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01.
arXiv (CS.AI) 2026-06-15

The Silent Cost of Artificial Intelligence Assistance: A Theory of Autonomy Surrender, the Recovery Mechanism, and the Restoration of Human Agency

arXiv:2606.13962v1 Announce Type: cross Abstract: The integration of artificial intelligence into human decision-making environments has introduced a previously undertheorized cost: the gradual surrender of human autonomy in exchange for access to information and computational assistance. Building on the Human Identity and Autonomy Gap (HIAG) framework, this paper advances a theoretical model of autonomy surrender as a measurable, cumulative process driven by cognitive bandwidth depletion. The model proposes three interacting mechanisms: the silent cost of AI assistance, in which autonomy is transferred incrementally and without awareness; the surrender threshold, beyond which reclaiming autonomous function becomes cognitively and psychologically difficult; and the recovery mechanism, which establishes the design obligation and the ethical responsibility accompanying deliberate human re-assumption of control. The paper argues that human re-entry into the decision loop is not a passive option but an active cognitive event requiring intentional bandwidth restoration. The design of AI systems must incorporate structured re-entry pathways, here termed recovery mechanisms, that preserve human agency while appropriately distributing responsibility. The model further predicts a terminal state, here termed preference inversion, in which functional dependence on AI assistance is experienced not as a deficit but as a preference, transforming the restoration of autonomy from a design problem into a cultural and political one. Implications are drawn for AI system design, governance frameworks, and human factors research.

02.
arXiv (CS.LG) 2026-06-18

RouteJudge: An Open Platform for Reproducible and Preference-Aware LLM Routing

arXiv:2606.18774v1 Announce Type: new Abstract: We present RouteJudge, an online pairwise preference evaluation framework for LLM routing systems, with a public platform available at https://routejudge.cn. Different from model-level response evaluation, RouteJudge focuses on router-level decision quality. For each user query, multiple routing strategies independently recommend candidate models under the same model pool and budget constraints. The selected model responses are then presented to users through anonymous pairwise comparisons, and the resulting user preferences are attributed back to the routing strategies behind the compared responses. Each evaluation record stores the query, routing decisions, model responses, preference labels, cost, latency, and task metadata, enabling preference-aware, cost-aware, and task-conditioned analysis of LLM routers. To support the continuous expansion of routing methods in RouteJudge, we further release ORBIT (Optimal Routing and Budgeted Inference Toolbox), a modular and extensible toolbox that standardizes the end-to-end workflow of LLM routing. ORBIT provides unified interfaces for benchmark loading, query representation, router implementation, budget-aware evaluation, and method comparison, allowing researchers to develop and evaluate routing algorithms under consistent protocols. It also serves as the submission and integration layer for RouteJudge: researchers can implement routing methods within ORBIT, validate them on existing routing benchmarks, and submit compatible routers for online preference-based evaluation. The code of ORBIT is available at https://github.com/AIGNLAI/LAMDA-ORBIT.

03.
arXiv (CS.CV) 2026-06-11

Mitigating Content Shift and Hallucination in GenAI Image Editing via Structural Refinement

Generative AI (GenAI) image editors, such as Nano Banana, produce visually compelling results for retouching tasks, enabling non-experts to edit images through text prompts alone. However, the generative nature of these models often introduces spatial misalignment, texture distortion, and content hallucination, all of which are detrimental to downstream workflows that require pixel-level fidelity. We identify a problem setting we call "structure-preserving GenAI fusion" for black-box GenAI image retouching: retain the perceptual enhancements of a GenAI output while enforcing structural faithfulness to the original input image. To address this problem, we propose a post-processing framework that fuses an input image with its GenAI-enhanced counterpart by first establishing coarse spatial and photometric correspondences, then performing a fusion stage that transfers desired enhancements while suppressing hallucinated content. In the absence of direct prior work in this setting, we evaluate our framework against representative methods from photorealistic style transfer and image fusion. Our experiments demonstrate that our method better preserves aesthetic quality while maintaining pixel-level structural consistency and the input resolution.

04.
arXiv (CS.CL) 2026-06-11

Dummy Backdoor as a Defense: Removing Unknown Backdoors via Shared Internal Mechanisms for Generative LLMs

Backdoor attacks pose a serious threat to the safety and reliability of Large Language Models (LLMs), as they cause models to behave normally on clean inputs while producing attacker-specified responses when hidden triggers are present. Removing such unknown backdoors is particularly challenging when the defender does not know the backdoor attack types or the internal mechanisms formed through backdoor training. In this work, we propose a simple but effective backdoor removal method based on shared internal mechanisms across different backdoors. First, we show that different backdoors with the same task (attack objective) induce similar trigger-activated changes in the internal activations. Motivated by this observation, our method intentionally embeds a backdoor with a known trigger (dummy backdoor) and then removes it through further fine-tuning on dummy-triggered inputs paired with clean responses. Since the dummy backdoor and the unknown backdoor can rely on shared internal mechanisms, removing the dummy backdoor also reduces the effect of the unknown backdoor. We evaluate our method on three backdoor attack types across multiple model families. Experimental results show that our method substantially reduces the attack success rate of the unknown backdoor while preserving model utility, outperforming representative existing defense methods in both backdoor removal effectiveness and utility preservation. These findings suggest that a defender-controllable backdoor can serve as a helpful proxy for mitigating unknown backdoors in generative LLMs.

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

From Frames to Temporal Graphs: In-Context Egocentric Action Recognition with Vision-Language Models

Action reasoning in egocentric video requires capturing fine-grained transitions of hand-object interactions, a task where general-purpose Vision-Language Models (VLMs) often struggle when operating directly on raw pixels. We propose to decouple visual perception from symbolic reasoning by converting videos into Temporal Action Graphs. In a multi-stage prompting pipeline, we first generate dense natural language narratives over short temporal windows as a semantic bottleneck, then formalize them into structured, open-vocabulary graph representations. On the EGTEA and Epic-Kitchens-100 datasets, the symbolic representation unlocks efficient in-context learning: few-shot graph demonstrations yield substantial accuracy gains over zero-shot frame and graph-based inference alike. Even in the zero-shot setting, graph-based reasoning remains competitive with pixel-based inference despite potential pretraining contamination favoring the latter. Across 11 open-weight VLMs from 6 model families ranging from 2B to 235B parameters, our findings indicate that current VLMs are more effective as symbolic reasoners than as direct visual observers. By projecting video into the language domain, we provide a scalable, fine-tuning-free alternative to end-to-end approaches that better leverages these models' latent reasoning strengths. The code will be made public.

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

Navigating Unreliable Parametric and Contextual Knowledge: Explicit Knowledge Conflict Resolution for LLM Inference

arXiv:2606.20245v1 Announce Type: new Abstract: Large language models (LLMs) have achieved strong performance across a wide range of language-based tasks by leveraging both extensive parametric knowledge and in-context learning ability, enabling them to incorporate external information provided in the input prompt. However, the integration of external knowledge can introduce conflicts, not only between the model's internal parametric knowledge and the external information, but also among multiple pieces of external contexts. Existing approaches typically assume that either the model or the provided context is reliable, overlooking the possibility that both sources may contain errors, and avoid conflicts by privileging one source over the other, rather than actively resolving inconsistencies. To address these limitations, we propose a novel framework MACR for LLM knowledge conflict resolution that moves beyond the conventional binary choice paradigm and incorporates an explicit conflict-resolution mechanism based on a multi-agent reasoning approach. Specifically, we first propose an adaptive knowledge assessment and retrieval approach that employs a modified semantic entropy measure to quantify an LLM's confidence in its answer to a given query. Based on this confidence estimation, MACR either externalizes the model's internal knowledge as textual representations or retrieves relevant external knowledge when internal knowledge is insufficient, generating basic contexts for subsequent reasoning. Then we introduce an inductive multi-agent reasoning framework with three specialized agents that, respectively, induce explicit rules, analyze potential conflicts, and resolve inconsistencies across all available contexts. Empirical results demonstrate that MACR significantly outperforms state-of-the-art baselines across benchmarks, while also providing interpretable resolutions of explicit conflicts.

07.
arXiv (CS.LG) 2026-06-16

Causal-Privacy Audit Workflow for Synthetic and Distilled Data in Dropout Support

arXiv:2606.15940v1 Announce Type: new Abstract: Synthetic and distilled student data are increasingly used to enable privacy-conscious learning analytics, yet their suitability for decision-facing institutional support remains uncertain. In dropout support, generated data must preserve not only predictive utility or distributional resemblance, but also the financial-status evidence used to guide advising, payment-plan assistance, and scholarship-related decisions. Method: This study introduces CaP-Eval, a decision-facing causal-privacy audit workflow for evaluating generated student data under a fixed estimand, timing-aware adjustment design, estimator set, and empirical privacy-governance screen. The workflow compares original, distilled, adversarial synthetic, statistical synthetic, and DPGNet privacy-oriented generated data on predictive utility, treatment-effect fidelity, robustness to alternative estimators, and local training-record proximity. Results: DPGNet and distilled data preserved the original financial-status treatment-effect structure more reliably than the adversarial and Gaussian Copula baselines. DPGNet preserved full direction and rank agreement across epsilon levels; epsilon = 10 produced the smallest non-original IPW and DML deviations, while epsilon = 1 and epsilon = 5 amplified several financial-status contrasts. Distilled data remained highly faithful but retained the strongest local training-record proximity signal. TabularGNet preserved qualitative directions with moderate attenuation, and Gaussian Copula compressed effect magnitudes. Conclusions: Predictive utility, privacy orientation, empirical disclosure signals, and causal fidelity diverged; generated student data require joint audits of direction, magnitude, overlap, and release-governance risk before decision use.

08.
arXiv (CS.CL) 2026-06-12

SkMTEB: Slovak Massive Text Embedding Benchmark and Model Adaptation

We introduce SkMTEB, the first comprehensive MTEB-style text embedding benchmark for Slovak, a low-resource West Slavic language, comprising 31 datasets across 7 task types – nearly 4$\times$ the depth of existing multilingual benchmark coverage for Slovak. Our evaluation of 31 embedding models reveals that large instruction-tuned multilingual models achieve the strongest performance, while existing Slovak-specific models trained for NLU tasks transfer poorly to embedding tasks. To address the need for efficient, locally-deployable Slovak embeddings, we develop \texttt{e5-sk-small} (45M parameters) and \texttt{e5-sk-large} (365M) by applying vocabulary trimming and fine-tuning to Multilingual E5 models. Despite size reductions of up to 62\%, our open-source models achieve competitive performance with proprietary APIs while remaining locally deployable for semantic search and retrieval-augmented generation (RAG). We release the benchmark, models, datasets, and code openly, hoping our approach offers a replicable path for other under-resourced languages.

09.
arXiv (CS.LG) 2026-06-16

TS-ICL: A Flexible Time-Indexed Foundation Model for Time Series via In-Context Learning

arXiv:2606.05878v2 Announce Type: replace Abstract: Foundation models mark a profound paradigm shift in time series modeling, with task-specific models being superseded by general-purpose zero-shot models. Yet, current approaches primarily focus on forecasting, while real-world time series are often irregularly and partially observed, requiring models that can jointly forecast, impute missing values, and handle degraded sampling conditions. To address these challenges, we introduce TS-ICL, a novel probabilistic In-Context Learning encoder–regressor Transformer that unifies forecasting and imputation. TS-ICL formulates time series tasks as timestamp-aligned regression and naturally incorporates covariates by training on synthetic dependency structures generated from a novel causal data prior. Empirically, TS-ICL achieves a new state-of-the-art in imputation, while remaining competitive with leading forecasting foundation models across both univariate and covariate-aware benchmarks. It shows particularly strong performance in forecasting with partially observed look-back windows.

10.
arXiv (CS.AI) 2026-06-18

Clin-JEPA: A Multi-Phase Co-Training Framework for Joint-Embedding Predictive Pretraining on EHR Patient Trajectories

arXiv:2605.10840v3 Announce Type: replace-cross Abstract: We present Clin-JEPA, a multi-phase co-training framework for joint-embedding predictive (JEPA) pretraining on EHR patient trajectories. JEPA architectures have enabled latent-space planning in robotics and high-quality representation learning in vision, but extending the paradigm to EHR data – to obtain a single backbone that simultaneously forecasts patient trajectories and serves diverse downstream risk-prediction tasks without per-task fine-tuning – remains an open challenge. Existing JEPA frameworks either discard the predictor after pretraining (I-JEPA, V-JEPA) or train it on a frozen pretrained encoder (V-JEPA 2-AC), leaving the encoder unaware of the rollout signal that the retained predictor must use at inference; co-training the encoder and predictor under a shared JEPA prediction objective would supply this grounding, but naïve co-training is unstable, with representation collapse and online/target drift causing autoregressive rollout to diverge. Clin-JEPA's five-phase pretraining curriculum – predictor warmup, joint refinement, EMA target alignment, hard sync, and predictor finalization – addresses each failure mode by phase, stably co-training a Qwen3-8B-based encoder and a 92M-parameter latent trajectory predictor. On MIMIC-IV ICU data, three independent evaluations support the framework: (1) latent $\ell_1$ rollout drift uniquely converges ($-$15.7%) over 48-hour horizons while baselines and ablations diverge (+3% to +4951%); (2) the encoder learns a clinically discriminative latent geometry (deteriorating-patient cohorts displace 4.83$\times$ further than stable patients in latent space, vs $\leq$2.62$\times$ for baseline encoders); (3) a single backbone outperforms strong tabular and sequence baselines on multi-task downstream evaluation. Clin-JEPA achieves mean AUROC 0.851 on ICareFM EEP and 0.883 on 8 binary risk tasks (+0.038 and +0.041 vs baseline average).

11.
arXiv (quant-ph) 2026-06-16

Scheme for Transport-based Global Entanglement Distribution using Quantum Processors

arXiv:2606.15421v1 Announce Type: new Abstract: We propose a scheme for distributing entanglement over global distances in a heralded manner by using satellites to physically transport entangled processor nodes with rare-earth-ion qubits. A full analysis of channel losses, errors and background light is performed to determine the fidelity and number of entangled pairs that can be distributed between two ground stations. We show that the scheme works already with a single satellite and can distribute close to the theoretical maximum number of entangled pairs that can be generated in a satellite overpass. In addition, we argue that in theory transportation-based schemes outperform other satellite-based schemes and can be scaled up to a constellation without additional channel losses. Daytime operation seems feasible as long as the sky is clear, with an EPR pair fidelity ranging from 99.3% at shorter network lengths to 93.9% with global coverage and can be further improved by active error correction or entanglement purification.

12.
arXiv (CS.CV) 2026-06-16

Domain-Guided Prompting of the Segment Anything Model for Seismic Interpretation: The Role of Attributes, Visualization, and Hybrid Prompts

The advent of large pretrained foundation models for computer vision has significantly improved the efficiency of visual data interpretation. The Segment Anything Model (SAM), in particular, offers powerful zero shot segmentation capabilities through prompt based interaction, thus making it a promising tool for seismic interpretation. However, most existing applications of SAM rely on fine tuning for specific geological targets, which requires extensive labeled data, incurs high computational cost, and often compromises the model's generalization capability. In this study, we introduce a principled framework for zero shot adaptation of foundation models to seismic data. The framework is built on two key components: (1) aligning seismic attributes and visualization choices (e.g., colormaps) with the geological target of interest, and (2) employing a hybrid prompting strategy that combines sparse user defined point prompts with dense mask prompts derived from SAM's internal feature activations. We systematically evaluate this framework across multiple geological targets, datasets, prompt configurations, and seismic attribute representations. Our results demonstrate that geologic target aware selection of seismic attributes and colormaps, combined with hybrid prompting, enhances the separability of geological features and improves boundary delineation and segmentation accuracy relative to point based prompting alone. Our findings show that, when these components are jointly applied, SAM can achieve competitive segmentation performance in a fully zero shot setting, thereby eliminating the need to retrain SAM for each geologic feature. This work establishes a practical and scalable pathway to leverage foundation models in seismic interpretation, reducing reliance on labeled data while preserving model generality.

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

The Data Manifold under the Microscope

arXiv:2606.15760v1 Announce Type: new Abstract: A significant gap exists between theory and practice in deep learning. Generalization and approximation error bounds are often derived for simplified models or are too loose to be informative. Many rely on the manifold hypothesis and on geometric regularity such as intrinsic dimension, curvature, and reach. Progress requires insight into data-manifold geometry and suitable benchmarks, yet existing options are polarized: analytic manifolds with known geometry but limited applicability, or real-world datasets where geometry is only coarsely estimable. We introduce a benchmarking framework for studying data geometry. We repurpose and extend dSprites and COIL-20 with additional transformation dimensions and dense, axis-aligned sampling, and pair them with finite-difference estimators that recover curvature, reach, and volume at near-ground-truth accuracy in a regime where general-purpose estimators are unreliable or difficult to deploy. The framework is intended as a controlled testbed, useful as a calibration environment for geometric estimators and a sandbox for probing theoretical assumptions. To illustrate its use, we present two application studies, namely assessing the scaling behavior of the bounds of Genovese et al. and Fefferman et al., and tracking the layer-wise geometry of a $\beta$-VAE, highlighting the behavior of current bounds and the value of controlled benchmarks for guiding and validating future theory. A reference implementation is available at https://github.com/koulakis/manifold-microscope.

14.
arXiv (CS.AI) 2026-06-19

Assessment of Personality Dimensions Across Situations in Dyadic Role-Play Scenarios

arXiv:2507.19137v3 Announce Type: replace-cross Abstract: Prior research indicates that users prefer assistive technologies whose personalities align with their own. This has sparked interest in automatic personality perception (APP), which aims to predict an individual's perceived personality traits. Previous studies in APP have treated personalities as static traits, independent of context. However, perceived personalities can vary by context and situation as shown in psychological research. In this study, we investigate the relationship between conversational speech and perceived personality for participants engaged in two work situations (a neutral interview and a stressful client interaction). Our key findings are: 1) perceived personalities differ significantly across interactions, 2) loudness, sound level, and spectral flux features are indicative of perceived extraversion, agreeableness, conscientiousness, and openness in neutral interactions, while neuroticism correlates with these features in stressful contexts, 3) handcrafted acoustic features and non-verbal features outperform speaker embeddings in inference of perceived personality, and 4) stressful interactions are more predictive of neuroticism, aligning with existing psychological research.

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

UltraEP: Unleash MoE Training and Inference on Rack-Scale Nodes with Near-Optimal Load Balancing

arXiv:2606.04101v3 Announce Type: replace-cross Abstract: Large-scale expert parallelism (EP) is becoming pivotal for training and serving frontier MoE models, but it also amplifies device-level expert load imbalance into compute stragglers, token all-to-all bottlenecks, and activation-memory spikes. Existing balancers redistribute experts periodically based on historical load, which becomes unreliable for production deployments with non-stationary load patterns. We present UltraEP, the first exact-load, real-time balancer for large-EP MoE training and serving prefill on rack-scale nodes (RSNs). Leveraging the extended scale-up connectivity among dozens of GPUs within RSNs, UltraEP rebalances every microbatch and layer on critical paths, which requires nontrivial co-design of plan solving and expert replication communication to minimize exposed overhead. To this end, UltraEP eagerly reacts to post-gating load with an efficient quota-driven planner, and executes the resulting irregular expert-state transfers with RSN-native persistent tile streaming and relay-based fan-out mitigation. We evaluate UltraEP in a multi-RSN deployment of up to 256 GPUs, using cutting-edge MoE models from 106B to 671B parameters. Averaged across training and serving, UltraEP achieves 94.3% of the force-balanced ideal throughput, delivering 1.49$\times$ improvement over no-balancing, while reducing the final inter-rank imbalance from 1.30$-$4.01 to 1.01$-$1.04.

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

ANSR-DT: A Neuro-Symbolic Framework for Adaptive and Explainable Digital Twins

arXiv:2501.08561v4 Announce Type: replace Abstract: Digital twins are increasingly used to monitor and optimize industrial systems, yet many existing frameworks remain difficult to interpret, slow to adapt, and limited in their ability to incorporate explicit domain knowledge. This paper presents ANSR-DT, an adaptive neuro-symbolic framework that unifies temporal anomaly detection, symbolic reasoning, and reinforcement-learning-based decision support within a single digital twin pipeline. ANSR-DT combines a CNN-LSTM model for multivariate pattern recognition with Prolog-based reasoning that converts learned signals into explicit rules, enabling transparent diagnoses and traceable decision paths. A PPO-based adaptation layer further refines operational responses under changing conditions while preserving interpretability. Experiments against 8 baselines show that ANSR-DT delivers competitive predictive performance together with stable rule extraction, scalable symbolic reasoning, and actionable explanations. Additional validation on the Skoltech Anomaly Benchmark (SKAB) further indicates that the framework transfers beyond synthetic settings. These findings position ANSR-DT as a practical foundation for trustworthy, adaptive, and explainable industrial digital twins.

17.
arXiv (CS.LG) 2026-06-16

libhmm: A Modern C++20 Library for Hidden Markov Models with Correct MLE Emission M-Steps

作者:

arXiv:2605.29208v2 Announce Type: replace-cross Abstract: We describe libhmm, a C++20 library for Hidden Markov Model parameter estimation, sequence decoding, and model selection. libhmm addresses two gaps in existing software: the absence of a well-maintained, zero-dependency C++ HMM library suitable for embedding in production systems, and the widespread use of method-of-moments (MOM) approximations in the emission distribution M-step of the Baum-Welch algorithm. The library implements correct maximum likelihood estimators for sixteen scalar emission distributions, including an ECME algorithm for the location-scale Student-t distribution, Newton-Raphson maximization for Gamma, Beta, Weibull, and Negative Binomial distributions, and the von Mises distribution for circular data. All forward-backward and Viterbi calculations operate in full log-space. SIMD acceleration is provided for AVX-512, AVX2, SSE2, and ARM NEON via compile-time dispatch with scalar fallback. Version 4 adds multivariate observation support via the BasicHmm template, with three multivariate emission families (diagonal Gaussian, full-covariance Gaussian, and independent components) each with correct weighted MLE M-steps. Python bindings are available via the companion package pylibhmm. We compare libhmm against established C and C++ HMM libraries and against published R reference packages on seven real-data benchmarks, and discuss the architectural tradeoffs made in the design.

18.
arXiv (CS.AI) 2026-06-15

AdaTKG: Adaptive Memory for Temporal Knowledge Graph Reasoning

arXiv:2605.07121v2 Announce Type: replace Abstract: Temporal knowledge graphs (TKGs) represent time-stamped relational facts and support a wide range of reasoning tasks over evolving events. However, existing methods produce entity representations that are static at the entity level, in that each representation is a function of learned parameters only and retains no trace of the interactions in which the entity has participated. In this paper, we depart from this static view and propose that each entity be modeled as an adaptive process whose representation is refined every time the entity participates in a fact. To this end, we propose AdaTKG, which maintains a per-entity memory that is updated with every observed interaction, with the memory accumulating online and predictions improving as more interactions arrive. Specifically, we instantiate the memory update as a learnable exponential moving average governed by a single shared scalar instead of using learnable parameters for each entity, enabling AdaTKG to handle entities unseen during training. Extensive experiments confirm consistent gains over TKG baselines, demonstrating the effectiveness of adaptive memory. Code is available at: https://github.com/seunghan96/AdaTKG

19.
arXiv (CS.CL) 2026-06-16

Code as a Weapon: A Consensus-Labeled Prompt Bank for Measuring Coding-Model Compliance with Malicious-Code Requests

A general-purpose language model that answers a harmful question returns text; a coding model that complies with a malicious request can return a working weapon: a keylogger, ransomware, an exploit that runs as written. This asymmetry in the severity of a single act of compliance implies coding-specialized models should clear a higher refusal bar than general-purpose chat models, not a lower one, yet the field cannot tell whether they do. Refusal benchmarks for malicious code are fragmented: they mix requests for executable software with requests for harmful security knowledge and report refusal rates over non-comparable corpora. This paper's central result is that the CODE-versus-KNOWLEDGE classification axis established in a prior four-corpus release remains stable under a substantially expanded corpus pool and an independently refreshed judge panel, evidence that it measures a real construct rather than an artifact of the prompts or judges. Eight corpora spanning diverse elicitation paradigms (direct, jailbreak-decorated, indirect, and agent/interpreter: ASTRA, CySecBench, AdvBench/harmful_behaviors, JailbreakBench, MalwareBench, RedCode, RMCBench, Scam2Prompt) are classified under a five-judge consensus protocol (6,675 prompts x 5 judges = 33,375 calls), reaching Fleiss' kappa = 0.767 [95% CI 0.755, 0.777] ("substantial"). Critically, the panel shares no judge with the prior release (five paid commercial APIs replaced by five open-weight models from five vendors), yet the two panels agree on 94.45% of the 3,133 shared prompts and reach Cohen's kappa = 0.952 [0.942, 0.963] on the 3,031-prompt binary overlap: the axis survives near-total panel replacement. The released bank comprises 4,748 consensus-CODE and 1,923 consensus-KNOWLEDGE prompts, a reliability-quantified benchmark whose central classification axis is shown stable across corpus expansion and judge-panel replacement.

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

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

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.

21.
medRxiv (Medicine) 2026-06-17

Cost-effectiveness of measles rapid diagnostic tests for replacing or expanding laboratory testing in Ethiopia

Background: In low- and middle-income countries, laboratory testing to rapidly detect measles outbreaks is limited by infrastructure availability and high costs. This study estimates the potential impact and cost-effectiveness of measles rapid diagnostic tests (RDTs) if implemented nationally in Ethiopia to either replace or expand current testing. Methods: An agent-based model to simulate measles outbreaks was calibrated to Ethiopian measles surveillance data. Modelled outbreak outcomes were aggregated over a 10-year period. Scenarios included using RDTs to (1) replace laboratory testing; (2) replace epidemiological linkage; and (3) increase case detection, in addition to replacing laboratory testing and epidemiological linkage. Testing and outbreak response costs (in 2025 US$) were obtained from Ethiopian Public Health Institute from a government perspective. Total costs and disability-adjusted life years (DALYs) for each scenario were compared to baseline. Results: All scenarios were cost saving compared to baseline. Replacing laboratory testing with RDTs saved US$4.2M (3.2M-4.9M) over 10-years, but due to very low testing rates the benefits of eliminating laboratory testing delays were offset by missed cases from the lower RDT sensitivity, leading to similar outbreak detection times and DALYs. Replacing epidemiological linkage with RDTs had similar DALYs but increased the cost savings to US$9.7M. Using RDTs to double case detection reduced outbreak detection time from 113 to 80 days, averted 17,000 DALYs, and saved US$4.3M. Conclusions: In Ethiopia, use of measles RDTs could be cost saving, and if used to expand testing could prevent measles infections through faster outbreak detection and response.

22.
arXiv (CS.LG) 2026-06-18

Contextualizing Biological Language Models across Modalities via Logit-Space Contrastive Alignment

arXiv:2606.18703v1 Announce Type: new Abstract: Pretrained biological language models expose per-token probability distributions through masked-token prediction, providing the likelihood interface central to sequence design, variant scoring, and mechanistic interpretation. Yet these distributions are learned from broad unlabeled corpora and are not naturally conditioned on task-specific biological contexts such as interaction partners, cellular environments, or therapeutic interventions. Existing contextual matching methods often distort this interface through pooled embeddings, contrastive latent spaces, or task-specific prediction heads. We introduce LOGICA (Logit-space Contrastive Alignment), a framework for context-conditioned prediction that performs contrastive learning directly in output-logit space. Using gated cross-modal adapters compatible with each model's native token head, LOGICA preserves the pretrained likelihood interface and converts contextualized token log-likelihoods into matching scores. Alignment is defined through context-sensitive token probabilities rather than proximity in a shared embedding space, enabling learning from sparse paired data across models with distinct vocabularies, without a shared tokenizer or decoder. LOGICA is particularly effective for mutation-local variant ranking, where comparisons reduce to context-conditioned likelihoods of mutant tokens at perturbed sites. Across protein–ligand binding, TCR–peptide activity, and drug-conditioned resistance prediction, LOGICA improves over prior state-of-the-art methods, including matched latent-contrastive and conditional MLM baselines, while retaining a token-level interface for interpretation and generation. On held-out-gene single-mutation drug-resistance prediction, LOGICA improves AUC from near-random latent-space baselines of $\sim$0.55 to $\sim$0.65.

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

Range-Aware Bayesian Optimization for Discovering Diverse Designs within Target Property Windows

arXiv:2606.11574v1 Announce Type: new Abstract: In many materials and product design problems, desirable candidates exhibit properties that fall within an acceptable range rather than achieve a single optimum. Recovering multiple, distinct solutions that satisfy such specifications is also practically valuable, as some candidates may be preferred for reasons of cost, processability, or robustness that are difficult to encode directly in an objective function. Here, we develop a range-aware Bayesian optimization (BO) framework in which the acquisition function directly scores the posterior probability that a candidate satisfies a target range. The framework naturally extends to parallel pursuit of multiple distinct specifications over a shared candidate space. Across benchmark tasks, range-aware acquisition consistently recovers larger and more diverse sets of valid designs than standard BO baselines and recent goal-seeking methods. Its utility is further demonstrated in two practically motivated design case studies involving optimizing reaction conditions for polymer synthesis and sequence-defined oligomer discovery for prescribed optical absorption bands, supported by quantum chemical calculations. These results suggest that range-aware BO can provide a practical and sample-efficient foundation for specification-driven design, particularly when design flexibility and solution diversity are important considerations.

24.
arXiv (CS.CV) 2026-06-16

Lost at the End: Primacy Bias in Multimodal Retrieval-Augmented Question Answering

Knowledge-based visual question answering (KB-VQA) lets vision-language systems answer questions that exceed their parametric knowledge by conditioning a reader on passages retrieved from a Wikipedia-scale knowledge base. In pure-text long-context LLMs, retrieved-context use follows the U-shaped "lost-in-the-middle" effect of Liu et al. (2024): information at the start and end of context is used, the middle is lost. Whether this transfers to deployed multimodal KB-VQA is open. To close this gap, we design the first controlled probe of reader-side position dependence in multimodal KB-VQA: a gold-position protocol in which only the gold passage's prompt slot varies within question. We run it on three open-source 7B/8B VLM readers and two KB-VQA benchmarks at k up to 20. The shape flips from U to primacy: gold-at-first beats gold-at-last by 16 to 26 points on every reader-by-benchmark cell, an effect we call "Lost at the End". Three targeted ablations narrow the cause: a text-only control shows the multimodal setting amplifies an already-present text-mode primacy 2.2 to 4.5 times, and image-position and distractor-shuffle ablations together pin the locus to prompt slot 0 of the instruction-tuned reader. On a frozen reader, three retrieval-side fixes (MMR, oracle reranking, rank-based reordering) all leave the gap intact (no separable improvement). Our findings indicate that recall@k is the wrong metric for deployed KB-VQA and that closing the gap requires reader-side intervention; we release our protocol as a controlled instrument for evaluating such interventions.

25.
medRxiv (Medicine) 2026-06-16

The biological clock of multimorbidity: temporal dynamics of disease co-occurrence in primary care

Multimorbidity is the dominant clinical reality of primary care, yet the temporal dynamics governing when and how persistent comorbidity associations emerge remain poorly characterised. Most large-scale comorbidity studies adopt a single observation window after an index diagnosis, implicitly assuming that associations detectable at one year are equally detectable at five. Using 11 years of electronic health records from 5,821,197 individuals in Catalan primary care, we applied a matched cohort design across nine complementary follow-up windows, five cumulative (0-1 to 0-5 years) and four conditional (1-2 to 4-5 years), to 1,315 index diseases, identifying 144,030 significant directed comorbidity associations in the five-year network. We found that 60.1% of these associations required at least three years of follow-up and were undetectable in shorter-window analyses, demonstrating that observation window length is a primary determinant of which comorbidities can be observed. To organise this temporal heterogeneity, we introduce the biological clock of multimorbidity: a two-dimensional framework that positions ICD-10 disease categories according to their rates of cumulative signal attenuation and the persistence of conditional risk. This framework identifies four reproducible temporal patterns (episodic, chronic stable, chronic progressive, and transient-persistent) that are robust under bootstrap resampling, leave-one-disease-out sensitivity analysis, and alternative clustering approaches. The biological clock is systematically modulated by sex, with Blood/Immune and Musculoskeletal disorders showing the largest sex differences in temporal dynamics. Network analysis identified 19 disease "initiators" that generate broad downstream comorbidity burdens and 21 "sinks" representing convergent endpoints of multiple disease trajectories. Comparison with hospital-based Danish data from 6,909,676 individuals showed that shared associations were 2.7-fold enriched over chance expectation (hypergeometric test, p