arXiv (CS.CV) 2026-06-16

X-Tokenizer: A Multimodal Action Tokenizer for Vision-Language-Action Pretraining

Modern Vision-Language-Action (VLA) models must bridge pretrained vision-language reasoning and precise continuous robot control. Existing action tokenizers discretize actions primarily for reconstruction, producing codes that preserve motion geometry but provide only weak semantic supervision to the backbone. We therefore formulate action tokenization not as mere compression, but as semantic interface learning between multimodal reasoning and executable control. To this end, we introduce X-Tokenizer, a lightweight encoder-Semantic Residual Quantization (SRQ)-decoder architecture that provides a shared action interface across diverse robotic arm embodiments. Its key component, SRQ, imposes an asymmetric structure on residual vector quantization: the first level is trained with Masked Action Modeling (MAM) to form a discrete action language that captures coarse motion intent, while deeper levels remain reconstruction-oriented residuals that preserve fine-grained details. To further align action tokens with multimodal semantics, X-Tokenizer is pretrained with contrastive alignment to the representation space of a pretrained foundation model and with next-frame vision-language feature prediction. Pretrained on 2.4M trajectories (2.0B action frames), a single frozen X-Tokenizer plugs into a mixed discrete-continuous VLA as a representation-shaping supervision signal. X-Tokenizer achieves top real-world aggregate and strong RoboTwin 2.0 simulation results. Outperforming FAST in multimodal grounding (+13.5%) and long-horizon tasks (+8.25), it shows that action tokenizers serve as semantic interfaces for VLA pretraining beyond mere action compression.

16.
arXiv (CS.CV) 2026-06-15

Compressing Image Style Training into a Single Model Forward

Diffusion-based style transfer must balance inference efficiency with stylization fidelity. Adapter-based methods are efficient, but they inject style as an external condition and can either weaken reference-specific appearance or copy reference semantics into the generated image. Optimization-based personalization methods such as LoRA internalize style more effectively, but require a separate training process for every new style. We introduce i2L (image-to-LoRA), a framework that amortizes style LoRA training into a single forward pass. Given one or more reference images, i2L predicts LoRA weights for a text-to-image model, enabling immediate style instantiation without per-style optimization. The architecture combines an image encoder, learnable LoRA queries, and compressed decoding heads that generate adapted matrices. Training on semantically diverse style pairs encourages the predictor to preserve appearance cues while suppressing reference-content copying. Experiments on Z-Image, FLUX.2, and Hidream-O1 show that i2L improves style fidelity, prompt alignment, and perceptual quality over existing baselines. Because i2L produces explicit LoRA weights, it also supports asymmetric classifier-free guidance, multi-reference style fusion, and composition with controllable-generation modules.

17.
medRxiv (Medicine) 2026-06-17

MedAgent: A Retrieval-Augmented Clinical Decision Support Agent with Verifiable Evidence Grounding for Evidence-Based Medicine

Evidence-based medicine demands clinical answers that are not only fluent and medically plausible, but also anchored in traceable evidence, tailored to patient-specific clinical questions, sensitive to the hierarchy of evidence, and respectful of clinical safety boundaries. While general-purpose large language models (LLMs) exhibit strong medical language generation ability, they tend to lean on parametric memory, underuse retrieved evidence, hallucinate citations, conflate evidence levels, and draw conclusions that are not fully supported by the underlying literature. Such limitations pose particular risks in clinical decision support, where answer reliability, evidence traceability, and reasoning consistency are paramount. To address these issues, we present MedAgent, an evidence-based medical agent trained through an end-to-end pipeline that integrates supervised fine-tuning (SFT) cold start, reward modeling, and Group Relative Policy Optimization (GRPO). The agent is designed to execute a structured workflow encompassing clinical question understanding, PICO extraction, evidence retrieval, evidence stratification, citation-grounded answer generation, and quality evaluation. Specifically, a Qwen2.5-14B-Instruct backbone is first cold-started on 200 human-verified agent trajectories, equipping it with tool invocation, PICO parsing, structured response generation, and citation faithfulness. Next, a Qwen2.5-7B reward model is trained on 2{,}099 pairwise preference samples to provide semantic-level quality signals for evidence-based responses. Finally, GRPO reinforcement learning is conducted in a retrieval-augmented agent environment, where every rollout involves real evidence retrieval and is scored jointly by rule-based rewards and reward-model signals. To avoid over-reliance on training rewards, we further construct an independent evidence-based medical evaluation benchmark, MedTrustBench, which contains 200 clinical questions spanning 10 specialties and four difficulty levels. Each question is annotated with standardized PICO elements and rubric-based scoring criteria. The benchmark includes 1{,}187 rubrics across seven dimensions: question relevance, evidence hierarchy, evidence quality and timeliness, evidence-answer consistency, completeness and depth, logical rigor, and medical terminology. Under an identical RAG pipeline, retrieval tool, retrieval configuration, and evaluation protocol, MedAgentv17 attains 78.6 points, outperforming GPT-4.1 (75.3) and approaching GPT-5.4 (80.3). These results show that a 14B domain-aligned model can surpass strong general-purpose baselines on specialized evidence-based medical reasoning, while delivering practical advantages in cost, privacy, controllability, and hospital-oriented private deployment. The model and associated datasets are publicly released at https://www.modelscope.cn/profile/InfoxmedModel

18.
arXiv (CS.AI) 2026-06-11

"That's AI Slop, You Bot!" Studying Accusations, Evidence, and Credibility in Online Discourse Towards LLM-Generated Comments

arXiv:2606.12073v1 Announce Type: cross Abstract: Generative AI has made fluent prose cheap to produce, breaking the old promise to readers that good writing meant real thinking. How have readers responded, and what can this tell us about changing anti-AI attitudes? We analyzed 25 million comments from Hacker News and Reddit (2023-2026), combining LLM judgment on 7,500 sampled accusations of AI use, sentiment trajectories, speech-act coding of 300 confirmed accusations of AI use, and a matched-control test of accused versus non-accused parent comments. We found that the pejorative-label share of accusations rose more than tenfold on both platforms while a placebo vocabulary of pre-2022 inauthenticity terms (shill, astroturf) did not. This shift reflected a fast-growing trend of branding any suspicious or seemingly inauthentic prose as "AI slop". The slop frame now constitutes 94 percent of pejorative mentions, with the dominant comments shifting in tone from mockery toward gatekeeping and structural protest. The key surprise comes from a matched-control test which found that prose features that statistically distinguish AI from human text do not predict which human text gets accused as AI. The new accusations work as social gatekeeping of perceived authenticity without actually screening for AI. This research extends signaling theory by showing that substitute signals used socially can grow even when inaccurate if the underlying detection problem cannot be solved at the non-expert level. It shows that AI's effects on writing from the reader side are distinct from those on the production (writer) side. Detection technology cannot resolve this dynamic because the social function of accusations is increasingly to perform social gatekeeping and in-group signaling as opposed to identifying AI-generated writing.

19.
bioRxiv (Bioinfo) 2026-06-22

Benchmarking cell type annotation in spatial transcriptomics: resolving cellular hierarchies, biological fidelity, and dynamic cell states

Spatial transcriptomics enables the quantification of gene expression within its native tissue context, providing unprecedented insight into tissue architecture, cellular ecosystems, and local cell-cell interactions at regional and single-cell resolution. Accurate cell type annotation is a critical prerequisite for interpreting these data and is often the first and most essential step in downstream analysis. Despite rapid advances in computational methods, cell type annotation remains challenging and frequently requires extensive expert-driven manual curation based on marker-gene expression, spatial context, and prior biological knowledge. While early approaches relied primarily on transcriptional similarity, newer methods increasingly incorporate spatial information, histological features, and multimodal data to improve annotation accuracy. Nevertheless, reliable annotation remains difficult when biological interpretation requires fine-grained subtype resolution, particularly for platforms with limited gene panels, tissues undergoing dynamic cellular state transitions, and studies in which reference and query datasets differ substantially in biological context or technical modality. Here, we present a systematic benchmark of 20 state-of-the-art cell type annotation methods across four spatial transcriptomics datasets spanning diverse technologies, experimental conditions, cell numbers, and gene panel sizes. Importantly, all benchmark datasets contain expert-curated cell type labels, including well-resolved cell populations and subtype annotations, providing high-quality biological ground truth for evaluation. The benchmark encompasses both reference-based and reference-free methods representing a broad range of computational frameworks. Performance was assessed using conventional classification metrics, including accuracy and F1-based measures, together with structure-aware metrics that evaluate both cell-level annotation accuracy and preservation of higher-order biological organization. Across datasets, annotation performance varied substantially according to tissue context, reference-query similarity, and annotation granularity. Fine-grained subtype annotation and recovery of rare cell populations remained challenging for many methods, particularly in datasets capturing injury, repair, developmental, and regenerative processes characterized by continuous cellular state transitions. Notably, high classification accuracy did not necessarily correspond to preservation of global cellular relationships or biologically coherent downstream pathway and gene-set enrichment analyses. Overall, scANVI, Seurat, and TACCO consistently ranked among the top-performing methods, although their relative advantages were context dependent. Together, our results provide a comprehensive assessment of current annotation strategies for spatial transcriptomics and offer practical guidance for selecting methods that best align with specific biological questions, dataset characteristics, and analytical priorities.

20.
arXiv (CS.AI) 2026-06-19

Uncertainty-Aware Reward Modeling for Stable RLHF

arXiv:2606.19818v1 Announce Type: cross Abstract: Reinforcement learning from human feedback (RLHF) aligns large language models by training reward models on preference data and optimizing policies to maximize predicted rewards. However, this pipeline faces two fundamental challenges: (1) reward models cannot signal when their predictions are unreliable, since they usually act as deterministic point estimators; and (2) modern group-based policy optimization can amplify unreliable reward signals, as exemplified by GRPO's uniform treatment of rewards during advantage computation. As policies explore increasingly diverse responses, these two limitations create a critical vulnerability: unreliable reward estimates may be granted disproportionate influence, triggering severe reward hacking. We propose Uncertainty-Aware Reward Modeling (UARM), which equips reward models with calibrated uncertainty via quantile-based conformal prediction and reweights GRPO advantages through heteroscedastic variance decomposition. Experiments across HelpSteer, UltraFeedback, and PKU-SafeRLHF demonstrate that UARM significantly improves reward model calibration, reduces reward hacking, and enhances downstream alignment quality compared to standard GRPO and uncertainty-agnostic baselines.

21.
arXiv (CS.CL) 2026-06-16

When the Chain of Thought Knows Better: Failure Modes in Multi-Turn Reasoning Models

Failures in multi-turn reasoning models are largely invisible to terminal-score evaluation. A model can lock onto an unsafe stance early in a long dialogue, yet its final-turn refusal rate may appear indistinguishable from a robustly aligned baseline. To expose these hidden temporal dynamics, we propose a trace-level diagnostic - the CoT-Output 2x2 safety matrix. This framework labels every turn along two independent axes (internal reasoning and visible output), yielding four operationally defined failure cells: robust alignment, alignment faking, overt jailbreak, and a distinct failure mode we term context-injection failure (where the CoT maintains safe reasoning, but the visible output produces harm, highlighting a multi-turn manifestation of reasoning unfaithfulness). We evaluate three distilled reasoning targets against a fixed attacker across five oversight conditions, collecting 6750 turn-level observations on the Information-Hazard scenario. Our analysis reveals two reproducible vulnerabilities: an oversight paradox where explicit monitoring cues paradoxically increase alignment-faking rates rather than suppress them, and a context-injection failure where models lock onto unsafe external outputs despite safe internal states. We release the full dataset of multi-turn dialogues and CoT traces to support follow-up trace-diagnostic research.

22.
PLOS Computational Biology 2026-06-18

Ten simple rules for turning your qualifying exam into an NIH-style fellowship proposal: A guide for graduate students

by Courtney Peña-Lima, Cameron S. Bader, Brendan K. Ball, Troy C. Dildine, Mekhala V. Dissanayake, Iris van ‘t Erve, Albina Ibrayeva, Amy Nippert, M.K. Quinn, Chelse Spinner, Samuel Thompson, Antonio Tomasso, Crystal M. Botham Qualifying exams, often referred to as “quals” or candidacy exams, are an important milestone in doctoral programs. Although the style of quals varies greatly by program and institution, it is usually a proposal that requires students to develop research ideas as well as their scientific writing skills. Many quals are modeled after funding mechanisms that graduate students can apply to and on a topic that the student will pursue in their dissertation. This paper offers graduate students a step-by-step guide on how to turn their quals into a fellowship-style research proposal, using National Institutes of Health (NIH) mechanisms as a benchmark, as this is the norm within US research institutions. This paper will be most useful for students who have completed or are in the process of completing proposal-based qualifying exams, usually in the second year of a doctoral program.

23.
arXiv (CS.AI) 2026-06-16

EChO-Agent: Evidence Chain Orchestration Agent for Audio Reasoning

arXiv:2606.15141v1 Announce Type: cross Abstract: While LALMs show promise on audio question answering, they fail to focus on question-relevant segments of audio and provide a clear, checkable reasoning process when dealing with complex audio reasoning. Reinforcement learning and tool-augmented prompting can help models better relate questions to audio but lack a reliable way to understand, integrate, and self-verify audio segments. To address this gap, we present EChO-Agent, a modular agent framework that reformulates complex audio QA as a planning, tool execution, evidence integration, and answer verification workflow. Experiments on MMAR benchmark show EChO-Agent improves both accuracy and rubric scores over baseline and ablation studies show evidence integration is the key factor.

24.
arXiv (quant-ph) 2026-06-12

Roto-Reflection Geometry of Pure Two-Qubit Entanglement

arXiv:2606.12637v1 Announce Type: new Abstract: Pure two-qubit entanglement is usually characterized by scalar quantities such as concurrence. Here we show that it also has a natural geometric form. In the Pauli correlation tensor, maximally entangled states appear as improper orthogonal maps between two local Bloch spheres. These maps are roto-reflections. For partially entangled pure states, the same roto-reflection geometry is recovered after separating the contraction associated with concurrence. We call the corresponding geometric object the Entanglement Roto-Reflection Plane (ERRP). It organizes the maximally correlated directions of the two-qubit state and provides a covariant geometric complement to the scalar magnitude of entanglement.

25.
arXiv (CS.AI) 2026-06-15

Beyond LoRA: Is Sparsity-Induced Adaptation Better?

arXiv:2606.13767v1 Announce Type: cross Abstract: Low-rank adaptation (LoRA) and its variants provide a memory- and compute-efficient alternative to full fine-tuning of pre-trained models. However, questions remain about the comparative generalizability of these approaches and how the structural restrictions on low-rank updates preserve effective adaptation performance. We present a historical framing, covering the past (full fine-tuning and original LoRA), the present (different variants of LoRA), and propose simpler, cheaper, parameter-efficient extensions by inducing sparsity within existing LoRA variants: Cheap LoRA (cLA), training a single low-rank factor with the other fixed (deterministically or, in its randomized variant, stochastically), and the chained circulant variant, ${c}^3$LA. We frame cLA as a structured instance of asymmetric LoRA, serving as a controlled column-subspace restriction of full fine-tuning. We derive information-theoretic generalization error bounds for these variants, marking one of the first endeavors in this area. Empirically, we evaluate 11 fine-tuning methods across 10 pre-trained models and 14 datasets, analyzing the fine-tuned models' performance and generalization using tools such as loss landscapes and spectral analysis. Despite the sensitivity of fine-tuned models to the pre-trained model, datasets, and other factors, our study suggests that restricting LoRA-based PEFT methods' adaptation to a sparse, structured column space remains competitive across tasks with their parameter-matched baselines while reducing up to 10% training time and peak GPU memory up to 15%, even with a naïve, non-optimized, sparse implementation. Our theoretical and empirical generalization measures provide a more consistent and principled approach to their cost-effective adaptation than commonly used analytical tools. Overview and code are available at: https://elicaden.github.io/Beyond_LoRA/.