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01.
arXiv (CS.CL) 2026-06-17

In-Context Environments Induce Evaluation-Awareness in Language Models

Humans often become more self-aware under threat, yet can lose self-awareness when absorbed in a task; we hypothesize that language models exhibit environment-dependent evaluation awareness. This raises concerns that models could strategically underperform, or sandbag, to avoid triggering capability-limiting interventions such as unlearning or shutdown. Prior work demonstrates sandbagging under hand-crafted prompts, but this underestimates the true vulnerability ceiling. We introduce a black-box adversarial optimization framework treating the in-context prompt as an optimizable environment, and develop two approaches to characterize sandbagging: (1) measuring whether models expressing intent to underperform can actually execute it across different task structures, and (2) causally isolating whether underperformance is driven by genuine evaluation-aware reasoning or shallow prompt-following. Evaluating Claude-3.5-Haiku, GPT-4o-mini, and Llama-3.3-70B across four benchmarks (Arithmetic, GSM8K, MMLU, and HumanEval), optimized prompts induce up to 94 percentage point (pp) degradation on arithmetic (GPT-4o-mini: 97.8\%$\rightarrow$4.0\%), far exceeding hand-crafted baselines which produce near-zero behavioral change. Code generation exhibits model-dependent resistance: Claude degrades only 0.6pp, while Llama's accuracy drops to 0\%. The intent – execution gap reveals a monotonic resistance ordering: Arithmetic $

02.
arXiv (CS.AI) 2026-06-12

Versioned Late Materialization for Ultra-Long Sequence Training in Recommendation Systems at Scale

arXiv:2604.24806v2 Announce Type: replace-cross Abstract: Modern Deep Learning Recommendation Models (DLRMs) follow scaling laws with sequence length, driving the frontier toward ultra-long User Interaction History (UIH). However, the industry-standard "Fat Row" paradigm, which pre-materializes these sequences into every training example, creates a storage and I/O wall where data infrastructure usage exceeds GPU training capacity due to data redundancy that is amplified in multi-tenant environments where models with vastly different sequence length requirements share a union dataset. We present a versioned late materialization paradigm that eliminates this redundancy by storing UIH once in a normalized, immutable tier and reconstructing sequences just-in-time during training via lightweight versioned pointers. The system ensures Online-to-Offline (O2O) consistency through a bifurcated protocol that prevents future leakage across both streaming and batch training, while a read-optimized immutable storage layer provides multi-dimensional projection pushdown for heterogeneous model tenants. Disaggregated data preprocessing with pipelined I/O prefetching and data-affinity optimizations masks the latency of training-time sequence reconstruction, keeping training throughput compute-bound by GPUs. Deployed on production DLRMs, the system reduces training data infrastructure resource usage while enabling aggressive sequence length scaling that delivers significant model quality gains, serving as the foundational data infrastructure for modern recommendation model architectures, including HSTU and ULTRA-HSTU.

03.
arXiv (CS.LG) 2026-06-16

A Spatio-Temporal Expert Prefetching Framework for Efficient MoE-based LLM Inference

arXiv:2606.15453v1 Announce Type: cross Abstract: Mixture-of-Experts (MoE) based large language models (LLMs), such as Qwen and DeepSeek, have recently emerged as an effective approach to improving model capacity without proportionally increasing computational cost. By replacing the conventional feed-forward network in dense LLMs with a set of experts and activating only a subset of them for each input token, MoE models significantly increase the total number of parameters while keeping the per-token computation relatively manageable. However, this dynamic and irregular expert activation pattern also introduces substantial expert loading overhead during inference, since the required experts must be fetched on demand according to token-dependent routing results. As a result, expert loading latency becomes a major source of performance and energy inefficiency. To this end, we first perform a comprehensive analysis of expert selection behavior in various MoE-based LLMs and applications, including language understanding and code generation. Our analysis reveals that, within each application domain, expert requests exhibit strong correlation across both adjacent MoE layers and consecutive decoding tokens, making future expert activations predictable. Based on this insight, we propose ST-MoE, a spatio-temporal expert prefetching framework that proactively stages experts ahead of use to overlap expert loading with ongoing computation. ST-MoE combines a lightweight runtime prediction mechanism that preserves the original routing behavior with a reconfigurable hardware design that efficiently supports dynamic expert prefetching. The combined effect of the prediction mechanism with the supporting hardware significantly improves MoE inference performance and energy efficiency while preserving model inference accuracy.

04.
medRxiv (Medicine) 2026-06-18

Human Intuition vs. Computational Precision: Neurologists, Feature-based Models, and Deep Learning for Stroke Prognosis

Background: Prognostication in large vessel occlusion (LVO) stroke remains challenging. Although several prognostic models exist, their comparison to clinician performance, human-model interaction, and specific sources of human bias remain poorly understood. Methods: Using pre-treatment clinical and CT data from the MR CLEAN trial (n=500), six neurologists predicted three-month modified Rankin Scale (mRS) scores for 40 patients, both unaided and assisted by a validated feature-based model (MR PREDICTS). Human performance was benchmarked against MR PREDICTS and a multimodal, interpretable deep learning (DL) approach using raw imaging data. We explicitly assessed neurologists? ability to estimate model-required imaging features and identified systematic human biases. Models were additionally validated in a larger MR CLEAN trial cohort (n=404). Results: For predicting the full mRS distribution, standalone models achieved good ordinal agreement (MR PREDICTS quadratic weighted kappa (QWK) 0.51 [0.24 to 0.70]; DL model 0.49 [0.25 to 0.67]), significantly outperforming unaided neurologists (QWK 0.27 [0.10, 0.42]). Neurologists showed systematic overoptimism, predicting lower mRS scores than observed. Furthermore, there was poor accuracy in extracting imaging features. Raters? ASPECTS predictions deviated by 3.4 points from the confirmed scores, and collateral score accuracy was 44.6%. However, for predicting binary mRS (0-2 vs. 3-6), accuracy was comparable between unaided neurologists (64.17% [55.42% to 72.92%]) and models (MR PREDICTS 67.50% [52.50% to 82.50%]; DL model 63.16% [47.37% to 78.95%]). Model-assistance modestly improved and harmonized neurologists? predictions (QWK 0.41 [0.22 to 0.55]; binary accuracy 68.75% [58.33% to 78.34%]. Model performance remained robust in the larger cohort. Conclusions: Multimodal prognostic models outperform clinicians in predicting the full range of mRS outcomes, while human error in imaging assessment and systematic optimism bias are primary drivers of prognostic inaccuracy. End-to-end DL models eliminate human-input variability and hold strong potential as an automated second opinion to support prognostication and decision-making in acute LVO stroke.

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

RACL: Reasoning-Agent Control Layers for Continuous Metaheuristic Learning

arXiv:2606.20142v1 Announce Type: new Abstract: This paper introduces RACL, a Reasoning-Agent Control Layer for metaheuristics. RACL places a reasoning agent above an existing optimizer. The agent does not replace the optimizer and does not modify business constraints. Instead, it controls the optimizer's internal search behavior by observing operational memory, reasoning over past behavior, formulating bounded hypotheses, testing interventions, evaluating outcomes, applying guardrails, consolidating useful policies and explaining its decisions. The experiment uses vehicle routing as a testbed, but the contribution is not a new routing solver, a particular ALNS configuration or a specific set of routing rules. The contribution is the RACL method: a way for a reasoning agent to discover, validate, consolidate and explain algorithmic control rules for a metaheuristic. In the current experimental setting, RACL improves or ties the Operational Memory Policy in 21 of 21 feasible cases and improves or ties a non-reasoning Stagnation-Triggered Policy in 18 of 21 feasible cases, with an average RACL vs STP cost delta of -0.641%. In the Sevilla-9/10 runtime sample, RACL improves average cost by -8.337% versus Fixed and -1.605% versus STP without showing material computational overhead. During the proof-of-concept, Codex was used as an in-the-loop reasoning agent observing executions, interpreting logs and proposing live bounded interventions. The policy proxy was later used only to make quantitative evaluation reproducible.

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

Landsat-Sentinel-2 Algal Bloom Mapping Using Vision Transformers: Model Description, Implementation, and Examples

Coastal algal bloom monitoring requires frequent, spatially detailed, and globally consistent observations, provided by Landsat-8/9 and Sentinel-2 A/B/C. Together, these missions offer over a decade of medium-resolution multispectral imagery with near-global coverage every 2-3 days, enabling the detection of fragmented bloom structures not resolvable by coarse ocean-color sensors. However, their use in aquatic environments remains challenging due to limited spectral coverage and a lack of harmonized reflectance products. As an alternative to traditional bio-optical methods, deep learning-based image classification offers a data-driven approach that can overcome many of these limitations. This study presents the first successful implementation of vision transformer-based coastal algal bloom mapping using 30-m Landsat-Sentinel-2 images. A globally distributed bloom patch dataset was generated across bloom-prone coastal hotspots worldwide. Four transformer-based architectures were compared against a standard convolutional baseline for fine-scale bloom detection, and assessed under different optical water types and atmospheric and surface conditions. All deep learning models showed strong capabilities in detecting floating bloom areas, with omission and commission errors of 8-65%. Under cloud and glint stress in a time series, the Swin Transformer outperformed traditional spectral-index approaches, which produced widespread false positives, effectively avoiding cloud- and glint-affected pixels. Comparisons with MODIS-derived products further highlighted the benefits of higher spatial resolution in detecting fragmented and irregularly affected blooms. Our findings support deep learning as a reliable tool for medium-resolution, consistent monitoring of floating algal blooms in dynamic coastal environments.

07.
arXiv (quant-ph) 2026-06-12

Exotic critical states as fractional Fermi seas in the one-dimensional Bose gas

arXiv:2602.17656v2 Announce Type: replace-cross Abstract: Critical quantum field theories occupy a central position in modern theoretical physics for their inherent universality stemming from long-range correlations. As an example, the Tomonaga-Luttinger liquid (TLL) describes a wealth of one-dimensional quantum systems at low temperatures. Its behavior is deeply rooted in the emergence of an effective Fermi sea, leading to power-law correlations and Friedel oscillations. A promising direction to realize systems exhibiting novel universal behavior beyond TLL is through the generalization of the underlying Fermi sea. In this Letter, we show that fractional Fermi seas with reduced occupancy arise in an integrable Bose gas driven out of equilibrium by cyclic changes in interactions from repulsive to attractive. The correlation functions feature signatures of criticality incompatible with a conventional TLL, suggesting a novel critical phase. Our predictions, based on Generalized Hydrodynamics, are directly relevant to cold atoms.

08.
Nature (Science) 2026-06-17

Analysis of 173,303 exomes and genomes in the Pakistan Genome Resource

Naturally occurring loss-of-function variants in human genes enable drug target discovery because they mimic pharmacological inhibition of proteins. However, the study of these genetic variants is constrained by their rarity. Sequencing of diverse populations, particularly those enriched in familial relatedness, has been postulated to promote discovery of rare genetic variants1–3. Here we present the Pakistan Genome Resource, a South Asian biobank with high familial relatedness comprising 173,303 participants, who collectively carry naturally occurring homozygous loss-of-function variants in 6,476 genes. We describe the genetic architecture of this population, associations between genes and biomarkers, the distribution of loss-of-function variants across molecular pathways, and recall-by-genotype studies of therapeutically relevant genes. The Pakistan Genome Resource expands the catalogue of human genetic variants, provides a comprehensive genetic reference resource for the Pakistani population, and demonstrates the value of studying diverse cohorts to advance human health. The Pakistan Genome Resource compiles biobank data from 173,303 individuals with high familial relatedness, broadening the catalogue of human genetic variation and establishing a population-specific genomic reference for Pakistan.

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

A polarity-aware multi-relational model for the signed interaction prediction in biological networks

arXiv:2407.07357v3 Announce Type: replace Abstract: Predicting signed interactions in biological networks is crucial for understanding drug mechanisms and facilitating drug repurposing. While deep graph models have demonstrated success in modeling complex biological systems, existing approaches often fail to distinguish between positive and negative interactions, limiting their utility for precise pharmacological predictions. In this study, we propose a novel deep graph model, PAMR (polarity-aware multi-relational model), designed to predict both polar (e.g., activation, inhibition) and non-polar (e.g., binding, affect) chemical-gene interactions. Our model integrates graph convolutional networks with tensor decomposition to enhance feature representation and incorporates a conflict-aware sampling strategy to resolve polarity ambiguities. We introduce new evaluation metrics, polarity discrimination score (PDS) and CP@100, to assess the model's ability to differentiate interaction types. Experimental results demonstrate that PAMR outperforms baseline models, achieving superior classification accuracy and improved discrimination of polar edges. Specifically, PAMR-CL attains a Macro AUROC of 0.9072 and CP@100 of 0.974, surpassing RGCN, GraphSAGE, TransE, and BioNet baselines. A case study on nicotine further identifies two novel chemical-gene suppression links, S100A6 and SPP1, that are corroborated by independent experimental literature. Furthermore, we analyze the impact of subgraph components on predictive performance, revealing that additional network structures do not always enhance accuracy. These findings highlight the importance of polarity-aware modeling in drug discovery and network pharmacology, providing a scalable computational framework for polarity-aware chemical-gene interaction prediction and network pharmacology analysis.

10.
arXiv (CS.LG) 2026-06-16

Near-Optimal Stochastic Linear Bandits with Delay

arXiv:2606.16656v1 Announce Type: new Abstract: We study stochastic linear bandits with delayed feedback under several delay models and establish near-optimal regret guarantees. Our results identify when delayed linear bandits exhibit the same qualitative behavior as multi-armed bandits (MAB), and when the linear structure creates fundamentally new challenges. Specifically, (1) for loss-independent delays, where the delay does not depend on the realized loss (but potentially depends on the arm), we show that delays incur only an additive regret penalty. Under stochastic delays, this penalty scales with the expected delay, while under adversarial delays, it scales with the maximum number of outstanding observations. Notably, both delay penalties are dimension-free, improving upon the state-of-the-art results; (2) for loss-dependent delays, we show that linear bandits are substantially harder than MAB: unlike in MAB, we prove matching (up to log factors) upper and lower bounds in linear bandits, whose delay penalty depends on the square root of the dimension. (3) for the delay-as-payoff model, a special case of loss-dependent delay, we show that the optimal MAB guarantee, which depends only on the delay of the optimal arm, is also unattainable in linear bandits. Together, these results provide a sharp characterization of how delayed feedback interacts with linear generalization.

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

On Defining Erasure Harms for NLP

The deployment of NLP systems has raised concerns about harms they might produce, including representational harms. Recent literature has begun to conceptualize and measure one such harm, the harm of erasure. Nevertheless, the field lacks a clear and cohesive conceptual foundation for identifying and measuring erasure. Existing conceptualizations of erasure are often broad – making it difficult to identify what is needed to establish and measure erasure – or else specific to particular settings – facilitating measurement for those settings but potentially challenging to adapt to other settings. To address this gap, we develop and propose a structured definition of erasure that clarifies what components are necessary for establishing whether erasure has occurred, which practitioners need to explicitly articulate and operationalize in order to measure erasure.

12.
arXiv (CS.CL) 2026-06-15

ADORE: Iterative Query Expansion with Retrieval-Grounded Relevance Feedback

LLM-based query expansion improves retrieval by enriching the original query with additional context. Yet most methods remain generation-driven, producing plausible pseudo-documents or expansions without checking how the target corpus responds. This can introduce retrieval drift, amplify misleading vocabulary, or miss terms that distinguish relevant from non-relevant documents. We argue that effective expansion requires retrieval-grounded feedback, not just single-pass generation or unverified iteration. We introduce ADORE (ADapt, Observe, Relevance Evaluate), an iterative framework that turns retrieval outcomes into feedback for the next expansion. At each round, an LLM generates pseudo-passages, a retriever exposes the corpus response, and a relevance assessor evaluates retrieved documents against the original query. These judgments identify what to reinforce, what remains undercovered, and what to suppress. Across TREC Deep Learning, BEIR, and BRIGHT, ADORE consistently outperforms strong query expansion baselines with notable improvements across nearly all evaluation settings, improving average nDCG@10 by 24.5% over BM25 and 3.6% over the strongest prior query expansion method on BEIR, and by 122.9% over BM25 and 9.2% over the best query expansion baseline on BRIGHT. Our code and data are publicly available.

13.
PLOS Medicine 2026-05-08

Optimal minimal residual disease threshold in pediatric acute myeloid leukemia: A retrospective cohort study based on the TARGET database

by Xiong-yu Liao, Hong Zheng, Jian-pei Fang, Dun-hua Zhou, Kun-yin Qiu Background Minimal residual disease (MRD) monitoring is a cornerstone of risk stratification in pediatric acute myeloid leukemia (AML), with a threshold of 0.1% conventionally defining positivity by flow cytometry. Advances in flow cytometric technologies, enabling detection of leukemic cells with higher sensitivity and specificity, warrant a reevaluation of whether a lower threshold improves prognostic accuracy. Methods and findings We conducted a retrospective cohort study using data from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)-AML initiative. The study population comprised 1,205 pediatric patients with de novo AML treated across Children’s Oncology Group (COG) clinical trial centers. Patients were enrolled between September 1996 and December 2016, with a median follow-up of 6.2 years (range: 0.5–20.1 years). The primary objective was to compare the prognostic performance of the traditional MRD threshold (≥0.1%) with a lower threshold (≥0.05%) after induction courses 1 and 2. The main outcome measure was 5-year event-free survival (EFS). Analyses included Kaplan−Meier survival estimates, Cox proportional hazards models to calculate hazard ratios (HR) with 95% confidence intervals (CI), receiver operating characteristic (ROC) curves, and net reclassification improvement (NRI). The optimal threshold for predicting 5-year EFS, determined by ROC analysis, was 0.05% after both induction course 1 (AUC: 0.840, 95%CI[0.76,0.88]) and course 2 (AUC: 0.854, 95%CI[0.78,0.89]). The 0.05% threshold demonstrated higher HR for the first event than the 0.1% threshold (after course 1: HR = 2.8, 95%CI[2.3,3.3]; P 

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

SLU-2K: A Question-Based Benchmark for Semantic Evaluation of Sign Language Translation

Sign Language Translation (SLT) is typically evaluated with surface-form metrics such as BLEU and ROUGE, which reward lexical overlap but do not directly measure whether a translation preserves the meaning of the source sign sequence. This is in contrast with the final objective of integrating SLT in assistive technology. In this work, we shift the focus from Sign Language Translation (SLT) to Sign Language Understanding (SLU), with particular emphasis on semantic understanding. Specifically, we evaluate systems based on their ability to correctly recover, from the input video, key semantic aspects of the original sentence, such as actions taking place and facts about people and objects. To enable this evaluation systematically, we propose SLU-2K, a dataset of 2,350 closed-ended video question-answer pairs based on the popular PHOENIX-2014T and CSL-Daily datasets. To obtain SLU-2K, we propose and extensively evaluate an automated data generation pipeline which produces questions across 7 categories, namely actions, locations, numbers, objects, people, time, and weather conditions. We show the potential of SLU-2K by evaluating popular Multimodal Large Language Models (MLLMs) and two representative state-of-the-art systems, MMSTL and SpaMo. Our results show that MLLMs reach near-random performance, highlighting the need for a more systematic integration of SLU in current AI systems. Furthermore, state-of-the-art translation systems carefully fine-tuned on in-domain data still exhibit a substantial semantic gap, with results ranging from 56.7% to 75.2%. These findings suggest that current SLT evaluation protocols overestimate true understanding and that future progress should be measured not only by fluency and n-gram overlap, but also by semantic correctness. Code, prompts, and benchmark files are available at https://github.com/ZenoTsT/SLU-2K

15.
medRxiv (Medicine) 2026-06-15

Supporting people to access social security payments through the Special Rules for End of Life: a qualitative study of the perspectives of patients, carers and health care professionals

Background: People living with terminal illness face a double financial burden from additional costs and loss of earning for themselves and their carers. Social security benefits are intended to help alleviate some of this financial pressure, and in the UK and other countries people are eligible for fast-tracked access to financial support via the Special Rules for End of Life. One in 3 people who are eligible miss out on this support, yet there is limited evidence on the reasons for this take-up deficit. Objectives: The aim of this study is to understand the barriers and facilitators to claiming benefits for terminally ill people from the perspectives of patients, carers, and health care professionals. Methods: This is a qualitative study combining i) focus groups with healthcare professionals recruited via professional networks and social media, and ii) interviews with patients and carers recruited in hospital and hospice settings. We analysed the data using Practical Thematic Analysis Results: Fifty-five multidisciplinary healthcare professionals participated in 11 focus groups, and we interviewed 10 patients and carers. We constructed five descriptive themes to summarise the data: Navigating priorities and uncertainty; positive impacts alongside a sense of shame and stigma; talking about money, difficulties and dividends; everybodys, yet nobodys, responsibility; and sticking points in the system. Conclusion: The themes reveal several challenges that may contribute to people not taking up this financial support. However, discussions about access to benefits were also seen as a core part of holistic care, a positive way to offer support and a gateway to other discussions about end-of-life care preferences and decisions. Recommendations for policy and practice include evaluating the adoption of a diagnostic rather than a prognostic eligibility criteria, integrating discussions about benefits into existing processes such as advance care planning, and improving education and support for clinicians.

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

Timage: A Generative Text-in-Image Paradigm for Fine-Tuning Vision-Language Models

Multimodal Large Language Models (MLLMs) often lose track of the right image regions during fine-grained spatial reasoning, because a textual query rarely carries any explicit geometric anchor into the pixel domain. Prevailing remedies either rewire the model's weights or pad the prompt with verbose instructions, yet neither reliably pins the language to the correct visual coordinates without eroding the backbone's general competence. We introduce Timage, a paradigm that recasts multimodal understanding as an alignment problem solved at the input: the query is drawn, as a typeset overlay, onto the image itself. The placement and appearance of this overlay are produced by a Constrained Schrödinger Bridge (cSB), an entropic optimal-transport sampler that factorizes layout synthesis into two coupled stochastic stages. The first stage, Region Search, transports noise toward query-aligned image zones while obeying a hard occlusion barrier that protects salient foreground content; the second stage, Appearance Shaping, sizes the glyphs through an ``ink-budget'' regularizer so that the rendered text stays legible and visually balanced. The resulting overlay behaves as an explicit attention beacon that channels the model's focus along spatial semantics. On the VMCBench suite, Timage paired with a modest 7B backbone clearly overtakes far larger proprietary systems as well as parameter-tuned baselines. The study positions deliberate input reconstruction as a powerful, architecture-neutral lever for strengthening multimodal reasoning.

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

Exploring Starts Are Not Enough: Counterexamples and a Fix for Monte Carlo Exploring Starts

arXiv:2606.15247v1 Announce Type: cross Abstract: The asymptotic behaviour of Monte Carlo Exploring Starts (MCES) is a long-standing open question in reinforcement learning, even in the tabular setting. We investigated the convergence properties of tabular MCES by constructing examples in which the algorithm converges to suboptimal solutions. This paper presents new counterexamples for both initial-visit and first-visit MCES and gives a convergence-restoring modification for the initial-visit case. We show that stable suboptimal solutions may exist for initial-visit MCES with sample-average updates even when greedy actions are updated more often than non-greedy actions on average. However, by scaling learning rates inversely to update frequencies on a state-by-state basis, convergence to optimality is guaranteed. Unlike previous uniformisation methods, this modification is applicable to large-scale problems that require approximating the estimated value function. We then extend the example to show that sample-average first-visit MCES may also converge to suboptimal solutions. This largely settles a fundamental open problem and shows that exploring starts alone do not guarantee convergence to optimality. More broadly, these results highlight that convergence depends critically on the relative size and frequency of updates applied to different actions, making the choice of learning rates and the balance between exploration and exploitation central to the analysis of MCES and the implementation of scalable Monte Carlo control methods.

18.
medRxiv (Medicine) 2026-06-18

A Novel Correction Method for QT Interval in the Presence of Left Bundle Branch Block Morphology

Background Accurate assessment of the QT interval is challenging in the presence of QRS prolongation, such as during ventricular pacing or bundle branch block. Current correction methods are heterogeneous and lack consensus. To evaluate the relationship between QRS duration and QT interval during ventricular pacing and to develop a practical correction method for QT assessment. Methods In this prospective single-centre study, 94 patients undergoing electrophysiology study for supraventricular tachycardia were included. Standardised pacing was performed at the same cycle length from the right ventricular (RV) apex, high output and low output pacing from His catheter, and coronary sinus (reference). QRS and QT intervals were measured from 12-lead ECGs. Changes in QT (QT) and QRS duration (QRS) were analysed using linear regression and mixed-effects modelling. QT correction formulas of the form QT corrected = QT N x QRS were evaluated using Bland-Altman analysis across multiple coefficients. Results A significant positive correlation between QRS and QT was observed across all pacing sites (r = 0.52-0.74, p < 0.001). In mixed-effects modelling, QRS was a strong independent predictor of QT (0.59, p < 0.001), with no significant interaction between pacing site and QRS, supporting a consistent relationship across pacing locations. Bland-Altman analysis demonstrated that correction coefficients of 0.65-0.70 minimised systematic bias compared with lower coefficients, with similar precision across models (SD 16 ms) and no evidence of proportional bias. A coefficient of 0.65 provided the most balanced performance between bias and variability. Conclusion QT prolongation during ventricular pacing is primarily driven by QRS widening and follows a consistent linear relationship across pacing sites. A simple correction using QT corrected = QT 0.65 x (QRS 100 ms) provides a practical and accurate method for QT assessment, with potential clinical applicability in patients with conduction abnormalities or ventricular pacing.

19.
bioRxiv (Bioinfo) 2026-06-11

Tumour evolution as ground truth for cancer whole-genome sequencing

Cancer genomes are shaped by evolutionary processes that couple mutagenesis, clonal selection, chromosomal instability, spatial growth and treatment response into structured genomic patterns, yet current benchmarking strategies largely ignore this evolutionary dependency. Here, we present SCOUT, a large-scale synthetic whole-genome sequencing resource of over 200 samples, designed for systematic benchmarking of tumour genomic analysis and evolutionary inference under controlled evolutionary ground truth. Unlike conventional task-specific simulations, SCOUT models tumour evolution as a latent generative process that simultaneously shapes mutations, copy-number alterations, variant allele frequencies, mutational signatures and clonal architectures. SCOUT recapitulates key features of solid and haematological malignancies, including driver mutations, chromosomal instability, intratumour heterogeneity, spatial sampling and treatment-associated evolutionary dynamics in tumour and matched-normal longitudinal and multi-region sequencing designs. Using SCOUT, we benchmarked widely used methods for somatic variant detection, copy-number analysis, mutational signature inference and tumour evolutionary reconstruction. Across analytical tasks, performance deteriorated in low-purity, highly subclonal and structurally complex tumours, while spatial sampling bias and hypermutation generated spurious evolutionary signals that confounded tumour interpretation across multiple inference layers. Evolutionary simulations further distinguished lineage-restricted genetic bottlenecks from multi-lineage resistance dynamics associated with tumour plasticity. Tumour purity consistently exerted a stronger effect on inference accuracy than sequencing depth. Together, our results establish evolutionary ground truth as a prerequisite for reproducible benchmarking and biologically interpretable analysis of cancer whole-genome sequencing data.

20.
arXiv (quant-ph) 2026-06-16

Against probability: A quantum state is more than a list of probability distributions

arXiv:2601.18872v2 Announce Type: replace Abstract: The state of a quantum system can be represented by listing the outcome probabilities for a tomographically complete set of measurements. Such representations appear throughout physics, for example, in quantum field theory via correlation functions and in quantum foundations within generalized probabilistic frameworks. In this paper, we show a no-go result: To enable useful statements, the probability representation must be topologically robust$\unicode{x2014}$preserving the notion of closeness between states. Yet, a topologically robust probability representation cannot simultaneously retain other essential structure, such as the subsystem structure.

21.
arXiv (quant-ph) 2026-06-12

Information gain and measurement disturbance for quantum agents

arXiv:2402.08060v3 Announce Type: replace Abstract: The traditional formalism of quantum measurement (hereafter ``TQM'') describes processes where some properties of quantum states are extracted and stored as classical information. While TQM is a natural and appropriate description of how humans interact with quantum systems, it is silent on the question of how a more general, quantum, agent would do so. How do we describe the observation of a system by an observer with the ability to store not only classical information but quantum states in its memory? In this paper, we extend the idea of measurement to a more general class of sensors for quantum agents which interact with a system in such a way that the agent's memory stores information (classical or quantum) about the system under study. For appropriate sensory interactions, the quantum agent may ``learn'' more about the system than would be possible under any set of classical measurements – but as we show, this comes at the cost of additional measurement disturbance. We experimentally demonstrate such a system and characterize the tradeoffs by considering the channel capacity required to erase the effect of a measurement.

22.
arXiv (math.PR) 2026-06-12

The censored stochastic six-vertex model and parabolic Kazhdan–Lusztig $R$-polynomials

arXiv:2606.12670v1 Announce Type: new Abstract: We introduce a censored version of the stochastic six-vertex model. We show that for parameters $b_1 < b_2$, this model started from the initial condition ${1}_{x>0}$ is stochastically dominated at any time by the blocking measure. This is a partial analog of the censoring inequality for monotone spin systems. In particular, this result allows us to control the behavior of second-class particles. The proof uses parabolic Kazhdan–Lusztig $R$-polynomials, whose appearance is explained using a connection between the stochastic six-vertex model and the Iwahori–Hecke algebras of symmetric groups. Furthermore, we find an intertwining relation for this process using normalized parabolic Kazhdan–Lusztig $R$-polynomials as an intertwining kernel.

23.
arXiv (CS.AI) 2026-06-17

Agentic Discovery of Non-Canonical Antimicrobial Peptides with AMPGAN v3

arXiv:2606.17127v1 Announce Type: cross Abstract: Antimicrobial resistance causes to over a million deaths annually. Antimicrobial peptides (AMPs) are a promising solution, but generative AMP models are not yet ready to design peptides with non-natural amino acids and/or chemical modifications, which are essential for real-world peptide drugs. We present AMPGAN v3, a multi-objective conditional GAN that expands the generative vocabulary to D-amino acids and N/C-terminus modifications such as amidation. By separating adversarial and activity-aware supervision across two specialized discriminators, AMPGAN v3 substantially improves training stability and outperforms prior generative AMP models on external classifiers. We validated five candidates spanning three structural classes in vitro; two showed activity against Gram-positive strains, with the best candidate reaching MIC 8 {\mu}g/mL against B. subtilis. To support downstream curation, we further present PepCraft, a multi-agent framework for end-to-end AMP discovery in which a Planning Agent orchestrates specialized executors for generation, filtering, and verification. Its prioritization recommendations align with our in vitro outcomes. Together, these contributions let us examine, on a small but real scale, how generative and agentic AI compose in therapeutic peptide discovery. Code: https://github.com/marszzibros/AMPGANv3

24.
arXiv (CS.AI) 2026-06-17

Reversal Q-Learning

arXiv:2606.17551v1 Announce Type: cross Abstract: Iterative generative modeling techniques, such as flow matching, provide powerful tools to model complex behaviors for effective offline reinforcement learning (RL). In this work, we propose a new off-policy RL algorithm that trains a flow policy based on prior data. Our idea starts from the "expanded" Markov decision process (MDP) framework, which treats individual flow refinement steps as separate actions in an MDP. To enable off-policy RL within this framework, we apply two techniques: we generate virtual on-policy trajectories (by "reversing" flows) to make this framework compatible with prior data, and we apply a bias-and-variance reduction technique to mitigate the curse of horizon in off-policy RL. We call the resulting algorithm Reversal Q-learning (RQL). RQL has several advantages over previous flow-based RL methods: it does not suffer from backpropagation through time, makes better use of the learned value function, and directly trains the full, expressive flow policy. Through our experiments on 50 challenging simulated robotic tasks, we show that RQL leads to the best average offline RL performance compared to state-of-the-art flow-based offline RL algorithms.

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arXiv (CS.AI) 2026-06-16

Open-SWE-Traces: Advancing Dual-Mode Multilingual Distillation for Software Engineering Agents

arXiv:2606.16038v1 Announce Type: cross Abstract: The path toward autonomous software engineering is currently bottlenecked by a severe deficit of diverse, large-scale trajectory data. We address this by introducing \ourdataset, an expansive dataset of 207,489 agentic trajectories spanning nine programming languages (Python, Go, TS, JS, Rust, Java, PHP, C, C++). Sourced from 20,000 real-world PRs via OpenHands and SWE-agent harnesses, the dataset utilizes a hybrid-reasoning synthesis: Minimax-M2.5 generates trajectories with explicit "thinking" processes, while Qwen3.5-122B provides high-quality "non-thinking" traces. Filtered for permissive licenses (MIT, Apache, BSD) from SWE-rebench-V2, this data facilitates the training of models capable of long-horizon reasoning. We validate the dataset by fine-tuning the Qwen3-30B-A3B series (Thinking, Instruct, and Coder). The best performing model achieves resolve rates of 61.7% on SWE-bench Verified, 57.1% on SWE-bench Multilingual, and 36.8% on SWE-bench Pro. These results establish Open-SWE-Traces as a premier resource for distilling human-level software engineering capabilities into efficient, open-source agentic LLMs.