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01.
arXiv (quant-ph) 2026-06-16

Instrument-based quantum resources: quantification, hierarchies and towards constructing resource theories

arXiv:2508.09134v3 Announce Type: replace Abstract: Quantum resources are certain features of the quantum world that provide advantages in certain information-theoretic, thermodynamic, or other useful operational tasks that are outside the realm of what classical theories can achieve. Quantum resource theories provide us with an elegant framework for studying these resources quantitatively and rigorously. While numerous state-based quantum resource theories have already been investigated, and to some extent, measurement-based resource theories have also been explored, instrument-based resource theories remain largely unexplored, with only a few notable exceptions. As quantum instruments are devices that provide both the classical outcomes of induced measurements and the post-measurement quantum states, they are quite important, especially for scenarios where multiple parties sequentially act on a quantum system. In this work, we study several instrument-based resource theories, namely (1) the resource theory of information preservability, (2) the resource theory of (strong) entanglement preservability, (3) the resource theory of (strong) incompatibility preservability, (4) the resource theory of traditional incompatibility, and (5) the resource theory of parallel incompatibility. Furthermore, we outline the hierarchies of these instrument-based resources and provide measures to quantify them. We then also established a relationship between our resource measure and the advantage in an information-theoretic task. In short, we provide a detailed framework for a wide variety of instrument-based quantum resource theories.

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

Nonlocal Bayesian Modeling of Continuous Spatio-Temporal Dynamics

arXiv:2606.14313v1 Announce Type: cross Abstract: Real-world spatio-temporal forecasting must handle irregular time points, spatially sparse observations, and the need for uncertainty quantification. This setting is often further compounded by nonlocal interactions (long-range spatial coupling). Modeling continuous-space, continuous-time nonlocal dynamics naturally leads to infinite-dimensional integro-differential equations (IDEs), making principled Bayesian inference intractable. We propose the NonLocal Bayesian Spatio-Temporal model (NLBST), a hierarchical Bayesian framework for continuous spatio-temporal fields that learns explicit nonlocal coupling while retaining tractable inference. NLBST represents the latent field via a coordinate-based spatial basis expansion and models the coefficient process with a continuous-time ODE whose learnable linear operator corresponds to a Galerkin reduction of a nonlocal IDE; a Neural ODE residual captures additional nonlinear dynamics. A linear-Gaussian observation model enables Kalman-style sequential updates under missing and irregular observations, while the spatial basis representation enables inductive prediction at unmeasured locations without retraining. Global parameters are learned via variational inference, and uncertainty is handled through a Bayesian hierarchy. Experiments on synthetic and real-world datasets demonstrate strong forecasting and spatial generalization with well-calibrated uncertainty, yielding substantial gains over baselines in strongly nonlocal and partially observed regimes.

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

Show the Signal, Hide the Noise: Spectral Forcing for Pixel-Space Diffusion

Pixel-space diffusion models are trained on full-bandwidth noisy images, yet the useful signal available to the denoiser is strongly frequency dependent. Under rectified-flow diffusion and natural-image power-law spectra, the per-band data-to-noise contour $k^{*}(t) = (1-t)^{-2/\alpha}$ separates a signal-bearing low-frequency region from a noise-dominated high-frequency region at each time $t$. We show that this implicit coarse-to-fine structure is not merely descriptive: it induces a capacity-allocation problem. A standard pixel-space denoiser must discover the moving bandwidth boundary internally and can spend computation on frequency-time regions where the optimal prediction collapses to deterministic baselines rather than data-distribution modeling. To make this boundary explicit, we introduce Spectral Forcing, a parameter-free, time-conditional 2D-DCT low-pass operator applied to the noisy input before the patch embedder. Its cutoff expands monotonically with the diffusion time and becomes the identity at the data endpoint. Through controlled synthetic experiments, we identify the regime in which the operator is beneficial: coarse patch tokenization and data whose high-frequency content is predominantly noise rather than essential signal. On ImageNet-256 with JiT-700M/32, Spectral Forcing consistently improves both FID and Inception Score across different training epochs, demonstrating robust gains throughout training; at finer tokenization, the spectral forcing is still competitive. We further insert the unchanged operator into SenseNova-U1, a unified text-to-image model, where it improves DPG-Bench and GenEval, showing that the input-side spectral prior transfers beyond class-conditional generation. These results suggest a route to capacity-efficient pixel-space diffusion by showing the signal and hiding the noise.

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

Finite-Time Convergence of Distributionally Robust Q-Learning with Linear Function Approximation

arXiv:2510.01721v3 Announce Type: replace Abstract: Distributionally robust reinforcement learning (DRRL) seeks policies that perform well when the deployment transition model differs from the nominal model generating the data. Most finite-sample guarantees for DRRL are tabular, model-based, rely on generative access, or obtain function-approximation guarantees only under additional structure, such as linear-transition models or restrictive discount-factor conditions. We study discounted model-free robust Q-learning under an $(s,a)$-rectangular chi-square uncertainty set, with linear approximation of the robust Q-function, using only a single Markovian trajectory from an unknown nominal model. Our algorithm combines a target-network outer loop with a dual function-approximation scheme for the chi-square robust Bellman update. The dual procedure uses moment-tracking critics, suffix averaging, a fresh-evaluation stage for the variance-like moment, and a tunable smoothing parameter to have a Lipschitz-continuous chi-square dual gradient. We prove a finite-time convergence bound to the optimal robust Q-function up to approximation error, without imposing a small-discount-factor assumption. Our results help close a gap between the empirical use of robust RL algorithms and the non-asymptotic guarantees available for their non-robust counterparts.

05.
medRxiv (Medicine) 2026-06-10

Development of a Novel Blood-Based Assay for Brain-Derived Tau and Its Validation in Traumatic Brain Injury

Brain-derived tau (BD-tau) is an emerging blood-based biomarker for neurodegeneration, yet there are currently limited well validated BD-tau assays available for research and clinical use. To enhance access to this vital biomarker for neurological disorders including traumatic brain injury (TBI), we developed a novel blood-based immunoassay for BD-tau on the ultra-sensitive Quanterix HD-X platform using Single Molecule Array technology. Analytical validation assessed dilution linearity, specificity, precision, detection limits, and spike recovery, each recording robust metrics in agreement with international expert recommendations. The assay demonstrated robust validation metrics, achieving between-run stability of 95% when analyzing aliquots from six independent plasma and serum samples across five analytical runs. It also showed strong dilution linearity when diluted four-fold and achieved over 90% recovery when spiked with cerebrospinal fluid. Next, we evaluated the clinical utility of the assay in cohorts of individuals with traumatic brain injury (TBI), where strong performances were recorded whether using the 2-step or 3-step assay formats ({rho}= 0.94; p < 0.0001). Furthermore, plasma BD-tau distinguished samples from TBI patients based on time from injury and severity (AUC=0.93). Plasma BD-tau differentiated between favorable and unfavorable functional outcomes in the acute-severe group. Our findings underscore the significant potential of the BD-tau assay as a biomarker for TBI in the severe phase.

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

CODA-BENCH: Can Code Agents Handle Data-Intensive Tasks?

Advanced agents are increasingly demonstrating the potential to operate as autonomous engineers, creating a growing demand for evaluation benchmarks that capture the complexity of real-world development. Such environments typically involve both complex code and large-scale data (i.e., file system). However, existing benchmarks usually evaluate code-centric or data-centric capabilities in isolation, leaving a clear gap with real development scenarios. In this paper, we bridge this gap by introducing CODA-BENCH, the first benchmark to jointly evaluate code and data intelligence in a data-intensive environment. We construct a data-intensive Linux sandbox based on the Kaggle ecosystem (containing hundreds of datasets), where agents must actively explore complex file hierarchies to identify relevant resources and generate code for data-driven analytical tasks. CODA-BENCH comprises 1,009 tasks spanning 31 communities, with each task environment containing an average of 980 files, simulating realistic data scale and noise. Evaluations of advanced agents reveal that even top-performing systems struggle to effectively integrate data discovery with code execution, achieving a success rate of only 61.1%. These results highlight a substantial gap in current agentic capabilities for data-intensive tasks and point to promising directions for future research.

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

The KG-ER Conceptual Schema Language

arXiv:2508.02548v3 Announce Type: replace-cross Abstract: We propose KG-ER, a conceptual schema language for knowledge graphs that describes the structure of knowledge graphs independently of their representation (relational databases, property graphs, RDF) while helping to capture the semantics of the information stored in a knowledge graph.

08.
arXiv (CS.CL) 2026-06-19

Before the Labels: How Dataset Construction Shapes Suicidality Detection in Clinical Text

Clinical NLP increasingly relies on electronic health record (EHR) data to detect suicidal behaviors, treating clinical documentation as more reliable ground truth than social media. We argue that this framing obscures how EHR-based suicidality datasets encode a particular operationalization of suicidality, shaped by who authors the data, how episodes are bounded, and how ambiguity is resolved. We ground this argument in a case study of the ScAN dataset, built over MIMIC-III clinical notes. We show how governance constraints, ICD-based cohort selection, single-annotator labeling, and hospital-stay-level aggregation produce labels that reflect clinician-documented judgments, treat suicidality as a bounded episode, and assume that intent can be reliably inferred from documentation. A linguistic analysis demonstrates that identical labels subsume heterogeneous clinical framings differing in temporality, negation, and uncertainty. We argue that clinical NLP should examine the assumptions embedded in suicidality datasets before interpreting their labels as ground truth.

09.
bioRxiv (Bioinfo) 2026-06-11

Pillbox: A Leakage-Aware Foundation-Model Predictor and Lineage-Ceiling Diagnostic for Cancer Drug Response

We present Pillbox, a predictor whose pipeline is audited against the six Asiaee leakage modes with the one residual pathway shown by per-fold ablation to be non-load-bearing on hard splits. Our model combines CpGPT methylation embeddings, CLAMP drug embeddings, and per-fold-fit gene-expression principal components which are fused by Feature-wise Linear Modulation (FiLM)-conditioned graph attention on the STRING v12 protein-protein interaction graph. Then we alpha-ensemble the model against a histogram-based gradient boosting regressor baseline. On GDSC GSE68379 (987 cell lines, 375 drugs) across seeds 42, 7, and 123, the ensemble reaches test R-Squared of 0.78, 0.77, and 0.76 on random, histology-blind, and site-blind splits respectively, with cell-aware lifts above the drug-mean floor of +0.054, +0.060, and +0.037. As a quantitative diagnostic for feature-stack saturation we propose the cross-architecture residual correlation, calibrated against a same-architecture-different-initialization control. On histology-blind splits the cross-architecture value of 0.939 falls short of the same-architecture ceiling of 0.974 by approximately 0.03 in residual correlation, a gap we interpret as the headroom available to architecture choice on top of the current foundation-model representation and consistent with the long-established observation that tissue lineage dominates cell-line drug response. We integrated curated mutation, methylation, and drug-target-expression channels, but these do not improve prediction once foundation-model embeddings are in place. Cross-screen validation against PRISM matches the GDSC-to-PRISM measurement reproducibility ceiling within 0.01 Spearman.

10.
arXiv (CS.AI) 2026-06-19

Cost-Optimal LLM Routing with Limited User Feedback under User Satisfaction Guarantees

arXiv:2606.19376v1 Announce Type: cross Abstract: Inference costs for large language model (LLM) applications are rapidly growing, driven by surging demand and rising infrastructure cost. Users expect high-quality responses, and in commercial settings this is formally codified in Service Level Agreements (SLAs), creating a fundamental tension between cost and quality. Recent progress on cost-aware LLM request routing has shown potential to resolve this tension, but existing approaches rely on complete feedback signals, offline training, extensive per-workload tuning, and most lack SLA guarantees or inference-time adaptivity. We introduce SLARouter, an online routing algorithm that learns a cost-optimal policy from the sparse, one-sided user feedback available in production systems. SLARouter provides theoretical guarantees for both cost optimality and strict SLA compliance. Experiments across a wide range of LLM benchmarks show that SLARouter satisfies SLA constraints without the need for per-benchmark tuning, reducing operating cost by up to 2.2x over existing baselines.

11.
arXiv (CS.LG) 2026-06-15

Deep Learning and Elicitability for McKean-Vlasov FBSDEs With Common Noise

arXiv:2512.14967v2 Announce Type: replace Abstract: We present a novel numerical method for solving McKean–Vlasov forward–backward stochastic differential equations (MV–FBSDEs) with common noise, combining Picard iterations, elicitability and deep learning. The key innovation involves elicitability to derive a pathwise loss function, enabling efficient training of neural networks to approximate both the backward process and the conditional expectations arising from common noise, without requiring computationally expensive nested Monte Carlo simulations. The mean-field interaction term is parameterized via a recurrent neural network trained to minimize an elicitable score, while the backward process is approximated through a hybrid feedforward and recurrent network representing the decoupling field. We validate the algorithm on a systemic-risk inter-bank borrowing and lending model, where analytical solutions exist, demonstrating accurate recovery of the true solution. We further extend the model to quantile-mediated interactions, showcasing the flexibility of the elicitability framework beyond conditional means or moments. Finally, we apply the method to a non-stationary Aiyagari–Bewley–Huggett economic growth model with endogenous interest rates, illustrating its applicability to complex mean-field games without closed-form solutions.

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

Entity Binding Failures in Speech LLM Reasoning: Diagnosis and Chain-of-Thought Intervention

Speech Large Language Models (SLLMs) underperform their text counterparts on complex reasoning. We reveal that this gap is not a uniform cognitive deficit. Evaluating two architecturally diverse SLLMs, we show speech-to-text (S2T) matches or exceeds text-to-text (T2T) on spatial, syntactic, and factual tasks. Yet on logical tasks requiring entity tracking, S2T accuracy collapses to chance. We diagnose this as an entity binding failure: continuous speech features blur precise entity-property associations during implicit reasoning. To validate this diagnosis, we introduce Entity-Aware Chain-of-Thought (EA-CoT), a lightweight inference-time intervention forcing SLLMs to enumerate entities and bind them to claims before reasoning. EA-CoT bridges the gap, even when spoken names are misrecognized, yielding up to a 24.4 percentage-point accuracy gain. Ablations confirm the gains stem from explicit semantic binding, reframing the gap as an elicitation failure rather than a missing capability.

13.
bioRxiv (Bioinfo) 2026-06-10

A Unified Spatial AI Framework for Cross-Domain Tissue-State Analysis in Trauma, Oral, and Cardiovascular Pathology

作者:

Objective: To develop a cross-domain spatial AI framework for identifying conserved tissue-state organisation across trauma, oral disease, and cardiovascular tissue using spatial transcriptomic data. Methods: Four public spatial transcriptomic datasets spanning wound healing, periodontitis, oral squamous cell carcinoma, and cardiac tissue were integrated using recurrence modelling, graph-based spatial learning, fuzzy tissue-state analysis, and tensor decomposition. Cross-domain coupling, spatial fragmentation, recurrence structure, and permutation-based topological validation were evaluated. Results: Six conserved fuzzy tissue states were identified, dominated by extracellular matrix remodelling, fibroblast/stromal activation, endothelial signalling, and inflammatory pathways. Latent embedding analysis demonstrated strong overlap between trauma and oral domains, while cardiovascular tissue exhibited more compact spatial organisation. Oral inflammatory tissue showed the highest fragmentation, whereas cardiovascular tissue demonstrated greater recurrence coherence. Tensor decomposition identified conserved stromal-remodelling programmes across domains. Permutation testing confirmed significantly elevated graph modularity and reduced spatial entropy relative to null distributions. Conclusion: The proposed framework identified conserved spatial tissue-state architecture linking wound healing, oral pathology, and cardiovascular tissue despite differences in tissue origin, pathology, and acquisition technology. Significance: These findings demonstrate the potential of spatial AI for investigating conserved stromal and inflammatory microenvironmental organisation across clinically related disease systems and may support spatial biology research in trauma–oral–systemic health.

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

All Eyes on the Workflow: Automated and Efficient Event Discovery from Video Streams

Disciplines such as business process management and process mining aid organizations by discovering insights about processes on the basis of recorded event data. However, an obstacle to process analysis is data multi-modality: for instance, data in video form are not directly interpretable as events. Existing approaches rely on a dictionary of activity label as input, cannot provide frame-by-frame labeling explanations, or rely on superseded computer vision techniques. In this work, we present SnapLog, an approach to extract event data from videos by converting frames to feature vectors using image embeddings and performing temporal segmentation through frame-wise similarity matrices. A generalized few-shot classification is then used to assign labels to the video segments, yielding labeled, timestamped sub-sequences of frames that are interpretable as events. Conventional process mining techniques can be used to analyze the resulting data. We show that our approach produces logs that accurately reflect the process in the videos.

15.
bioRxiv (Bioinfo) 2026-06-21

SPA-C: an hybrid tool to accurately scaffold genomes using Hi-C and Deep-Learning

Genome assembly is a computational pipeline designed to reconstruct chromosomes from small sequencing reads. Following their assembly, contiguous sequences (contigs) are arranged into chromosome-long sequences during scaffolding. Hi-C, a long-range linkage information between regions of the genome widely used in recent large sequencing projects, is often required to correctly order contigs. Several tools have been developed to automate this task following either statistical or deep-learning approaches. Statistical approaches summarise 2D Hi-C matrices into contact densities across sequences, thus ignoring informative visual patterns. The sole existing deep-learning tool uses a transformer-based computer vision model to correct the assembly. It has been trained on several species and uses Hi-C matrices directly. Yet it comes as a supplementary step in the scaffolding process, introducing extra computation time, and has been trained on a dataset that might contain labelling errors, which could provide sub-optimal results. We propose SPA-C, an hybrid pipeline combining the strengths of both approaches. Linkage prediction is handled with a frugal CNN-based model and a graph-solving algorithm is used to generate the scaffolds. Through our input's design, the model is able to both correct errors within assemblies and link contigs, leveraging small, local Hi-C contact matrices. We handled low-complexity regions that might induce erroneous predictions using an external tool, improving the overall accuracy of generated assemblies. On a benchmark of six various genomes and four standard metrics, SPA-C outperformed four out of four state-of-the-art methods while achieving comparable start-to-end computation time.Python and Bash scripts are available on GitHub (https://github.com/SPA-C/SPA-C.git) and Zenodo (https://doi.org/10.5281/zenodo.19000361).

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

SPEAR: A System for Post-Quantization Error-Adaptive Recovery Enabling Efficient Low-Bit LLM Serving

arXiv:2606.11244v1 Announce Type: cross Abstract: Efficient large language model (LLM) serving is increasingly constrained by deployment cost. Quantization is a key technique for reducing serving cost, yet even state-of-the-art 4-bit quantizers exhibit a noticeable quality gap from FP16, particularly for smaller models where low-bit serving is most beneficial. We identify a fundamental cause of this gap: quantization error is highly input-dependent and varies substantially across tokens, while existing post-quantization compensation methods are static and apply identical corrections to all inputs. As a result, easy tokens are over-corrected while hard tokens remain under-corrected. We present SPEAR, a system for post-quantization error-adaptive recovery that improves low-bit LLM serving. SPEAR introduces lightweight Error Compensators (ECs) modulated by per-token gates and places them only at the most error-sensitive layers identified through a CKA-guided entropy-aware diagnostic. This focuses a small parameter budget where it is most effective. Efficient deployment of ECs presents several systems challenges, including additional computation, tensor-parallel synchronization caused by input-dependent gating, and latency instability across configurations. SPEAR addresses these issues through adaptive kernel-fusion dispatch, combining an epilogue-integrated peer-reduction kernel with P2P dual-write to fuse the post-EC computation into low-bit GEMMs, and an SLO-constrained EC-aware scheduler for predictable serving performance. Across challenging per-channel quantization settings, SPEAR recovers 56-75% of the perplexity gap between W4 and FP16 while adding less than 1% model memory overhead and maintaining latency comparable to a widely used 4-bit serving deployment.

17.
arXiv (math.PR) 2026-06-11

Large deviations for marked sparse random graphs with applications to interacting diffusions

arXiv:2204.08789v2 Announce Type: replace Abstract: We consider the empirical neighborhood distribution of marked sparse Erdős-Rényi random graphs, obtained by decorating edges and vertices of a sparse Erdős-Rényi random graph with i.i.d. random elements taking values on Polish spaces. We prove that the empirical neighborhood distribution of this model satisfies a large deviation principle in the framework of local weak convergence. We rely on the concept of BC-entropy introduced by Delgosha and Anantharam~(2019) which is inspired on the previous work by Bordenave and Caputo~(2015). Our main technical contribution is an approximation result that allows one to pass from graph with marks in discrete spaces to marks in general Polish spaces. As an application of the results developed here, we prove a large deviation principle for interacting diffusions driven by gradient evolution and defined on top of sparse Erdős-Rényi random graphs. In particular, our results apply for the stochastic Kuramoto model. We obtain analogous results for the sparse uniform random graph with given number of edges.

18.
arXiv (CS.LG) 2026-06-19

VIMPO: Value-Implicit Policy Optimization for LLMs

arXiv:2606.20008v1 Announce Type: new Abstract: Reinforcement learning with verifiable rewards has become a central tool for improving the reasoning ability of large language models, but current methods face a trade-off between simplicity and credit assignment. Group-relative methods such as GRPO avoid training a critic, but typically assign a trajectory-level advantage to every token. Actor-critic methods provide denser learning signals, but require a learned value function with its own training instability. We introduce VIMPO, a critic-free policy optimization method that derives a policy-implied value function from the optimality conditions of KL-regularized reinforcement learning. For autoregressive generation, the resulting value recurrence can be written in terms of policy-reference log-ratios and anchored by the terminal condition that no future reward remains at the end of a trajectory. This gives a simple value loss that incorporates outcome-level verifiable rewards without training a critic. The same derivation also yields a critic-free actor advantage, allowing VIMPO to separate reward incorporation through the value loss from policy improvement through a PPO-style actor update. On mathematical RLVR benchmarks, VIMPO improves over GRPO across MATH-500, AIME 2024, AIME 2025, and OlympiadBench, with especially larger gains on competition-style evaluations. Under noisy rewards, VIMPO retains a consistent advantage over GRPO, suggesting that policy-implied value optimization can provide finer credit assignment while preserving the practical simplicity of critic-free training.

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

Structured Noise Adaptation for Sequential Bayesian Filtering with Embedded Latent Transfer Operators

arXiv:2606.14195v1 Announce Type: new Abstract: Kalman filters based on the Embedded Latent Transfer Operators (ELTO) emerge as novel statistical tools for sequential state estimation. However, a critical limitation stems from their use of simplified noise models, which fail to dynamically adapt to non-stationary processes. To address this limitation, we introduce an ELTO-based Bayesian filtering approach with a new structured parameterization for the filter's noise model. This parameterization enables structured noise adaptation, which couples the data-driven learning of an optimal time-invariant noise model with dynamic parameter adaptation that responds to changes in dynamics within non-stationary processes. Empirical results show that our structured noise adaptation improves the filter's dynamic state estimation performance in noisy, time-varying environments.

20.
arXiv (quant-ph) 2026-06-17

Probes of chaos over the Clifford group and approach to Haar values

arXiv:2603.29695v3 Announce Type: replace Abstract: Chaotic behavior of quantum systems can be characterized by the adherence of the expectation values of given probes to moments of the Haar distribution. In this work, we analyze the behavior of several probes of chaos using a technique known as Isospectral Twirling [1]. This consists in fixing the spectrum of the Hamiltonian and picking its eigenvectors at random. Here, we study the transition from stabilizer bases to random bases according to the Haar measure by T-doped random quantum circuits. We then compute the average value of the probes over ensembles of random spectra from Random Matrix Theory, the Gaussian Diagonal Ensemble and the Gaussian Unitary Ensemble, associated with non-chaotic and chaotic behavior respectively. We also study the behavior of such probes over the Toric Code Hamiltonian.

21.
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.

22.
arXiv (CS.AI) 2026-06-15

Evidence-Gated LLM Priors for Multi-Objective Bayesian Optimization

arXiv:2606.01730v2 Announce Type: replace Abstract: Large language models (LLMs) are increasingly used as heuristic advisors for black-box optimization, yet their suggestions and self-reported confidence are not necessarily calibrated to downstream objective values. This issue becomes more pronounced in multi-objective Bayesian optimization, where different objectives may require different expert knowledge and where an LLM expert can be useful for one objective but misleading for another. We study how to use LLM-generated expert priors in discrete multi-objective Bayesian optimization without blindly trusting them. We propose an objective-wise reputation-market mechanism that treats each expert-objective pair as a falsifiable prior source. Expert weights are updated online from observed objective feedback, discounted over time, and gated by market-level trust. We then introduce a decoupled counterfactual gate that can use the LLM prior without confidence, use it with confidence, or abstain from the LLM prior entirely. Across controlled synthetic stress tests and three molecule optimization benchmarks with \qwenflash{}-generated expert priors, we find that dynamic objective-wise calibration improves robustness over fixed LLM priors. However, raw LLM confidence is not reliably beneficial: on ESOL, confidence is positively correlated with prediction error; on FreeSolv, confidence can help; and on Lipophilicity, ignoring confidence remains strongest. Our fixed three-arm counterfactual gate improves over the first counterfactual variant on ESOL and FreeSolv, while an attempted margin portfolio exposes a useful negative result: margin selection should be acquisition-aware rather than based only on one-step prior error.

23.
arXiv (quant-ph) 2026-06-19

Efficient classical representation and quantum state preparation of complete active space wavefunctions

作者:

arXiv:2606.19457v1 Announce Type: new Abstract: Quantum computers promise to solve the electronic structure problem for a large class of molecules. However, the performance of relevant quantum algorithms hinges on preparing initial states with substantial overlap with the target eigenvector. For classically challenging molecules with strong electron correlation, starting from multi-reference states, such as complete active space (CAS) wavefunctions is necessary. Unfortunately, the most advanced state preparation protocols applied to such states result in a gate complexity that scales exponentially with the active space size $d$. In fact, even encoding a CAS state classically is traditionally believed to be intractable for chemically relevant systems. Here, we draw insights from the recently introduced Quantum Paldus Transform (QPT) to show that there exists an efficient classical representation of CAS states and to design a new state preparation routine outperforming previous ones. The QPT represents a transformation from the Fock basis to a friendlier symmetry-adapted basis. Our main contribution consists in showing that CAS states expanded in this basis can efficiently be represented as a matrix product state (MPS) with a bond dimension scaling as $O(d^2)$. One can then efficiently load the MPS on a quantum computer and use the inverse QPT to transform the state to the Fock basis. Moreover, our method can easily be extended to the efficient preparation of CAS states in first quantisation with similar complexity. Crucially, we demonstrate that the complexity of both state preparation protocols only grows polynomially as $O(d^3)$ , which constitutes to the best of our knowledge an exponential improvement over the state of the art.

24.
arXiv (CS.CL) 2026-06-12

Layer-Resolved Optimal Transport for Hallucination Detection in NMT and Abstractive Summarization

Optimal transport (OT) has been shown to detect hallucinations in neural machine translation (NMT) by measuring the geometric distance between cross-attention distributions and a reference distribution, without any supervision. We extend this analysis to all six decoder layers of the Fairseq DE-EN model ($N=3{,}414$), showing that Wass-to-Unif and Wass-to-Data are complementary detectors specialised across hallucination types, that detection is concentrated in layers L1–L4 with L5 anti-predictive for subtler types, and that hallucinated translations lack the exploratory attention phase present in correct translations from the first decoding step. We further evaluate whether the geometric signal transfers to abstractive summarization faithfulness detection: our unsupervised OT detector on AggreFact ($N=1{,}116$) achieves $57.2\%$/$57.6\%$ balanced accuracy on CNN/XSum – above chance but substantially below supervised MiniCheck-Flan-T5-L($69.9\%$/$74.3\%$). This gap is principled: unlike NMT hallucinations, unfaithful summaries can attend correctly to source tokens while misrepresenting their content, a failure mode invisible to concentration-based OT metrics by construction. Structural experiments on T5-base confirm consistent decoder organisation across depth, with Layer~3 showing peak concentration and Layer~12 being most critical for generation quality. Together, the results establish OT on cross-attention as a reliable detector when the failure mode is source disengagement, a principled interpretability tool regardless of task, and fundamentally limited when faithfulness failures occur downstream of attention.

25.
medRxiv (Medicine) 2026-06-15

Multi-domain AD risk burden and plasma biomarkers in cognitively unimpaired adults

Introduction: Alzheimer's disease (AD) pathology accumulates decades before symptom onset, yet how the cumulative effect of genetic, familial, and modifiable lifestyle risk burden jointly affects plasma biomarker levels and trajectories in cognitively unimpaired older adults remains unknown. Methods: We analyzed data from 261 participants in the PREVENT-AD cohort. A composite risk score integrating APOE e4 status, polygenic score, family history, and modifiable/lifestyle risk was examined against six plasma biomarkers using linear regression and linear mixed-effects models. Results: APOE e4 was the strongest predictor of plasma biomarker levels. Higher composite risk burden was associated with elevated ptau181, ptau217, ptau217/Ab42, and GFAP levels, and lower Ab42/40 levels. A higher risk burden was predictive of accelerated ptau181 accumulation. Discussion: Cumulative AD risk burden is broadly associated with plasma biomarker levels and specifically predicts accelerated ptau181 accumulation in cognitively unimpaired older adults, supporting structured composite risk profiling as a framework for AD risk stratification.