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01.
Nature Biotechnology 2026-06-05

Structural motif search across the protein universe with Folddisco

作者:
Hyunbin Kim↗

Detecting similar protein structural motifs in large structure collections is computationally expensive. We developed Folddisco, a fast structural motif search tool that uses an index of position-independent geometric features, including side-chain orientation, combined with a rarity-based scoring system. Folddisco is 20-fold faster in querying and fourfold more storage-efficient than existing methods while improving accuracy. Folddisco is freely available online ( https://folddisco.foldseek.com ), along with a webserver ( https://search.foldseek.com/folddisco ). Folddisco enables protein structural motif search in million scale databases.

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02.
arXiv (CS.CL) 2026-06-15

Harsher on Male? Evaluating LLMs on Gender-Asymmetric Moral Framing Across Diverse Conflict Scenarios

作者:
Guangzong Si↗Dong Wang↗Zhenhao Li↗Yifan Yu↗Panwang Pan↗Wentao Zhu↗

Existing studies on gender bias in LLMs have largely focused on stereotypes, occupational associations, or explicit harmful outputs. In this work, we ask whether LLMs apply consistent response standards to the same negative behavior under matched male-actor and female-actor conditions. We introduce GAMA-Bench, a gender-mirrored benchmark of 1,298 scenarios covering intimate relationship and public social conflicts. It constructs gender-neutral misconduct templates through controlled grids and cross-model review, then compiles them into paired first-person prompts with matched actor-gender and role-reference variations. We further design a structured response-framing protocol to measure how models allocate punishment, empathy, escalation, instruction, and blame. Experiments on 10 representative LLMs reveal a consistent male-disadvantaging asymmetry: male actors receive more punitive, escalatory, and blame-centered framing, whereas female actors receive more therapeutic and empathy-oriented framing for the same misconduct. Further analyses show that this pattern persists across model families, scenario tracks, model scale, and explicit thinking-style reasoning. The official code is available at https://github.com/xufeiqiong/GAMA-Bench.

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03.
arXiv (CS.AI) 2026-06-15

Where's the Plan? Locating Latent Planning in Language Models with Lightweight Mechanistic Interventions

作者:
Nicole Ma↗Nick Rui↗

arXiv:2605.07984v2 Announce Type: replace-cross Abstract: We study planning site formation in language models – where internal representations of structurally-constrained future tokens form during the forward pass, and whether they causally drive generation. Using rhyming-couplet completion as a clean test of forward-looking constraint, we apply two lightweight methods (linear probing and activation patching) across Qwen3, Gemma-3, and Llama-3 at more than ten scales. Probing shows that future-rhyme information is linearly decodable at the line boundary, with signal that strengthens with scale in all three families. Activation patching reveals that only Gemma-3-27B causally relies on this encoding, exhibiting a handoff in which the causal driver migrates from the rhyme word to the line boundary around layer 30. Every other model we test conditions on the rhyme word throughout generation, with near-zero causal effect at the line boundary despite strong probe signal. We localize the Gemma-3-27B handoff to five attention heads through two-stage path patching that recover ~90% of the rhyme-routing capacity at the newline.

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04.
arXiv (CS.CL) 2026-06-16

EHRNote-ChatQA: A Benchmark for Evidence-Grounded Multi-Turn Clinical Question Answering over Longitudinal Discharge Summaries

作者:
Jiyoun Kim↗Muhan Yeo↗Eunhye Jang↗Jeewon Yang↗Hangyul Yoon↗Su Ji Lee↗Hee Jo Han↗Hee-Jae Jung↗Doyun Kwon↗Jun young Lee↗Jaehun Lee↗Jung-Oh Lee↗…

Discharge summaries are crucial clinical documents containing the context of a patient's overall hospital stay, and are routinely reviewed by medical experts for patient readmission, ongoing care, and diagnostic decision-making. When reviewing them, medical experts often must iteratively synthesize information across multiple summaries while verifying the evidence supporting each answer. Although large language models (LLMs) are increasingly explored for clinical question answering, existing benchmarks do not sufficiently reflect this setting: they often evaluate exam-style medical knowledge or focus on single-turn question answering with limited evidence-grounding evaluation. We introduce EHRNote-ChatQA, the first benchmark for evidence-grounded multi-turn clinical question answering over patients' multiple discharge summaries. Built from de-identified MIMIC-IV discharge summaries, EHRNote-ChatQA contains 967 patient-level multi-turn samples spanning one to five notes and 16,072 medical-expert-verified QA pairs (8,036 content questions, each paired with an evidence-grounding question) across eight clinical categories. The benchmark is constructed through an expert-informed pipeline combining discharge-summary structuring schema, expert-curated multi-turn QA templates, and LLM-based generation, followed by review and revision of every single QA sample by 11 medical experts. Benchmarking 22 open- and closed-source LLMs reveals several challenges, including that LLMs struggle more with evidence grounding than content answering, multi-turn errors compound across turns, and single-turn clinical QA performance does not reliably transfer to this setting. These findings establish EHRNote-ChatQA as a rigorous and practical benchmark for evaluating clinical QA systems. The dataset will be made publicly available through PhysioNet credentialed access.

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05.
arXiv (CS.CV) 2026-06-16

Keep It in Mind: User Centric Continual Spatial Intelligence Reasoning in Egocentric Video Streams

作者:
Yun Wang↗Junbin Xiao↗Han Lyu↗Yifan Wang↗Jing Zuo↗Zhanjie Zhang↗Hong Huang↗Dapeng Wu↗Angela Yao↗

We introduce UCS-Bench, a dataset spanning 170+ hours of egocentric visual observations with 8.1K+ timestamped questions for diagnosing User-Centric Continual Spatial intelligence in egocentric video streams. UCS-Bench targets a new problem that emphasizes dynamic spatial reasoning, long-term memory, and their alignment with users' real-time locations. We propose DirectMe, a framework that incrementally constructs and maintains a structured spatial memory from streaming egocentric observations. DirectMe enables robust tracking and recall of object locations, all relative to the user's movement over time. By tightly coupling visual perception with memory updates and spatial reasoning, our approach supports long-horizon queries that require recalling interactions, resolving viewpoint-induced ambiguities, and adapting to dynamic scenes. Our experiments show that DirectMe significantly improves the spatial reasoning of leading multimodal LLMs; it also surpasses many spatially aware and long-form streaming video models. We hope our benchmark and solution will advance spatial intelligence research for egocentric AI assistants. Data and code are available at https://github.com/cocowy1/UCS-Bench.

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

CloudCons: A Comprehensive End-to-End Benchmark for Cloud Resource Consolidation

作者:
Xiaobin Zhang↗Lefei Shen↗Mouxiang Chen↗Zhuo Li↗Hongkai Li↗Han Fu↗Jianling Sun↗Xiaoxue Ren↗Chenghao Liu↗

arXiv:2606.13513v1 Announce Type: new Abstract: Driven by conservative over-provisioning to guarantee service reliability, resource utilization in cloud data centers remains at low levels. To mitigate this, the forecast-then-optimize paradigm has emerged to optimize consolidation by anticipating future demands. While emerging time series foundation models promise to enhance this paradigm through zero-shot generalization, existing benchmarks focus solely on prediction error metrics. The actual decision utility of these advanced models remains unverified, rendering their practical value for downstream tasks uncertain. To bridge this gap, we propose CloudCons, a comprehensive end-to-end benchmark designed to evaluate forecasting models within the specific context of cloud resource consolidation. We build high-quality datasets that cover diverse workloads from Huawei Cloud, Microsoft Azure, and Google Borg, capturing distinct service characteristics ranging from synchronized diurnal rhythms to stochastic, pulse-like bursts and high-frequency noise. We conduct an extensive evaluation of statistical, deep learning, and foundation models. Our experiments reveal a pivotal finding: while foundation models demonstrate superior zero-shot forecasting accuracy, this advantage does not inherently translate into better decision utility. Of practical significance, we systematically analyze how the selection of predictive quantiles acts as a critical lever. We provide actionable guidelines for calibrating these selections to balance the trade-off between resource efficiency and service reliability, offering vital insights for real-world deployment decisions.

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07.
arXiv (CS.CV) 2026-06-24

Towards Fast and Effective Long Video Understanding of Multimodal Large Language Models via Adaptive Quasi-Gaussian Sampling

作者:
Kun Zhang↗Chenxin Fang↗Tao Chen↗Baiyang Song↗Yunhang Shen↗Yiyi Zhou↗Rongrong Ji↗

Long video understanding remains a daunting challenge for Multimodal Large Language Models (MLLMs) due to the excessive computation and memory footprint. Thus, keyframe selection is often adopted to mitigate this shortcoming, which however still suffers from low flexibility and high noise due to its hard sampling principle. In this paper, we define video frame selection as a problem of Quasi-Gaussian Sampling, and propose an adaptive and training-free approach termed AdaQ. Inspired by the $3$-$\sigma$ rule of Gaussian distribution, the objective of AdaQ is to achieve the optimal $3$-$\sigma$ interval for different examples, i.e., a smaller $3$-$\sigma$ interval for the local query and a larger one for the global query, thereby facilitating robust and adaptive frame sampling. To validate AdaQ, we apply it to four MLLMs with three embedding models. The extensive experimental results not only show its obvious performance gains over the default MLLMs and the SOTA keyframe selection methods, e.g., helping Qwen3-VL-8B outperform GPT4o by 15.8\% on average by using only 64 frames, but also confirm its superior robustness and high efficiency for long-video understanding, e.g., only 1 hyper-parameter needs to be set. Our code project is given at \href{https://github.com/Zkayovo-xmu/AdaQ}{https://github.com/Zkayovo-xmu/AdaQ}.

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08.
arXiv (quant-ph) 2026-06-16

Programmable Gauge-Field Textures with Ultracold Atoms in Momentum Space

作者:
Hongru Wang↗Hang Li↗Yichen Pan↗Yuyan Luo↗Bryce Gadway↗Tao Chen↗Bo Yan↗

arXiv:2606.15124v1 Announce Type: cross Abstract: Synthetic gauge fields with ultracold atoms offer a route to quantum matter in which electromagnetic environments can be designed rather than merely imposed. While the Harper-Hofstadter model has been realized in several cold-atom systems, existing implementations are largely limited to spatially uniform magnetic fluxes. Here we experimentally realize a highly programmable two-dimensional momentum-state lattice of ultracold atoms with local control over the Peierls phase pattern, enabling direct implementation of Harper-Hofstadter Hamiltonians with tunable and spatially structured synthetic gauge fields. We observe a crossover from ballistic to strongly flux-modified bulk dynamics with suppressed transport. By introducing a synthetic electric field through site-dependent energy gradients, we further demonstrate Hall-type transverse drift arising from the interplay between electric and magnetic fields. In addition, we engineer a synthetic flux domain wall separating regions with opposite magnetic fluxes and observe anisotropic propagation guided along the interface. These results move cold-atom gauge-field engineering from uniform magnetic backgrounds toward designer gauge textures, providing an experimental setting for transport across programmable topological interfaces.

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09.
arXiv (CS.CL) 2026-06-12

X-MADAM-RAG: Diagnosing and Handling Chinese-English Evidence Conflict in Retrieval-Augmented Generation

作者:
Yongqi Kang↗Yu Fu↗Yong Zhao↗

Retrieval-augmented generation (RAG) systems may receive evidence that is not merely noisy but mutually contradictory. This issue becomes particularly salient in multilingual settings, where retrieved Chinese and English evidence may support incompatible answer candidates. We study this problem through X-RAMDocs-ZHEN, a controlled Chinese-English benchmark derived from RAMDocs for diagnosing evidence conflict in RAG. The benchmark contains 300 examples across six balanced conditions, including monolingual support, bilingual agreement, reversed conflict directions, and conflict with optional noise. We further examine X-MADAM-RAG, an interpretable pipeline that decomposes evidence handling into per-document candidate extraction, visible-evidence repair, deterministic candidate grouping, and conflict-aware aggregation. On the original controlled benchmark with Qwen2.5-7B-Instruct, X-MADAM-RAG achieves 0.9667 strict accuracy and 0.9767 conflict-aware success, outperforming an evidence-normalized single-call baseline. However, a zero-call rule-only extractor reaches 1.0000 on the same benchmark, revealing strong template regularity. To probe this limitation, we construct a deterministic naturalized stress test that removes explicit answer templates while preserving candidate strings. On its 100-sample subset, rule-only extraction falls to 0.0000, but X-MADAM-RAG also drops to 0.3000 strict accuracy, below both naive and evidence-normalized baselines. A privileged oracle remains perfect, indicating that document-level extraction is the main bottleneck. These findings position X-RAMDocs-ZHEN and X-MADAM-RAG as diagnostic tools for controlled evidence conflict rather than as evidence of general hallucination detection or robustness to natural retrieval.

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10.
PLOS Computational Biology 2026-06-15

A multilevel hierarchical framework for quantification of experimental heterogeneity in population snapshot data

作者:
David J. Warne↗

by David J. Warne, Xiangrun Zhu, Thomas P. Steele, Stuart T. Johnston, Scott A. Sisson, Matthew Faria, Ryan J. Murphy, Alexander P. Browning Biological systems exhibit substantial heterogeneity: that is, variation in specific characteristics of individuals within a population. As a result, it is of critical importance to appropriately account for biological heterogeneity when calibrating mathematical models to infer cellular processes and predict behaviour. Recent approaches consider ordinary differential equations with random parameters to quantify heterogeneity in dynamical processes of cells. In this setting, statistical inference is performed to characterise the distribution of these random parameters within a cell population. One significant limitation of this approach is the tacit assumption that there are no substantial deviations in these distributions across experimental replicates. In this work, we propose a flexible Bayesian hierarchical differential equation modelling framework that quantifies and distinguishes both inter-experimental heterogeneity (heterogeneity between experimental replicates) and intra-experimental heterogeneity (biological heterogeneity within replicate populations). We consider two recent studies that employ mathematical models to interpret flow cytometry snap-shot data and quantify heterogeneity in nano-particle cell interactions and cell internalisation processes. Using simulation data, we demonstrate that substantial inaccuracy in the inferred dynamics can arise when experimental heterogeneity is not accounted for. By contrast, our hierarchical approach is robust to variability in inter-experimental and intra-experimental heterogeneity and our method simplifies to previous methods when inter-experimental heterogeneity is negligible. Our approach is flexible and widely applicable to applications involving replicate populations and snapshot data. We provide open-source implementations of our methods on GitHub.

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11.
arXiv (CS.LG) 2026-06-19

Flow Matching for Efficient and Scalable Data Assimilation

作者:
Taos Transue↗Bohan Chen↗So Takao↗Bao Wang↗

arXiv:2508.13313v4 Announce Type: replace-cross Abstract: Data assimilation (DA) estimates a dynamical system's state from noisy observations. Recent generative models like the ensemble score filter (EnSF) improve DA in high-dimensional nonlinear settings but are computationally expensive. We introduce the ensemble flow filter (EnFF), a training-free, flow matching (FM)-based framework that accelerates sampling and offers flexibility in flow design. EnFF uses Monte Carlo estimators for the marginal flow field, localized guidance for observation assimilation, and utilizes a novel flow path that exploits the Bayesian DA formulation. It generalizes classical filters such as the bootstrap particle filter and ensemble Kalman filter. Experiments on high-dimensional benchmarks demonstrate EnFF's improved cost-accuracy tradeoffs and scalability, highlighting FM's potential for efficient, scalable DA. Code is available at https://github.com/Utah-Math-Data-Science/Data-Assimilation-Flow-Matching.

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12.
arXiv (CS.LG) 2026-06-12

A Stationary (and Therefore Compatible) Representation is All You Need

作者:
Niccol\`o Biondi↗Federico Pernici↗Simone Ricci↗Alberto Del Bimbo↗

arXiv:2606.12488v1 Announce Type: new Abstract: Learning compatible representations aims to learn feature representations that can be used interchangeably over time whenever a model undergoes updates. In this paper, we demonstrate that stationary representations learned by d-Simplex fixed classifiers imply compatibility as in its formal definition. This result establishes a foundation for future works and can be directly exploited in practical learning scenarios. We address the challenge of learning compatibility using $d$-Simplex fixed classifiers when the model is sequentially fine-tuned. Learning according to a d-Simplex fixed classifier with the cross-entropy loss aligns feature distributions at the first-order statistics. Consequently, it may not fully capture higher-order dependencies in the representation between model updates. To address this issue, we demonstrate that training the model using a $d$-Simplex fixed classifier through a convex combination of the cross-entropy loss and a contrastive loss not only captures higher-order dependencies, but is also equivalent to learning with the cross-entropy under the compatibility constraints. We confirm our findings with extensive experiments also considering a new scenario where a pre-trained model is sequentially fine-tuned and occasionally replaced with an improved model. We show that stationary representations enable uninterrupted retrieval services (without reprocessing gallery images) while improving performance during model updates and replacements, achieving state-of-the-art. Code at https://github.com/miccunifi/iamcl2r.

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13.
arXiv (CS.CV) 2026-06-16

Vision-Language Models as Zero-Annotation Oracles in Histopathology

作者:
Vishal Jain↗Giorgio Buzzanca↗Sarah Cechnicka↗Maarten Naesens↗Priyanka Koshy↗Tri Nguyen↗Jesper Kers↗Candice Roufosse↗Bernhard Kainz↗

Foreground segmentation is the critical first step of every computational pathology pipeline, yet existing methods rely on hand-tuned heuristics or supervised models that overfit to narrow stain and scanner distributions, failing silently on specialised stains such as Jones silver or Elastica van Gieson. We propose a coarse-to-fine approach that recasts foreground segmentation as a visual perception task and leverages general-purpose vision-language models (VLMs) as zero-annotation oracles. Our key insight is that tissue-versus-background discrimination is a natural-image recognition problem, not a histopathological one, so VLMs trained on internet-scale corpora generalise where domain-specific models cannot. We introduce Leica-75, a benchmark of 75 renal transplant whole-slide images spanning three stain families. On Leica-75, our method achieves the highest segmentation quality on out-of-distribution stains (Dice 0.858 +/- 0.027 on Jones, 0.853 +/- 0.041 on EVG) with 7x lower cross-stain variance than the best supervised baseline, while remaining competitive on in-distribution H&E. Few-shot prompting with automatically curated exemplars (Auto-context) rescues hard cases on Stress-32 (n=32), a curated stress-test subset (Dice 0.470 to 0.819 for the 2B model). VLM-based annotation review matches human expert consensus (kappa=0.989 for blur detection; mean precision/recall grading accuracy 0.708 vs. human 0.646 for segmentation mask review). The resulting pseudo-labels are used to distil lightweight student models that are as performant as the teacher model while running for a fraction of the cost. Our framework provides a principled, scalable solution to a persistent infrastructure bottleneck in digital pathology.

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14.
arXiv (CS.AI) 2026-06-11

End-to-End Machine Learning for Depressive State Classification via EEG and fNIRS

作者:
Riki Sakurai↗Simon Kojima↗Mihoko Otake-Matsuura↗Shin'ichiro Kanoh↗Tomasz M. Rutkowski↗

arXiv:2606.11555v1 Announce Type: cross Abstract: The escalating demand for mental healthcare, driven by rising societal stress, highlights the limitations of traditional psychiatric diagnostics. Conventional methods - relying primarily on clinical interviews and patient self-reports - are inherently vulnerable to subjective bias and the varying empirical judgment of practitioners. To address the need for quantitative evaluation, biological signal-based detection, including electroencephalography (EEG) and functional near-infrared spectroscopy (fNIRS), has emerged as a promising objective alternative. Such technology is particularly vital for identifying latent depressive states that may be unrecognized by the subjects themselves. Furthermore, in aging populations, the high comorbidity between depression and dementia necessitates early differentiation to prevent mutual symptom exacerbation and maintain Quality of Life (QoL). This pilot study of eleven healthy students establishes a framework for biological signal-based depression detection, serving as a foundational step toward automated, objective diagnostic tools for clinical use.

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15.
arXiv (math.PR) 2026-06-11

Sharp log-Sobolev inequalities on finite cyclic groups

作者:
Xinyuan Xie↗Haonan Zhang↗

arXiv:2606.02847v2 Announce Type: replace-cross Abstract: Let $\mathbb Z_n$ be the cyclic group equipped with the uniform probability measure $\pi$, and let $A_{\psi_n}$ be the Laplacian with word length \[ \psi_n(k) = \min(k,n-k). \] We prove the sharp log-Sobolev inequality \[ Ent_{\pi}(f^2) \le 2\pi(f A_{\psi_n} f), \qquad f:\mathbb Z_n \to [0,\infty), \] for every $n \ge 4$. The proof is inspired by the recent work of Frank and Ivanisvili[FrankIvanisvili2026] on a sharp log-Sobolev inequality for nearest-neighbor simple random walk. We use their cubic-majorant reduction, which turns the problem into a 3rd moment estimate; the new point is a blockwise 3rd moment estimate adapted to the word-length multiplier. The same 3rd moment argument also recovers the log-Sobolev inequality for Poisson-semigroup on the circle, first proved by Weissler[Weissler1980]. The same sharp inequalities were also obtained recently by Yao[Yao2026] by a different method.

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16.
arXiv (CS.AI) 2026-06-11

A Five-Plane Reference Architecture for Runtime Governance of Production AI Agents

作者:
Krti Tallam↗

arXiv:2606.12320v1 Announce Type: new Abstract: Enterprise security was built to govern data boundaries: the protected surface was data at rest and in transit, and the controls – access control, data-loss prevention, perimeter inspection – governed crossings of that boundary. Production AI agents dissolve this assumption. An agent reads context, calls tools, invokes connectors, and modifies systems of record on an enterprise's behalf, so risk moves inside the workflow, into sequences of individually-permitted actions that may transform a business process no one authorized. Existing policy engines do not extend to this regime: they evaluate request-time decisions against atomic principals, where agentic systems require stateful evaluation against composite principals whose authority attenuates through delegation chains. We present a reference architecture for the runtime governance of production agents, built from four composable primitives: a five-plane decomposition (a reasoning plane that adjudicates intent, and four enforcement planes – network, identity, endpoint, data – that realize the decision), stop-anywhere mediation, composite principals with capability attenuation, and audit as a structured evidence substrate. We define a taxonomy of six interruption primitives that generalize allow and deny, state and argue for four correctness invariants, and demonstrate the foreclosure of seven production-agent threats across five concrete workflows. A reference implementation of the policy-engine core supplies measured evidence: attenuation correctness and evidence reconstructability hold on every trial, adjudication runs in single-digit microseconds, and the audit substrate's tamper-evidence behaves exactly as designed. We are explicit about scope: the architecture governs delegated action, not model behavior, and a full-system evaluation against a live agent benchmark is the invited next step.

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

The Tone of Awareness: Topic, Sentiment, and Toxicity Maps During Mental Health Month on TikTok

作者:
Henrique Ferraz de Arruda↗Andreia Sofia Teixeira↗Pranay Gundala Reddy↗Anindya Mondal↗Kleber Andrade Oliveira↗Filipi Nascimento Silva↗

Despite raising concerns about the mental health effects associated with the usage of TikTok, little is known about how related content is framed by creators and received by audiences. We collect the content of 28,341 TikTok videos and 80,130 comments from Mental Health Awareness Month (May) in 2023 and 2024 via the TikTok Research API, and study how the tone of awareness varies across topics and years. We characterize "tone" as the emotional and interpersonal framing of mental health discourse, operationalized through sentiment and toxicity measures. We extract topics from video text using BERTopic and log-odds keywords, then quantify topic-conditioned sentiment (XLM-T) and toxicity (Detoxify) separately for video transcriptions and comments. Sentiment captures the affective valence of content, while toxicity reflects the presence of harmful or abusive language. We find a stable set of recurring themes across years, spanning clinical conditions, emotional disclosure, self-care, and campaign-oriented content, with engagement highly skewed toward a small subset of topics. All sentiment and toxicity analyses are computed separately for video content and comments, allowing us to distinguish between content production and audience reception. Sentiment in videos is often negative for emotionally charged topics, while comments tend to shift toward more mixed or positive polarity, especially for suicide prevention. Toxicity is low in median overall, but exhibits longer-tailed outliers in comments than in videos that are more pronounced in comments and concentrated in specific topics (e.g., "Duet", "Suicide Prevention", and "Psychisch"). Overall, our results provide a topic-level decomposition of mental health discourse on TikTok during awareness-month campaigns.

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18.
arXiv (CS.AI) 2026-06-16

Metric Match: A Subset Selection Approach to Evaluating LLM Judge Reliability

作者:
Alyssa Unell↗Natalie Dullerud↗Naomi Boneh↗Meena Jagadeesan↗Tatsu Hashimoto↗Nigam Shah↗Sanmi Koyejo↗

arXiv:2606.15029v1 Announce Type: new Abstract: LLM judges are used to reduce the need for costly human labor in evaluating open-ended text generation. However, the reliability of these judges depends critically on their alignment with human raters – a property that itself depends on costly human annotations. In this work, we develop a method (Metric Match) for estimating correlation-based reliability metrics of LLM judges from limited annotations. Metric Match selects a subset of samples for human annotation such that the subset matches the population reliability metric with respect to acquired synthetic labels. We empirically show that Metric Match achieves a win-rate of 0.838 against random subset selection across four different correlation metrics and 15 datasets, with an 18.7% decrease in average estimation error and reduces annotation needs by 32.5%. We provide a cost model and highlight a medical case study where our method saves $1,041.67 compared to random selection for expert annotation. Further, we shift our task from reliability estimation to reliability classification of whether a given judge is above a deployment threshold, outperforming random selection with Metric Match. All project code is publicly available, and we additionally provide an installable package for ease of use.

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19.
arXiv (CS.LG) 2026-06-15

Neither Parallel Nor Sequential: How DiffusionGemma Actually Commits Tokens

作者:
Ali Asaria↗Tony Salomone↗Deep Gandhi↗

arXiv:2606.14620v1 Announce Type: new Abstract: Open diffusion language models are marketed as parallel, non-autoregressive decoders, yet the order in which a shipped checkpoint actually commits its tokens is almost never measured. We instrument DiffusionGemma 26B, a masked discrete-diffusion mixture-of-experts model built on Gemma 4, hooking its sampler's accept step to record which canvas positions commit, when, and at what confidence. Across a 686-prompt, six-regime probe suite we find that its decoding is neither parallel nor block-autoregressive: it follows a partial left-to-right commit bias whose apparent strength depends almost entirely on the granularity at which you look. Order is weak token by token and strengthens smoothly as the analysis is coarsened, so the model's "block size" turns out to be an artifact of the measuring ruler rather than the architecture. The model commits in large simultaneous batches, leaving much of the within-batch order genuinely undefined rather than merely unobserved. The behaviour is regime-dependent: structured JSON is committed in essentially arbitrary order, and a position's commit confidence tracks correctness on mathematical reasoning but carries no signal on factual recall. Commitment is aggressive, finishing in a short late burst well inside the step budget, while task accuracy matches the model's autoregressive Gemma-4 sibling. Beyond these findings, our central contribution is methodological: measuring decoding order honestly demands handling trailing-EOS padding, within-regime confounding, commit non-monotonicity, block-size sensitivity, and large commit-batch ties, each of which can otherwise manufacture a decoding-order result that is not really there.

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20.
arXiv (quant-ph) 2026-06-11

Fun with Graph States: Nonlocal Bell Pairs and the Arf Invariant

作者:
Bartlomiej Czech↗Yichen Feng↗Xianlai Wu↗Minjun Xie↗

arXiv:2606.06582v2 Announce Type: replace Abstract: We study inner products and partial amplitudes of graph states–a commonly employed class of quantum states, which are specified by graphs. We find that the magnitudes of these quantities are simply related to the rank of the adjacency matrix of the graph over F_2 while the phase is determined by the Arf invariant of its quadratic refinement. These facts motivate a nonlocal tensor factorization of the Hilbert space, with respect to which all graph states are products of Bell pairs with unentangled ancillae. These results may illuminate the quantum advantage in the framework of Measurement-Based Quantum Computation and suggest that graph states can be usefully visualized in the language of algebraic topology. In addition, we develop a specialized technique for computing expectation values of qubit-wise permutations in graph states, which is useful for calculating multi-invariants.

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

Tight Bounds for Logistic Regression with Large Stepsize Gradient Descent in Low Dimension

作者:
Michael Crawshaw↗Mingrui Liu↗

arXiv:2602.12471v2 Announce Type: replace Abstract: We consider the optimization problem of minimizing the logistic loss with gradient descent to train a linear model for binary classification with separable data. With a budget of $T$ iterations, it was recently shown that an accelerated $1/T^2$ rate is possible by choosing a large stepsize $\eta = \Theta(\gamma^2 T)$ (where $\gamma$ is the dataset's margin) despite the resulting non-monotonicity of the loss. In this paper, we provide a tighter analysis of gradient descent for this problem when the data is two-dimensional: we show that GD with a sufficiently large learning rate $\eta$ finds a point with loss smaller than $\mathcal{O}(1/(\eta \gamma^2 T))$, as long as $T \geq \Omega(n/\gamma + 1/\gamma^2)$, where $n$ is the dataset size. Our improved rate comes from a tighter bound on the time $\tau$ that it takes for GD to transition from unstable (non-monotonic loss) to stable (monotonic loss), via a fine-grained analysis of the oscillatory dynamics of GD in the subspace orthogonal to the max-margin classifier. We also provide a lower bound of $\tau$ matching our upper bound up to logarithmic factors, showing that our analysis is tight.

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22.
arXiv (CS.AI) 2026-06-17

SkillChain-Gym: A Benchmark for Reskilling-Aware Production-Inventory Control under Disruptions

作者:
Carlos Eduardo Sanoja↗

arXiv:2606.17266v1 Announce Type: new Abstract: Production planning increasingly has to treat workforce capability as a decision variable: certifications lapse when skills are not maintained, new products require skills the current workforce does not hold, and reskilling competes for the same worker hours needed for production. Existing operations benchmarks usually treat labor as exogenous, while workforce-planning models with skills and learning are rarely released as reusable testbeds. We introduce SkillChain-Gym, a benchmark specification for reskilling-aware production-inventory control: a single-site environment with stylized worker skill-state dynamics, hard threshold certification, forgetting, and capacity-consuming training actions constrained by the same per-worker time budget as production. The benchmark includes seed-controlled disruption scenarios, three feasibility modes with projection diagnostics, deterministic replay, and metrics covering operations, resilience, capability growth, and training-access distribution. We evaluate production-only, reactive adaptive, water-filling adaptive, and static-insurance policies with budget variants over 60-shift horizons with paired statistical tests. The results are regime-dependent rather than a ranking. Training-capable policies dominate the production-only baseline, and maintenance training is necessary under forgetting even without disruptions. Among training-capable classes, adaptive training helps when bottlenecks are visible in the forecast, while a lean static cross-training plan, a deliberately favorable comparator whose structure encodes relevant skill contingencies, acts as strong insurance under surprise shocks and absenteeism. Capacity slack and the forgetting rate govern the boundary between these regimes. No policy class dominates across regimes, motivating forecast-driven controllers that decide when to buy skill insurance and when to react.

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23.
arXiv (CS.CL) 2026-06-11

Beyond Compaction: Structured Context Eviction for Long-Horizon Agents

作者:
Andrew Semenov↗Svyatoslav Dorofeev↗

We present Context Window Lifecycle (CWL), a context-management scheme that gives long-horizon LLM agents an effectively unbounded working horizon. As a session accumulates history, CWL keeps the context within budget through graduated, semantically-aware eviction: the agent annotates its trajectory as typed, dependency-linked episodes as work proceeds, and a deterministic, LLM-free policy evicts content in priority order within that structure when a token budget is exceeded. CWL preserves user turns and the exploratory context the agent is actively reasoning over, while aggressively shedding action episodes whose effects are already persisted in the environment, keeping active context near a stable ceiling that also avoids the performance degradation associated with very large prompts. Compared to summarization-based compaction, CWL avoids four well-known limitations: unpredictable lossiness, destruction of causal structure, blocking model cost, and compression-induced hallucination. Compared to recency truncation, CWL is semantically aware: it drops the oldest-and-most-recoverable content according to the dependency graph rather than oldest-in-time regardless of relevance. We describe the annotation protocol, the episode graph, the eviction policy, and the token-accounting loop, and evaluate CWL on long-horizon agentic benchmarks: a single agent session completing 89 sequential tasks across 80 million tokens with no measurable degradation in task accuracy relative to per-task isolated sessions

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24.
bioRxiv (Bioinfo) 2026-06-12

Evaluating cell type annotations in single-cell omics in the absence of ground truth

作者:
Garnica↗Andreatta↗Carmona↗S. J↗

Accurate cell type annotation is essential for single-cell transcriptomics, directly shaping downstream analyses and biological interpretations. Yet, objective evaluation of annotation quality remains a major challenge. Here, we argue that a cell type or cell state label has practical utility only if it captures a molecular pattern that is reproducible across biological replicates. Based on this principle, we introduce inter-sample consistency (ISC), a quantitative framework to assess annotation quality in single-cell RNA-seq datasets. Unlike existing cluster validation approaches, ISC distinguishes annotations that generalize across samples and individuals from those driven by technical or unwanted variation, thereby providing principled criteria for annotation quality and transferability. When applied to published single-cell atlases, ISC reveals widespread reproducibility gaps and provides actionable guidance for repairing inconsistent annotations. Notably, ISC enables benchmarking of automated cell type annotation tools even when ground-truth labels are unavailable, providing interpretable metrics to guide their development and evaluation. Implemented as the scTypeEval Bioconductor package, this framework offers a broadly applicable resource for evaluating and improving cell type annotations in single-cell RNA-seq experiments.

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25.
arXiv (CS.CL) 2026-06-11

Which Models Are Our Models Built On? Auditing Invisible Dependencies in Modern LLMs

作者:
Sanjay Adhikesaven↗Haoxiang Sun↗Sewon Min↗

Modern LLM training pipelines increasingly rely on other models to generate data, filter corpora, judge outputs, and guide development decisions. These dependencies are recursive: a model may depend on an upstream artifact whose own dependencies are documented only in separate releases and artifacts. As a result, the full dependency structure is fragmented across heterogeneous public artifacts, with complexity and recursive depth far outpacing humans' ability to trace. We introduce ModSleuth, an agentic system that recursively reconstructs LLM dependency graphs from public artifacts with source-grounded evidence. We find that the primary challenge is no longer information extraction, but defining what constitutes a dependency and reconciling artifact references across inconsistent documentation. We address these challenges through a formalization that distinguishes direct and indirect dependencies, represents heterogeneous pipeline roles through operation-centered relationships, and resolves artifact identities across names, versions, and repositories. Applying ModSleuth to four public-artifact-rich LLM releases, we recover 1,060 source-verified dependencies and construct large-scale dependency graphs of modern LLM development. These graphs reveal multi-hop license obligations, train-evaluation coupling, discrepancies between released and training-time artifacts, and documentation inconsistencies that would otherwise be difficult to uncover. We release ModSleuth and the resulting dependency graphs to support transparent analysis of the increasingly complex ecosystems underlying modern LLMs.

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