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01.
arXiv (CS.AI) 2026-06-16

Critically Engaged Pragmatism: Scientific Norm and Social, Pragmatist Epistemology for AI Science Evaluation Tools

作者:
Carole J. Lee↗

arXiv:2601.09753v2 Announce Type: replace-cross Abstract: AI science evaluation tools aim to assess research credibility. As with traditional metrics such as impact factors, their edicts can be decontextualised and repurposed in problematic ways. To address this, I propose Critically-Engaged Pragmatism as a scientific norm enjoining scientific communities to scrutinise the purposes and purpose-specific reliability of AI science evaluation tools. To foster Critically Engaged Pragmatism, creators of AI science evaluation tools should transparently and fully report design, training, and benchmarking details to facilitate assessments of purpose-specific reliability, liability to different types of error, and bias. What count as best practices for the transparent reporting of AI science evaluation tools should be updated as new forms of error, bias, and gamesmanship are discovered. Under this framework, AI science evaluation tools are not objective arbiters of scientific credibility. Rather, they are the object of critical discursive practices that ultimately ground the credibility of scientific communities.

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02.
arXiv (CS.CV) 2026-06-16

UniDDT: Unifying Multimodal Understanding and Generation with Decoupled Diffusion Transformer

作者:
Shuai Wang↗Liang Li↗Yang Chen↗Ruopeng Gao↗Yao Teng↗Limin Wang↗

Unified Multimodal Models (UMMs) have emerged as a critical direction for general-purpose multimodal intelligence, integrating understanding and generation into a single framework. However, existing UMMs face prominent challenges: (1) the inherent learning conflicts between visual understanding and generation tasks, leading to suboptimal modeling in both tasks; (2) different understanding and generation visual spaces impeding scalability; (3) over-reliance on task-specific data that neglects the duality of text-image understanding and generation. To address these challenges, we propose UniDDT, which leverages a Noisy ViT encoder along with an LLM to unify semantic encoding for visual generation and understanding tasks, while employing a separate diffusion decoder to decouple diffusion decoding from text decoding. With this Noisy ViT encoder, UniDDT is able to leverage the latent space as a unified visual representation, enabling seamless compatibility between understanding and generation tasks. Thus, the scalability within the generation tasks and the semantic expressiveness within understanding tasks can be balanced. Also, we construct dual data structures from the same image-text pairs, fostering interdependence between the generation and understanding data to exploit their inherent duality. Extensive experiments demonstrate that UniDDT achieves effective unification of multimodal understanding and generation with enhanced semantic consistency and scalability. For visual generation tasks, our UniDDT achieves 0.87 GenEval score and 86.9 DPG overall score. For multimodal understanding tasks, our UniDDT achieves 1699.5 score on MME benchmark and 76.5 overall score on SEEDbench.

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03.
medRxiv (Medicine) 2026-06-20

EpiLink: a simulation-based compatibility model for genomic transmission clustering in infectious disease surveillance

作者:
Arthur↗Banks↗C. J↗Kao↗R. R↗

Identifying recently linked infections from pathogen genome sequences is central to infectious disease surveillance, yet many clustering approaches rely on fixed genetic distance thresholds whose relationship to transmission is often unclear. This limitation is especially important in rapidly growing outbreaks and superspreading events, where many cases may be sampled close together in time and share little genetic variation, making true transmission links difficult to distinguish from other closely related infections. Supervised models can improve discrimination, but they require labelled transmission data that are rarely available during outbreak response. We developed EpiLink, a threshold-free method that estimates whether two cases are compatible with recent transmission. Here, compatibility means how well the observed genetic distance and sampling-time difference between two cases fit what would be expected if they were linked by defined recent transmission scenarios. EpiLink simulates plausible recent transmission histories while accounting for uncertainty in infection timing, testing delay, and mutation accumulation, then assigns higher scores to pairs whose observed differences are typical of those simulations. EpiLink was evaluated using both synthetic and empirical SARS-CoV-2 outbreak data from the 2020 Boston epidemic. Two EpiLink variants were compared to a logistic regression model trained on labelled transmission data. One EpiLink variant assumed deterministic mutation accumulation, with genetic differences proportional to elapsed evolutionary time; the other accounted for stochasticity by sampling mutation counts from a Poisson distribution. The logistic regression model performed better at distinguishing linked from unlinked pairs, but EpiLink achieved comparable clustering accuracy. In the Boston data, EpiLink recovered clusters enriched for documented conference and skilled nursing facility outbreaks. EpiLink thus provides an interpretable, simulation-based approach for identifying recent transmission clusters when fixed thresholds are difficult to justify and labelled transmission data are unavailable.

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04.
arXiv (CS.AI) 2026-06-12

Geometric and Quantum Kernel Methods for Predicting Skeletal Muscle Outcomes in chronic obstructive pulmonary disease

作者:
Azadeh Alavi↗Hamidreza Khalili↗Stanley H. Chan↗Fatemeh Kouchmeshki↗Muhammad Usman↗Ross Vlahos↗

arXiv:2601.00921v3 Announce Type: replace-cross Abstract: Chronic obstructive pulmonary disease (COPD) affects hundreds of millions of people worldwide, and skeletal-muscle dysfunction is clinically important. Quantum machine learning is increasingly explored for biomedical prediction, but its value in small biomarker cohorts requires benchmarking against strong classical baselines. We analysed a cigarette-smoke COPD cohort of 213 animals with blood and bronchoalveolar-lavage biomarkers to predict tibialis anterior muscle weight, muscle quality, and force. We developed a kernel-geometric quantum hybrid method in which synthetic symmetric positive definite (SPD) references are mapped through a reproducing kernel Hilbert space, compressed using train-only random projection, normalised, and supplied to low-dimensional quantum regression circuits. We benchmarked this approach against classical ridge/kernel models, SPD relational representations, and quantum-kernel regression (QKR). All methods were evaluated using condition-stratified repeated cross-validation. The largest numerical improvement was observed for muscle weight, where the proposed method had the numerically lowest mean root mean squared error (RMSE), approximately 1.8% below the best classical comparator; paired fold-level testing did not establish statistically significant superiority after Holm adjustment, but the endpoint is biologically meaningful. The method also had the numerically lowest mean RMSE for muscle quality. For force, biomarker-only Ridge performed best, suggesting a more linear endpoint structure.

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05.
arXiv (quant-ph) 2026-06-24

Logical qubits with erasure conversion using metastable neutral atoms

作者:
Bichen Zhang↗Genyue Liu↗Guillaume Bornet↗Sebastian P. Horvath↗Pai Peng↗Shuo Ma↗Shilin Huang↗Shruti Puri↗Jeff D. Thompson↗

arXiv:2506.13724v2 Announce Type: replace Abstract: Implementing large-scale quantum algorithms with practical advantage will require fault-tolerance achieved through quantum error correction, but the associated overhead is prohibitive. This overhead can be reduced by engineering physical qubits with fewer errors, and by shaping the residual errors to be more easily correctable. In this work, we demonstrate quantum error correcting codes and logical qubit circuits in a metastable ytterbium-171 nuclear spin qubit with a noise bias towards erasure errors. These errors can be located separately from any syndrome information diagnosing the error, and we demonstrate adaptive circuit execution based on erasure information. We show that dephasing errors on the qubit during coherent transport can be strongly suppressed, and implement entangling gates that maintain a high fidelity in the presence of gate beam inhomogeneity or pointing errors. Furthermore, we demonstrate logical qubit encoding in the [[4, 2, 2]] code, with error correction during decoding based on mid-circuit erasure measurements despite the fact that the code is too small to correct any Pauli errors. Finally, we demonstrate logical qubit teleportation between multiple code blocks with conditionally selected ancillas based on mid-circuit erasure checks, a key part of leakage-robust error correction schemes using neutral atoms.

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

EvoTrainer: Co-Evolving LLM Policies and Training Harnesses for Autonomous Agentic Reinforcement Learning

作者:
Guhong Chen↗Yingcheng Shi↗Yongbin Li↗Binhua Li↗Xander Xu↗Hu Wei↗Shiwen Ni↗Min Yang↗Jieping Ye↗

arXiv:2606.03108v2 Announce Type: replace Abstract: Autonomous LLM training is often framed as recipe search, which leaves the training harness largely static. This limitation sharpens in agentic RL, where shifting bottlenecks and scalar rewards mask diverse failure modes. We introduce EvoTrainer, an autonomous training framework that co-evolves LLM policies and training-side harnesses through empirical feedback: it diagnoses rollout-level evidence, revises diagnostics, backtests interventions, and accumulates reusable skills. Evaluated on mathematical reasoning, competitive-programming code generation, and repository-level software engineering, EvoTrainer matches or exceeds the human-engineered RL references under the same data, codebase, and evaluation protocol, with the largest gain on long-horizon agentic SWE. Trajectory analyses show that retained strategies diverge across domains, evolving diagnostics prevent invalid high-scoring branches from being promoted, and reusable skills shape later search. Autonomous LLM RL should move beyond recipe search toward joint evolution of policies and the training harnesses that interpret them.

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07.
arXiv (CS.LG) 2026-06-17

Conditional Local Importance by Quantile Expectations

作者:
Kelvyn K. Bladen↗Adele Cutler↗D. Richard Cutler↗Kevin R. Moon↗

arXiv:2411.08821v4 Announce Type: replace-cross Abstract: Global variable importance measures are commonly used to interpret the results of machine learning models. Local variable importance techniques assess how variables contribute to individual observations. Current, popular methods, including LIME and SHAP, provide useful measures of feature contribution in the prediction space, while leaving opportunities for improved characterization of local structure in the model loss space. Additionally, they are not natively adapted for multi-class classification problems. We propose a new model-agnostic method for calculating local variable importance, CLIQUE, that highlights locally dependent relationships, provides improved stability over permutation-based methods, and can be directly applied to multi-class classification problems. Simulated and real-world examples show that CLIQUE emphasizes locally dependent information, captures interaction behavior beyond what can be evaluated by correlations, and assigns zero importance in regions where the response is invariant to changes in variables.

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

Scaling LLM Reasoning from Minimal Labels: A Semi-Supervised Framework with a Lightweight Verifier

作者:
Keizo Kato↗Chenhui Chu↗Yugo Murawaki↗Sado Kurohashi↗

For the development of Large language models (LLMs), recent approaches to generating pseudo intermediate reasoning have shown remarkable progress. But they typically rely on large numbers of correctly annotated answers to assess reasoning quality. This paper presents a semi-supervised framework that scales reasoning learning from minimal supervision, turning reasoning verification itself into a data creation mechanism. We train a lightweight reasoning-correctness classifier on only a few labeled samples, which judges whether intermediate reasoning traces generated by an LLM are valid. Furthermore, an entropy-based confidence threshold filters out unreliable samples, and the remaining high-confidence reasoning traces are used to fine-tune the model. Experiments on Verifiable Math Problems (Orca-Math subset) and Question Answering on Image Scene Graphs (GQA) with Visual Programming show that our method achieves accuracy comparable to using 10-15x more labeled data. Ablation analyses confirm that both the classifier and entropy filtering are essential for scalable and noise-resistant pseudo-labeling. By replacing expensive answer-level supervision with lightweight reasoning verification, our method provides a practical path toward constructing large-scale reasoning resources and paves the way for future autonomous reasoning systems that learn from minimal human input.

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

Fin-RATE: A Real-world Financial Analytics and Tracking Evaluation Benchmark for LLMs on SEC Filings

作者:
Yidong Jiang↗Junrong Chen↗Eftychia Makri↗Jialin Chen↗Peiwen Li↗Ali Maatouk↗Leandros Tassiulas↗Eliot Brenner↗Bing Xiang↗Rex Ying↗

arXiv:2602.07294v4 Announce Type: replace-cross Abstract: With the increasing deployment of Large Language Models (LLMs) in the finance domain, LLMs are increasingly expected to parse complex regulatory disclosures. However, existing benchmarks often focus on isolated details, failing to reflect the complexity of professional analysis that requires synthesizing information across multiple documents, reporting periods, and corporate entities. Furthermore, these benchmarks do not disentangle whether errors arise from retrieval failures, generation inaccuracies, domain-specific reasoning mistakes, or misinterpretation of the query or context, making it difficult to precisely diagnose performance bottlenecks. To bridge these gaps, we introduce Fin-RATE, a benchmark built on U.S. Securities and Exchange Commission (SEC) filings and mirroring financial analyst workflows through three pathways: detail-oriented reasoning within individual disclosures, cross-entity comparison under shared topics, and longitudinal tracking of the same firm across reporting periods. We benchmark 17 leading LLMs, spanning open-source, closed-source, and finance-specialized models, under both ground-truth context and retrieval-augmented settings. Results show substantial performance degradation, with accuracy dropping by 18.60% and 14.35% as tasks shift from single-document reasoning to longitudinal and cross-entity analysis. This degradation is associated with increased comparison hallucinations, temporal and entity mismatches, and is further reflected in declines in reasoning quality and factual consistency–limitations that existing benchmarks have yet to formally categorize or quantify.

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10.
bioRxiv (Bioinfo) 2026-06-23

Automated Segmentation of Prostatic Gold Fiducial Markers for MR-Only Radiotherapy Planning Using Multi-Modal Consensus Deep Learning

作者:
Stewart↗A. W↗Goodwin↗Richardson↗Robinson↗S. D↗O'Brien↗Jin↗Barth↗

Purpose: To develop and evaluate a multi-model consensus deep learning approach for automated gold fiducial marker (FM) segmentation in T1-weighted prostate MRI. Materials and Methods: In this retrospective study, T1-weighted MRI and CT-derived reference standard segmentations were collected from 127 prostate cancer patients (all male; mean age, 70 years +/- 7 [standard deviation]; age range, 50-88 years; collected between October 2020 and January 2026) who each had three implanted gold FMs. A 3D U-Net was trained on 93 subjects using four random seeds to produce an ensemble. At inference, marker-class probability maps were averaged across models and the top three connected components selected. Performance was evaluated on 34 temporally held-out subjects (9 tuning, 25 test) using marker-level sensitivity and precision with exact (Clopper-Pearson) 95% confidence intervals (CIs). A model count ablation study was performed. The pipeline was deployed for on-scanner processing on Siemens MRI systems via the OpenRecon framework and as a browser-based application using WebAssembly, executing entirely client-side. Results: The four-model consensus achieved 96% (70 of 73) sensitivity and 95% (70 of 74) precision on 25 test subjects, with 29 of 34 (85%) subjects achieving perfect marker detection. Single models had a mean sensitivity of 84% (SD, 9%), improving to 96% with four-model consensus (SD,

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

Latent Geometric Chords for Query-Efficient Decision-Based Adversarial Attacks

作者:
Ei Hmue Khine↗Yao Li↗Jiebao Sun↗Shengzhu Shi↗Zhichang Guo↗Boying Wu↗

While decision-based black-box adversarial attacks present a severe security threat, current methodologies suffer from fundamental limitations. Pixel-wise attacks frequently introduce unnatural, high-frequency visual artifacts, while latent-space frameworks are confined by the limited search space of low-dimensional manifolds and inherent reconstruction flaws. To resolve these limitations, we propose Latent Geometric Chords (LGC) for Query-Efficient Decision-Based Adversarial Attacks alongside a variant, LGC-H. At its core, LGC navigates decision boundaries by executing a curvature-aware geometric search within a compressed semantic manifold. To guarantee high visual fidelity and circumvent dimensionality bottlenecks, we introduce a Residual-based Adversarial Generation (RAG) mechanism. RAG isolates semantic perturbations as geometric chords and superimposes them directly onto the original source image. RAG substantially resolves baseline reconstruction flaws and effectively doubles the permissible search space dimensions. Experimental results demonstrate that LGC achieves robust cross-dataset transferability and substantially outperforms state-of-the-art baselines. Notably, our method, LGC, minimizes perturbation magnitudes while achieving state-of-the-art visual fidelity–with a Structural Similarity Index Measure (SSIM) exceeding 0.99 and a Learned Perceptual Image Patch Similarity (LPIPS) below 0.01 at 5000 queries–and sustaining high attack success rates under stringent perceptual constraints, successfully compromising adversarially trained robust models. The source code is available at: https://github.com/eihmuekhine/Latent-Geometric-Chords.

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

Learning Red Agent Policy from Observations for Neurosymbolic Autonomous Cyber Agents

作者:
Ankita Samaddar↗Sandeep Neema↗Daniel Balasubramanian↗Xenofon Koutsoukos↗

arXiv:2606.18223v1 Announce Type: cross Abstract: With sophisticated cyber-attacks becoming increasingly prevalent, modern networks require intelligent autonomous cyber-defense agents trained via Reinforcement Learning (RL). These agents employ neurosymbolic approaches such as behavior trees with learning-enabled components (LECs) to learn, reason, adapt, and implement security rules while maintaining critical operations. However, these autonomous networks are partially observable systems, i.e., the cyber-attacker's (red agent's) actions are not observable, making it difficult for the defender to predict red actions, learn red policies, or assess the attacker's intrusion levels. To address this, we propose a Policy Learning Technique using imitation learning to learn policies for partially observable RL agents with discrete states and discrete actions. We apply this technique in an autonomous cyber environment to predict red agent's actions from network observations and defender actions. Integrated with a neurosymbolic cyber-defense agent, our method effectively handles different red policies and achieves high prediction accuracy across diverse simulated scenarios.

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

PathRouter: Aligning Rewards with Retrieval Quality in Agentic Graph Retrieval-Augmented Generation

作者:
Bo Wang↗Heyan Huang↗Yaolin Li↗Wei Tang↗Yuan Zhang↗Wenbo Li↗Mingze Gao↗Ge Shi↗Chong Feng↗

Agentic GraphRAG trains language-model agents to iteratively retrieve and reason over graph-structured evidence, enabling more accurate and context-aware decision-making by efficiently navigating complex information networks. However, outcome-only reinforcement learning suffers from answer-path reward aliasing, where correct answers may come from shortcuts rather than useful evidence paths. It also exhibits search-update ambiguity, as scalar trajectory-level feedback does not indicate which retrieval actions to adjust. To mitigate these shortcomings, we present PathRouter, a path-aware training framework for agentic GraphRAG. PathRouter jointly evaluates each trajectory along answer correctness and evidence-path overlap, yielding four trajectory categories with differentiated GRPO advantage scaling that suppresses shortcut reinforcement while preserving evidence-seeking behavior. For evidence-poor trajectories, a frozen gold-evidence teacher provides token-level KL guidance on reasoning and search-query tokens, excluding answer tokens to avoid direct response imitation. Experiments on six QA benchmarks across three model sizes show that PathRouter consistently improves answer F1 and evidence-path overlap, achieving average F1 gains of 3.1 on 3B and 4.9 on 7B models compared to a strong baseline.

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14.
arXiv (CS.CL) 2026-06-15

Dialogue SWE-Bench: A Benchmark for Dialogue-Driven Coding Agents

作者:
Brendan King↗Jeffrey Flanigan↗

AI coding agents have rapidly transformed software engineering, powering widely used interactive coding assistants. Despite their interactive real-world use, existing benchmarks evaluate them as fully-autonomous systems. In this work, we introduce Dialogue SWE-Bench, an automatic benchmark dataset for evaluating the ability of coding agents to resolve real-world software engineering problems through dialogue with a user. We design a novel, persona-grounded user simulator to support our task evaluation, and augment our task evaluation with automatic evaluations of dialogue quality. We also propose a new schema-guided agent, aimed at improving the dialogue capabilities of off-the-shelf coding agents, which improves over strong baselines by 3-14%. Our results indicate that better coding models do not always correspond to better dialogue models, suggesting that dialogue capability is a distinct and currently understudied dimension of coding agent performance.

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

SAGE: Stochastic Prompt Optimization via Agent-Guided Exploration

作者:
Ziyi Zhu↗Luka Smyth↗Saki Shinoda↗Jinghong Chen↗

Context engineering has emerged as a primary lever for improving AI systems without parameter updates. Recent work showing that textual gradients do not function as real gradients motivates treating automatic prompt optimization (APO) as black-box search. We introduce SPO (Stochastic Prompt Optimization), a framework for stochastic search over prompt space, and compare three strategies of increasing sophistication: error-informed random search, a genetic algorithm with evolutionary operators, and SAGE (SPO via Agent-Guided Exploration), a multi-agent pipeline with diagnostic code execution. Across three benchmarks, no single strategy dominates; effectiveness depends on the interaction of landscape structure with error type. We further deploy SAGE on a mental-health chatbot under a continuous optimization paradigm, where it compounds eight cycles of individually-noisy A/B tests into a statistically robust gain in next-day retention. We argue that coupling qualitative diagnosis with quantitative validation is what makes agentic optimization effective for open-ended task-oriented dialogue.

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

Not all Jensen-Shannon Divergence Estimators are Equal

作者:
Alba Garrido↗Alejandro Almod\'ovar↗Mar Elizo↗Patricia A. Apell\'aniz↗Santiago Zazo↗Juan Parras↗

arXiv:2606.16411v1 Announce Type: new Abstract: The Jensen-Shannon divergence is widely reported as a scalar measure of fidelity for synthetic tabular data. Yet, in practice, it is estimated from finite samples using protocols that are often underspecified. This creates a measurement problem. Although the population divergence is well defined, the empirical value depends on the estimator family, sampling protocol, calibration, dimensionality, and class balance. We show that different protocols can yield non-comparable values: marginal-based estimators ignore dependencies in the joint distribution and can severely underestimate divergence, while classifier-based estimators capture joint structure but exhibit strong estimator dependence. We systematically study this behavior across controlled settings with reference divergences and real-world synthetic tabular benchmarks. Our analysis reveals dependence blindness in marginal estimators, prior-shift bias under class imbalance, and estimator sensitivity in high dimensions. To address prior shift, we derive a closed-form posterior correction for classifier-based Jensen-Shannon estimation. Our results show that empirical Jensen-Shannon divergence values are inherently protocol-dependent, making explicit specification of the estimation procedure necessary for meaningful comparison. We provide practical guidelines and an open-source tool for estimator-aware Jensen-Shannon evaluation.

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17.
arXiv (CS.LG) 2026-06-15

DTVEM-RE: A Hierarchical Random-Effects Extension of the Differential Time-Varying Effect Model for Person-Specific Multi-Lag Estimation in Intensive Longitudinal Data

作者:
Amartya Bhattacharya↗

arXiv:2606.14116v1 Announce Type: new Abstract: The Differential Time-Varying Effect Model (DTVEM) of Jacobson et al. (2019) is a popular tool for finding the best time lag in intensive longitudinal data, but it assumes everyone shares the same lag structure. The original authors named fixing this as future work, and it clashes with the premise of modern clinical research, which is that people differ. We present DTVEM-RE, an extension that lets each person have their own lag coefficients, with two versions of the confirmatory step: a discrete-time hierarchical Bayesian VAR in Stan, which pools across people and gives calibrated uncertainty, and a continuous-time per-person Ornstein-Uhlenbeck model in ctsem, which handles unevenly spaced beeps directly. We report four results. A simulation shows the Bayesian version recovers the between-person spread tau_a with bias below 0.01 and coverage of 90 to 93 percent. On the Fisher et al. (2017) EMA dataset (N=40), person-specific lag-1 effects vary by an order of magnitude across three mood items, the Bayesian and GAMM estimates agree closely (r=0.87 to 0.92), and DTVEM-RE gives the best one-step-ahead prediction among four discrete-time methods. A multi-lag version shows all nine tau_k values have credible intervals excluding zero, and the lag where people differ most changes across items, something lag-1-only methods like mlVAR cannot detect. Finally, the two versions agree almost exactly on person-specific lag-1 estimates (r >= 0.995), differing only as shrinkage predicts. DTVEM-RE is, to our knowledge, the first person-specific implementation of DTVEM-style lag detection, and it contains standard DTVEM as a special case.

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

On the QUEST for Uncertainty Quantification via Highest Density Regions

作者:
Sam Goring↗Tom Kuipers↗Nicola Paoletti↗David S. Watson↗

arXiv:2606.19569v1 Announce Type: new Abstract: Uncertainty quantification (UQ) is essential for reliable decision-making in safety-critical applications in probabilistic machine learning. For regression problems, dominant scalar UQ approaches - notably, those based on proper scoring rules - measure uncertainty via pointwise predictive risk. This can lead to counterintuitive results when the target statistic is not the conditional expectation. We propose an alternative framework, in which uncertainty is characterised by the volume of the most probable subset of a distribution's support. QUEST (Quantifying Uncertainty via highest dEnSiTy regions) is a novel approach to UQ based on the concentration of Lebesgue measure at a distribution's peak(s), evaluated at one or more values of a robustness parameter $\alpha$. We establish connections between our measures and classical statistics from information theory and economics. We show that, unlike popular alternatives based on proper scoring rules, QUEST measures of epistemic and aleatoric uncertainty satisfy a set of axioms adapted from the UQ literature, including monotonicity under distributional spread and invariance to location shifts. Selective prediction benchmarks confirm that QUEST performs favourably against standard measures such as variance and differential entropy.

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

Learning Hybrid Biophysical Neuron Models with Neural ODEs

作者:
Jonas Beck↗Michael Deistler↗D\'ora Vikt\'oria Moln\'ar↗Jakob H. Macke↗Philipp Berens↗

arXiv:2606.16693v1 Announce Type: cross Abstract: Biophysical neuron models link measurements of neural activity to underlying cellular mechanisms. Yet, a central challenge is that the kinetics of many ion channels are poorly characterized, and practical simplifications – omitting channels or reducing morphological detail – introduce systematic gaps between model and biology. Bridging these gaps requires approaches that can flexibly discover unmodeled dynamics while preserving mechanistic interpretability. Here, we introduce a hybrid modeling framework that embeds neural ordinary differential equations into conductance-based biophysical models to capture unknown currents or mis-specified channel kinetics. By parameterizing the neural ODE in terms of voltage-dependent steady-state and time-constant functions, we recover interpretable gating dynamics directly from voltage recordings without assuming a functional form. We show that the hybrid model fits the gating kinetics of 2400 ion channel models and recovers unknown gating dynamics from single current-clamp recordings, generalizing to out-of-distribution stimulus regimes under realistic inputs and parameter misspecification. We also use our method to reduce a multicompartment model of a cortical neuron into a single-compartment hybrid model with a learned axial current, yielding up to an order of magnitude lower computational cost. Together, our results establish a plug-and-play framework for selectively replacing unknown components of conductance-based models with neural ODEs while preserving their mechanistic structure.

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20.
arXiv (CS.CL) 2026-06-24

Dialogue to Discovery: Attribute-Aware Preference Elicitation for Conversational Product Search Assistants

作者:
Sarthak Harne↗Natwar Modani↗Debabrata Mahapatra↗Shubham Agarwal↗

Conversational product search assistants offer a more expressive, natural, and interactive alternative to traditional keyword-based product search. With limited screen space, showing only a few items increases the need for precise preference elicitation, which can prolong conversations, leading to user frustration and session abandonment. Conversely, rushing to recommend items without a clear understanding of preferences risks poor matches and a degraded user experience. We present Dialogue to Discovery (D2D), an attribute-oriented preference elicitation framework that dynamically exploits the structure of product attributes to efficiently steer conversations toward the user's desired item. D2D adaptively prioritizes the most informative queries and strategically times product recommendations, reducing premature or off-target suggestions that harm engagement. To evaluate D2D, we curate three datasets from the Amazon Reviews corpus. In simulated conversations modelled using a multi-factor utilitarian patience framework, D2D achieves a 22.2-29.9% improvement in target-finding accuracy, 6.6-16.1% reduction in abandonment, and 27.5% shorter average conversations over the state-of-the-art baselines. A complementary user study further confirms significant gains in both user satisfaction and perceived efficiency.

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21.
medRxiv (Medicine) 2026-06-23

Blood-brain barrier dysfunction in cerebral amyloid angiopathy is associated with disseminated cortical superficial siderosis

作者:
Bay↗Pfister↗Mattern↗Bernal↗Neumann↗Doerner↗Meuth↗S. G↗Schreiber↗Arndt↗

Background: Blood-brain barrier (BBB) dysfunction is increasingly recognized as a feature of cerebral amyloid angiopathy (CAA) and has been linked to hemorrhagic imaging manifestations such as cortical superficial siderosis. However, it remains unclear whether neurovascular barrier dysfunction can be captured by routinely available fluid biomarkers and whether such markers identify clinically relevant hemorrhage-prone CAA phenotypes. The CSF/serum albumin quotient (QAlb) is an established marker of neurovascular barrier dysfunction. We investigated QAlb levels in CAA and their association with imaging markers of disease severity. Methods: We included 225 participants (115 with CAA, 72 with Alzheimers disease [AD], 38 healthy controls) with CSF biomarkers and standardized MRI evaluation. Pathologic QAlb levels were identified via the age-corrected Reiber-formula. Group differences and determinants of pathological QAlb were assessed using uni- and multivariable regression analyses. The diagnostic relevance was assessed by receiver operating characteristic analysis. Results: QAlb levels were higher in CAA than in controls (ratio of means [RoM] 1.43, 95% CI 1.28-1.58) and patients with AD (RoM 1.22, 95% CI 1.10-1.35; both p

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22.
arXiv (quant-ph) 2026-06-11

Split-Evolution Quantum Phase Estimation for Particle-Conserving Hamiltonians

作者:
Megan Cerys Rowe↗Carlo A. Gaggioli↗Ludmila Szulakowska↗David Mu\~noz Ramo↗David Zsolt Manrique↗

arXiv:2604.14921v2 Announce Type: replace Abstract: We present a hardware demonstration and resource analysis of split-evolution quantum phase estimation (SE-QPE) on a Quantinuum System Model H2 quantum computer. SE-QPE is a modification to canonical QPE for particle-conserving Hamiltonians in which controlled time evolution is replaced by CSWAP-based interference between a target register and a reference register. For factorizations of time evolution with a shared eigenbasis, SE-QPE preserves the phase-register outcome distribution of canonical QPE and, unlike with compute–uncompute substitutions, it remains compatible with non-exact eigenstates. The substitution removes controlled-simulation overhead and enables parallel evolution on two registers, reducing the depth of each phase-kickback block. Resource analysis for Trotterized double-factorized chemistry Hamiltonians shows that the substitution becomes increasingly favorable at higher phase powers and combining QPE and SE-QPE implementations can be a useful option. Over a range of FeMoco active spaces, SE-QPE reduces time evolution resources, with asymptotic reductions of about 33% in CX count, 25% in $T$ count, and an asymptotic depth ratio of $3/N$ for CX layers. On Quantinuum H2-2, a four-qubit model ethylene demonstration with explicit inverse QFT and repeated phase-kickback steps up to 8 phase bits yields distinct energies and shows the auxiliary registers provide useful error detection filters.

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23.
bioRxiv (Bioinfo) 2026-06-20

The recount3 Python package for programmatic access to uniformly processed RNA-seq data

作者:
Alsalihi↗Flight↗R. M↗Moseley↗H. N. B↗

The recount3 online resource provides tens of thousands of uniformly processed RNA-seq samples across human and mouse from major sequencing repositories like the Sequence Read Archive. While access to these datasets has traditionally been centered in the R/Bioconductor ecosystem, the growing prominence of Python in bioinformatics and machine learning necessitates native, efficient tooling for Python users. Therefore, we present the recount3 Python package with robust application programming interface (API) and command-line interface (CLI) for discovering, downloading, and materializing recount3 resources. The software orchestrates uniform resource locator (URL) resolution, persistent on-disk caching, and the automatic parsing of data into analysis-ready data structures, including Pandas DataFrames and BiocPy RangedSummarizedExperiment objects. The recount3 Python package drastically lowers the barrier to entry for large-scale utilization of RNA-seq data in Python-based computational pipelines, bridging the gap between massive public transcriptomic data and modern machine learning ecosystems.

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24.
bioRxiv (Bioinfo) 2026-06-15

DAQplugin: Deep Learning based Real-time Model Evaluation Plugin for ChimeraX

作者:
Terashi↗Zhu↗Kihara↗

Although an increasing number of protein structures are determined by cryogenic electron microscopy (cryo-EM), protein structure modeling frequently suffers from residue misassignments and sequence register shifts, particularly in regions with ambiguous density. Here, we present DAQplugin, a ChimeraX plugin that performs real-time evaluation of protein models against cryo-EM density maps using the deep-learning-based residue-wise model quality (DAQ) score. Unlike existing validation tools that are typically applied after model construction, DAQplugin enables real-time deep-learning-based validation during model building and refinement. To our knowledge, DAQplugin is the first tool that provides real-time deep-learning based validation of protein models for cryo-EM map within an interactive modeling environment. In addition to identifying potential modeling errors, DAQplugin also provides guidance for correcting sequence register shifts by suggesting alternative residue placements along the backbone. The computation in this plugin is designed to run efficiently on general CPUs without requiring GPU hardware. Using DAQplugin, users can perform deep-learning-based validation on standard laptops during interactive model building, model-map fitting, and refinement. DAQplugin is able to facilitate more accurate interpretation of cryo-EM density maps and improve the reliability assessment of protein structure models.

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25.
arXiv (CS.AI) 2026-06-24

THEIA: Learning Complete Kleene Three-Valued Logic in a Pure-Neural Modular Architecture

作者:
Augustus Haoyang Li↗

arXiv:2604.11284v5 Announce Type: replace-cross Abstract: We present THEIA, a 2.75M-parameter modular neural architecture that learns the complete Kleene three-valued logic (K3) truth table from task data without external symbolic inference or hand-encoded K3 gate primitives. Across 5 seeds it passes all 39 K3 rules at >99% per-rule accuracy. K3 learnability is not the central finding: Transformer baselines also pass all 39 rules, and flat MLPs match THEIA on Phase-1 accuracy within 0.04pp. The contributions are two properties of the learned system. (1) Uncertainty-verdict asymmetric propagation. THEIA preserves Has-Unknown at every upstream boundary (80.0/91.1/90.8/99.7% across Arith/Order/Set/Logic vs. ~52% majority) while final-verdict decodability stays at or below a 73.4% U-vs-non-U oracle reference under linear and nonlinear probes. Activation patching on non-absorbent T->U cases flips 4,898/4,898 OR and 4,719/4,719 AND pairs across 5 seeds, ruling out residual shortcuts. (2) Reliability spectrum under discretized end-to-end training, on tasks decomposable along the engine boundaries. A mod-3 sequential composition task generalizes from 5- to 500-step evaluation at 99.96+-0.04% (5 seeds). Under identical Gumbel-softmax training, flat MLPs collapse to chance by 50 steps; a 2x2 ResMLP grid reaches >=99% on only 3/20 (config, seed) trials; a pre-LN Transformer reaches 99.24+-0.34%. Straight-through discretization prevents 0.999^500 compounding; the architectural separator is sustaining Phase-1 accuracy under Phase-3 training, where flat MLPs fail. Auxiliary: under per-architecture development defaults (not optimizer-controlled), THEIA reaches 12/12 Kleene coverage 6.5x faster than a parameter-comparable 8L Transformer; this narrows to ~3.6x with Transformer-standard tuning and 4.93x with the same recipe on both. Ratios are config-specific, not asymptotic.

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