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01.
arXiv (CS.CL) 2026-06-11

Measuring Semantic Progress in Multi-turn Dialogue via Information Gain

Evaluating multi-turn dialogue is challenging because quality emerges across turns rather than within individual responses. We focus on a key dimension of information-seeking dialogue: semantic progress, defined as the accumulation of new, question-relevant, and non-redundant information over the course of a conversation. We formalize semantic progress as question-conditioned uncertainty reduction and introduce an information-theoretic metric that approximates it in embedding space. Our main estimator uses a tractable Gaussian formulation with closed-form updates, while a complementary maximum-entropy argument shows why log-determinant structure arises more broadly when only second-order embedding information is retained. This formulation yields desirable theoretical properties, including monotonicity, additive decomposition of total information gain across turns, and diminishing returns for redundant evidence. Unlike LLM-as-a-judge approaches, our metric requires no autoregressive inference at evaluation time and is fully reproducible for a fixed embedding model. Experiments on MT-Bench, Chatbot Arena, and UltraFeedback show that the proposed metric achieves competitive agreement with human judgments despite targeting only semantic progress, with improved alignment on MT-Bench and UltraFeedback compared to several LLM-based judges. Notably, the method remains effective with lightweight embedding models under CPU-only execution, indicating that semantic progress can be captured without reliance on large model capacity.

02.
arXiv (CS.CL) 2026-06-24

Prague Dependency Treebank – Consolidated 2.0: Enriching a Complex Annotation Scheme

The Prague Dependency Treebank framework is unique in its attempt to systematically include and link different layers of language, including a meaning representation with several types of inter-sentential phenomena, especially coreference and discourse relations. We present its second consolidated version (PDT-C 2.0), which concludes almost 30-years long project of sustained development of the resource to a uniformly and coherently annotated, genre-diversified, almost 4 million token language resource of Czech language, with accompanying fully compatible lexicons. In addition to continuous linguistic research, the richly linguistically annotated corpus is also widely used in international comparisons of the development of traditional and novel NLP tools as well as in conversions into other formalisms. The corpus and the trained parsers are available under the CC BY-NC-SA licence.

03.
arXiv (CS.AI) 2026-06-19

Interpretable and Verifiable Hardware Generation with LLM-Driven Stepwise Refinement

arXiv:2606.19387v1 Announce Type: cross Abstract: Large language models (LLMs) have achieved remarkable success in software development. However, they are susceptible to hallucinations, meaning that they can introduce subtle semantic and logical errors. Due to the high stakes in chip design and manufacturing, hardware engineers are still reluctant to rely on LLMs for register-transfer level (RTL) generation. In this paper, we propose a hardware generation framework that combines the creativity and broad knowledge of LLMs with the explainability and mathematical rigor of formal methods. Specifically, we devise a set of transformation rules that cover various design decisions and hardware features. By iteratively applying these rules, an LLM agent can convert a design specification into an RTL program with guaranteed correctness. Experimental results demonstrate the effectiveness and efficiency of the framework.

04.
arXiv (quant-ph) 2026-06-16

Adiabatically-induced Kawaguchi geometry and jerk in quantum-classical systems

arXiv:2606.16037v1 Announce Type: new Abstract: Adiabatically eliminating the quantum degrees of freedom in a mixed quantum-classical system produces an effective force in the classical equation of motion. The elimination can be made to any order in the adiabatic parameter, generating a series of higher order forces. By applying a sequence of near-identity unitary transformations to the quantum state, we derive a hierarchy of increasingly accurate effective actions for the classical variables. The third order Euler-Lagrange equation is non-Newtonian as the force depends on the jerk, the third order time derivative of position. We find that the third order terms induce a special kind of Kawaguchi geometry on the space of classical variables. This geometry is characterized by an almost symplectic structure and a differential line element that depends on the acceleration in addition to the velocity. Our results can be used to efficiently capture higher order nonadiabatic effects in molecular dynamics simulations.

05.
medRxiv (Medicine) 2026-06-18

Personalizing Suicide Risk Assessment: Machine Learning Extraction of Cross-Modal Interactions Between Psychosocial and Demographic Factors in Veterans

Background: Veterans face an elevated risk of suicide compared to the general population, motivating national efforts to develop predictive models that can guide proactive care. Current models used by the U.S. Department of Veterans Affairs (VA) rely primarily on structured electronic health record (EHR) data, though clinical notes contain rich contextual information that can be quantified using natural language processing (NLP) to derive psychosocial variables that may improve risk detection. Machine learning methods, particularly classification and regression trees (CART), can also uncover interactions between clinical and psychosocial variables, enabling identification of patient characteristics that modify suicide risk factors. However, integrating structured and unstructured data presents challenges because NLP features often greatly outnumber traditional clinical variables, potentially biasing interaction discovery. In prior work, we addressed this imbalance by introducing a weighted CART framework that balances structured variables with NLP-derived psychosocial features from semantic lexicons (SEANCE). While effective, semantic approaches summarize language into predefined constructs and may overlook important lexical variation present in clinical narratives. Methods: In this study, we extend that framework by replacing semantic features with a high-dimensional bag-of-words (BoW) representation of clinical notes and by evaluating models across cohorts defined by structured suicide risk stratification (low, medium, high) and varying temporal lookback windows. Using a cohort of 27,241 veterans, we analyzed clinical documentation collected up to 30, 90, or 270 days prior to death (or a matched index date for controls), enabling temporally flexible risk modeling. XGBoost models were trained to balance structured and unstructured features and identify cross-modal interactions between textual and clinical variables. Results: When incorporated into generalized linear models, these interactions improved predictive performance, particularly among low- and medium-risk patients, and substantially reduced the performance gap between interpretable and more complex models. Notably, the BoW representation outperformed our prior semantic index-based approach. Discussion and Conclusions: Together, these findings demonstrate the utility of interpretable NLP methods for uncovering clinically meaningful interactions between psychosocial and demographic factors in suicide risk and establish a strong benchmark for future deep learning approaches aimed at capturing richer contextual and temporal information from clinical narratives.

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

Viral Proteins Reveal Geometry of Protein Language Models

arXiv:2606.12609v1 Announce Type: new Abstract: Protein language models are trained on highly imbalanced datasets, raising the question of how they represent underrepresented biological sequences. Using viral proteins as a case study across ESM model families, we identify a dominant nativeness axis in embedding space, aligned with masked reconstruction perplexity, that orders sequences from well-modeled cellular proteins through viral proteins to shuffled and random sequences. Scaling contracts this axis unevenly across viral families. Despite this, protein language model embeddings retain viral-specific signal: viral proteins remain linearly separable beyond zero-shot perplexity and shallow sequence features. Together, these results suggest that pLM representations are structured by a general notion of nativeness while preserving information specific to distinct biological groups.

07.
arXiv (math.PR) 2026-06-12

Fourier Dimensions of Mandelbrot Cascades under Minimal Integrability

Authors:

arXiv:2606.08703v2 Announce Type: replace Abstract: This note announces exact Fourier dimension formulas for canonical Mandelbrot cascade measures under the minimal Kahane Peyriere integrability condition and records the canonical b adic extension on cubes. In the dyadic interval setting, the theorem is proved in a balanced vector weight model allowing dependence between sibling weights. Almost surely on non extinction, the Fourier, energy, and L2 dimensions all equal the energy exponent. The scalar specialization gives the canonical Mandelbrot Kahane Fourier dimension formula under the minimal integrability condition. On the circle, the endpoint formula is given by the endpoint lower local dimension exponent. For the b adic Mandelbrot cascade on cubes, the Fourier dimension is the minimum of 2 and the energy exponent, with the universal Fourier barrier at dimension two providing the high dimensional obstruction.

08.
arXiv (math.PR) 2026-06-19

The t-Split Two-Periodic Aztec Diamond Model

Authors:

arXiv:2606.19507v1 Announce Type: new Abstract: In this work we consider an Aztec diamond model split into two unequal regions which are asymptotically fixed in size. Each region is weighted with a distinct two-periodic weighting. We refer to this model as the t-split two-periodic Aztec diamond, to signify its difference from the previous work title Split Two-Periodic Aztec Diamond, where the model was split into two equal regions. We derive an integral expression for the correlation kernel of the model and give a partial description of the scaling limit behavior, along with a conjecture for the remainder. We refer to the larger and smaller sides of the model as the dominant and non-dominant sides, and to the location of the weight change as the interface. The dominant side exhibits a limit shape that depends only on its own weighting and is identical to that of the two-periodic Aztec diamond, while the non-dominant side appears to have a novel limit shape that depends on both weightings and the location of the interface. Lastly, we consider the complete limit shape in the case where the dominant side two-periodic parameter goes to 0.

09.
arXiv (CS.LG) 2026-06-15

XRDiff: Crystal Structure Prediction from Powder X-Ray Diffraction Data Using Diffusion Models

arXiv:2606.14003v1 Announce Type: cross Abstract: Determining the crystal structure of a material from its powder X-ray diffraction (PXRD) pattern is a central challenge in materials science. PXRD is an accessible and widely used characterization technique, yet recovering the atomic structure from diffraction data requires solving an underdetermined inverse problem due to the loss of phase information. Generative modeling can provide a prior over atomic structure and learn the mapping from PXRD patterns to crystal structures via simulated structure-spectrum pairs. We present XRDiff, a diffusion model that recovers crystal structures from PXRD given either the stoichiometry or, in a more challenging setting, the elemental constituents and total number of atoms in the unit cell. We evaluate on datasets where each stoichiometry has multiple polymorphs and all polymorphs of a given composition are held out together, ensuring that high performance reflects genuine use of the diffraction signal. XRDiff achieves strong structure recovery rates on simulated benchmarks, indicating that the model learns a spectrum-to-structure mapping precise enough to differentiate between polymorphs. To address generalization to experimental data, we compare a full-spectrum encoding against an encoding based on peak descriptors. The peak-based encoding generalizes substantially better, outperforming even a model trained on full spectra with augmentations fitted to the experimental noise distribution. These results demonstrate that representations robust to the noise and artifacts present in real-world PXRD offer a practical and scalable path toward closing the simulation-to-experiment gap, enabling zero-shot crystal structure solution from experimental PXRD with full or partial chemical composition input.

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

Multi-Class Brain Tumor Classification Using Advanced Deep Learning Models: A Comparative Study

Despite recent advancements in deep learning, accurately classifying brain tumors from MRI images continues to pose challenges. In this research, we present a comprehensive evaluation of five different convolutional neural networks (CNN) architectures, including a customized baseline model and four pre-trained models - for use in classifying multi-class brain tumors using a clinically-sourced dataset of approximately 10,000 MRI images. We have utilized five different architectures; VGG16, VGG19, DenseNet121, and EfficientNetB0, which were all tested and trained within an identical experimental framework. Performance was measured by both overall accuracy and tumor-wise recall as a means to measure the clinically-relevant performance of each architecture. We found that EfficientNetB0 had the best overall classification accuracy at 95%, when compared to the other architectures tested; specifically VGG16 (94.37%), VGG19 (92.29%), DenseNet121 (90.91%) and the customized CNN (78.00%). An especially important finding of our research was the considerable improvement in detecting meningiomas; specifically, while simple CNNs could detect meningiomas with a recall rate of approximately 20%, EfficientNetB0 was able to detect meningiomas with a recall rate of 89%. Meningiomas are often difficult to detect because they can appear very subtly on MRI images. Additionally, an interesting finding was that the deeper VGG19 performed worse than the shallower VGG16. This indicates that in many cases the architectural efficiency of a CNN model may be more important than its depth when working with medical images. Overall, EfficientNetB0 appears to provide the optimal trade-off between classification accuracy, number of parameters used in the model and clinically meaningful performance.

11.
arXiv (math.PR) 2026-06-12

Symmetric Cooperative Motion in Higher Dimensions

arXiv:2606.13459v1 Announce Type: new Abstract: We prove a distributional convergence result for a multidimensional version of symmetric cooperative motion which was introduced and studied in one dimension in [HRW, SCM1]. Our approach relies on framing the associated recursive distributional equation as a discretization of the porous medium equation. A major challenge is to analyze the behaviour of finite difference schemes which approximate weak solutions of the porous medium equation with unbounded initial data. In overcoming this difficulty, we perform a detailed analysis of the probability mass function of symmetric cooperative motion, in which we introduce several new comparison arguments for the discrete process. Consequently, along the way, we establish a novel multidimensional convergence result for a finite difference scheme approximating the ZKB/Barenblatt solution of the porous medium equation, which is of independent interest.

12.
bioRxiv (Bioinfo) 2026-06-21

ReSeT: a taxonomy-aware reference genome selection tool

Motivation: Reference genome composition determines which taxa a profiling pipeline can detect and distinguish, and becomes of critical importance for high-resolution profiling where taxonomic boundaries begin to blur. Existing selection tools optimize within-taxon representativeness but disregard discrimination across taxa, leaving open whether explicitly accounting for inter-taxon discrimination during selection improves profiling. Results: Here we present ReSeT, a facility-location-based reference genome selection tool that operates on arbitrary pairwise distance matrices, extended with a tunable inter-taxon discrimination term and per-genome selection cost, and solved by local search. We benchmark ReSeT against established selection methods on three viral datasets spanning varying degrees of taxonomic ambiguity. On the high-ambiguity SARS-CoV-2 datasets, appropriately tuned ReSeT selections matched or exceeded the strongest alternatives in terms of profiling accuracy, whereas on the low ambiguity IAV dataset VSEARCH remained dominant. Interestingly, we find that the novel inter-taxon discrimination term contributed weakly, indicating that ReSeT's facility-location formulation and selection cost drives ReSeT's performance. We further propose a novel taxonomic ambiguity index, computable from ReSeT's inputs, that summarizes the taxonomic ambiguity of reference genomes and aligns with where ReSeT improves over existing selection methods. Availability and implementation: ReSeT is implemented in Python ([≥]3.10) and is freely available under the MIT license. The source code is available on GitHub at https://github.com/JaspervB-tud/ReSeT and ReSeT can also be installed directly from the Python Package Index (PyPI) via pip install reset-bio.

13.
arXiv (CS.AI) 2026-06-12

Transformer Field Theory: A Response-Theoretic Approach to Mechanistic Interpretability

arXiv:2605.25225v2 Announce Type: replace-cross Abstract: Mechanistic interpretability often studies Transformer behavior by intervening on internal activations through activation patching, causal tracing, path patching, and steering directions. This paper develops Transformer Field Theory: a response-theoretic framework in which the residual stream of a fixed forward pass is treated as a Transformer field over layer depth and token position. In this formulation, patching becomes a localized source insertion into the Transformer field, first-order sensitivity fields predict patch effects, Green functions describe downstream propagation, and patch selection is posed as an adjoint inverse problem. Empirically, we test the theory's forward response objects in GPT-2-style autoregressive Transformers. Localized Transformer-field interventions exhibit a bounded local linear regime; first-order sensitivities predict patch effects across layer-token sites; localized sources generate structured anisotropic Transformer-field propagation; high-sensitivity sites and sliced Green operators provide reduced response descriptions; and prompt-induced Transformer-field displacements partially transfer answer behavior. These results establish sensitivities, Transformer-field responses, and sliced Green operators as practical objects for organizing patching experiments, while providing the forward mathematical basis for patch-site inference and cross-scale response transfer.

14.
medRxiv (Medicine) 2026-06-10

Impact of Early Treatment on Symptom Improvement and Procedural Events among Men with BPH and Bothersome Lower Urinary Tract Symptoms: A Contemporary Analysis of the American Urological Association Quality (AQUA) Registry

PURPOSE: As the armamentarium of BPH therapies continues to expand, it remains imperative to maximize patient satisfaction and minimize decisional regret. We sought to determine the impact of time from BPH diagnosis to index treatment on symptom improvement and subsequent procedural events. MATERIALS AND METHODS: We queried the American Urological Association Quality Registry for men [&ge;] 40 years old with BPH, available IPSS data, and no receipt of prior BPH treatment. Index treatment included medication, surgery, or minimally invasive surgical therapy (MIST). Outcomes included IPSS over 3 years of follow-up, change in percentage of mild lower urinary tract symptoms (LUTS) by 3 months, and time to procedural event. Patients were stratified by time from index diagnosis to treatment by 3 years. Outcomes were compared across time-to-treatment cohorts with appropriate statistical tests with p < 0.05 as significant. RESULTS: 43,919 patients met criteria with 19,642 pursuing treatments. Patients pursued treatment at comparably lower baseline IPSS compared to prior prospective series. Patients undergoing surgery and MIST had significantly higher baseline IPSS, while medical comorbidities were significantly more common among men initiating pharmacotherapy. Early surgery and MIST were associated with significant improvement in IPSS within 6-12 months and an increase in mild LUTS by 3 months. All forms of early treatment were associated with delayed time to procedural events, including catheterization and fulguration. CONCLUSIONS: Early procedural intervention for BPH is associated with early symptom improvement and delayed time to procedural events among real-world, contemporary practice.

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

ZIVARI-TLBO: A Zero-Cost Inter-Group Evaluated-Elite Relay Mechanism for Teaching-Learning-Based Optimization

arXiv:2606.17087v1 Announce Type: cross Abstract: ZIVARI-TLBO is a grouped Teaching-Learning-Based Optimization (TLBO) method that augments an existing population-state controller with a fixed inter-group evaluated-elite relay. At each scheduled event, every group offers its already evaluated elite to the next group in a fixed ring; the elite replaces the receiver's worst eligible learner only when its stored objective value is better. Because the exact relay copies an already evaluated solution and its stored fitness, it requires no additional objective-function calls. The frozen gts-v4-cm-fixed implementation is evaluated under equal 10,000-evaluation budgets on eight classical functions at dimensions 10, 30, 50, and 100, with 30 matched seeds, and on five constrained engineering problems. A direct ablation against the same grouped landscape-aware controller without relay records 728/11/221 wins/ties/losses and a rank-biserial effect size of 0.624 across dimensions. In an eight-method multidimensional comparison, WOA obtains the best average rank (2.914) and ZIVARI-TLBO ranks second (3.382); ZIVARI-TLBO significantly outperforms TLBO, MCTLBO, DE, PSO, and GWO, loses significantly to WOA, and is not significantly different from HHO after Holm adjustment. Feasibility-aware engineering results are mixed and sensitive to the current static-penalty formulation. The evidence supports a scoped relay contribution and budget-consistent information-sharing mechanism, but not universal state-of-the-art, global-convergence, engineering-dominance, or CEC superiority claims.

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

Physics-IQ Verified

Video generative models ( VGMs) have become a new frontier that can be used not just for video generation but for a multitude of downstream tasks, including world modeling. To advance these tasks, a good video model must understand the physical reality of the world. Evaluating this understanding is an emerging field and has led to the Physics-IQ benchmark, which quantifies this explicitly by comparing model-generated videos to real-world videos of physical experiments. In this work, we present a systematic audit of the Physics-IQ benchmark, expose shortcomings and propose three solutions that sharpen how we can measure physical understanding of VGMs. Specifically, we improve prompt and ground-truth quality to reduce the influence of confounding factors and further introduce a sample-level scoring system that weights each sample and metric equally. Our resulting benchmark, Physics-IQ Verified, refines 57.6\% of all samples and improves over 34.8\% of prompts. In a comparison study using six image-to-video generative models, we observe moderate but meaningful ranking changes (Kendall's $\tau = 0.46$). We hope Physics-IQ Verified advances the community by providing a more reliable signal toward physically accurate VGMs. The code for the benchmark can be accessed at https://github.com/google-deepmind/physics-iq-benchmark

17.
arXiv (CS.AI) 2026-06-19

Which Pairs to Compare for LLM Post-Training?

arXiv:2606.19607v1 Announce Type: new Abstract: Preference-based post-training has become a central paradigm for aligning language models. A common data-collection strategy is to generate a small set of completions for each prompt and label the resulting comparison pairs. However, human preference labels are often much more expensive than generating additional completions, suggesting a different use of the same labeling budget: generate a larger pool of completions, but label only the most informative comparison pairs. This paper studies which pairs should be compared in preference-based post-training. We formulate comparison curation as a sampling-design problem and evaluate designs by the quality of the final policy under the preference-based post-training objective. We instantiate this framework for Direct Preference Optimization (DPO), analyzing how the choice of labeled pairs propagates through DPO training to downstream policy performance. Our main results provide matching upper and lower bounds on the post-training optimality gap of the DPO-trained policy. The bounds show that comparison selection affects downstream performance through a single design-dependent information matrix, which links label allocation to parameter estimation error and policy suboptimality. This yields an explicit optimization criterion for budgeted comparison curation and motivates practical sampling designs for selecting informative pairs from large generated completion pools. Experiments on synthetic settings and language-model post-training benchmarks show that the proposed designs consistently improve sample efficiency over common comparison-selection heuristics.

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

DeFAb: A Verifiable Benchmark for Defeasible Abduction in Foundation Models

arXiv:2606.18557v1 Announce Type: new Abstract: A rule-based logic solver resolves every instance in our benchmark in under 50 microseconds with 100% accuracy; the best frontier language model reaches 65% at best and drops to 23.5% under rendering-robust evaluation (worst case over four surface renderings). We introduce DeFAb (Defeasible Abduction Benchmark), a dataset and generation pipeline that converts four decades of publicly funded knowledge bases into formally grounded instances for defeasible abduction: constructing hypotheses that explain anomalies by overriding defaults while preserving unrelated expectations. Because every hypothesis must pass polynomial-time checks for valid derivation, conservativity, and minimality, DeFAb makes logical rigor the instrument for measuring creativity and theoretical reasoning, scoring the disciplined construction of theory revisions rather than fluent but theory-destroying prose. The pipeline pairs taxonomic hierarchies (OpenCyc, YAGO, Wikidata) with behavioral property graphs (ConceptNet, UMLS) to produce 372,648+ instances across 33.75M materialized rules from 18 sources, in three levels with polynomial-time verifiable gold standards. Four frontier models do not reliably internalize defeasible reasoning: rendering-robust Level 2 accuracy is 7.8-23.5%; chain-of-thought variance (~36 pp) exceeds any inter-model gap; and a matched contamination control isolates a +19.4 pp Level 3 gap. We further release DeFAb-Hard (a 235-instance Level 3 difficulty variant; best model 53.3% vs 100% symbolic) and CONJURE (a kernel-verified transformative-creativity variant of 560 Lean 4/Mathlib instances whose gold answers are definitions the proof kernel did not previously contain, judge-free verifier; a pilot finds zero novel concepts). The same verifier doubles as an exact reward for preference optimization (DPO, RLVR/GRPO). Released under MIT at https://huggingface.co/datasets/PatrickAllenCooper/DeFAb.

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

Understanding Cross-Sensor Feature Variations for Generalizable 3D Perception

Radar-camera BEV perception often suffers from degraded performance when evaluated across datasets, as changes in driving scenes, sensor configurations, and environmental conditions can alter both the input observations and the internal fused representations. This work studies this issue from the perspective of source-domain variation modeling, aiming to improve the robustness of BEV-based 3D detectors without relying on target-domain samples. We introduce a framework that characterizes visual scene variations in the frequency domain and uses them to synthesize diverse source-domain views. By comparing the resulting fused BEV representations, the framework further captures how image-level variations influence multi-modal BEV features. These variation patterns are then used to regularize the detector, encouraging the learned fusion space to remain stable under latent scene changes. The proposed method is applied only during training and leaves the inference pipeline unchanged. Experiments on cross-dataset radar-camera 3D detection between View-of-Delft and TJ4DRadSet demonstrate consistent improvements over multiple BEV fusion backbones, and the gains remain effective when a small amount of target-domain data is available.

20.
medRxiv (Medicine) 2026-06-15

Repurposing cardiovascular disease risk models to predict incident and co-occurring cardiovascular, cardiometabolic and neurocognitive outcomes.

Background: Cardiovascular disease (CVD), cardiometabolic and neurocognitive conditions share risk factors and frequently co-occur. We evaluated whether four established CVD risk prediction models (QRISK3, PCE, SCORE2, SCORE2-OP) can be repurposed to predict 10-year risk of these conditions and their co-occurrence with CVD. Methods: The models were recalibrated using 20% of the UK Biobank (UKB) and evaluated in the remaining 80%. We performed external validation using data from Clinical Practice Research Datalink (CPRD) Aurum, assessing model discrimination (c-statistics) and calibration (intercept and slope). We used permuted feature importance to determine the influence of each individual predictor in the models. Results: Depending on the model, the c-statistics for incident CVD ranged from 0.71 to 0.74 in the UKB test set (16,137 events). Discrimination was equal to or higher than CVD when evaluated against non-traditional CVD outcomes: 0.74 to 0.77 for heart failure (3,471 events), 0.72 to 0.73 for atrial fibrillation (9,213 events), 0.73 to 0.75 for peripheral arterial disease (1,927 events) and 0.80 to 0.82 for abdominal aortic aneurysm (595 events). For the multimorbidity endpoints, model discrimination ranged from 0.74 for the composite of CVD and T2DM (SCORE2-OP) to 0.83 for the composite of CVD and dementia or Parkinson's disease (QRISK3). When considering the onset of any cardiovascular, cardiometabolic, or neurocognitive outcome discrimination ranged from 0.71 to 0.72. The repurposed models slightly underestimated the predicted risk in the CPRD compared to the UKB: average difference in calibration intercept was at most -0.64. After age and sex, smoking status and systolic blood pressure contributed most to model predictions. Conclusions: Repurposed CVD models can be used to identify 10-year risk of many CVD-related conditions and their multimorbidity. These may be used to support risk-based approaches to prevention and screening. The repurposed models have been made available at: https://repurposed-cvd-risk-models.shinyapps.io/cvd_cmd_dementia_app/ Keywords: Risk prediction; cardiovascular disease; cardiometabolic disease; dementia; disease prevention.

21.
medRxiv (Medicine) 2026-06-16

Presurgical immune biomarkers associated with pain intensity and pain interference recovery after total knee arthroplasty: findings from the PRIME-KNEE study

Chronic postsurgical pain (CPSP) prevalence after total knee arthroplasty (TKA) is >20%. Circulating immune biomarkers are known factors of musculoskeletal pain but poorly understood as CPSP predictors. This prospective, longitudinal study of 203 patients s/p TKA tested presurgical plasma biomarkers associated with 6-month CPSP, using promising approaches from geriatrics biomarker research: expected recovery differential (ERD; resilience outcome) and penalized, machine-learning regularization modeling (elastic net and LASSO regression). Forty-nine presurgical candidate biomarkers were considered. CPSP was operationalized using ERDs built around PROMIS pain intensity and pain interference, which quantified the difference between observed and expected recovery after accounting for demographic, comorbidity, reserve, and perioperative factors. Plasma/ERDs from ~130 patients revealed 13 biomarkers with the highest selection stability criteria, and either positive or negative (+/-) associations with ERDs. Interleukin (IL) 5 (-) and Lipopolysaccharide-Binding Protein (LBP; +) were associated with both ERDs. Unique associations with pain intensity ERD included Cytomegalovirus-Specific IgG Negative (CMV IGg-; -), Macrophage Inflammatory Protein-1 Beta (MIP1b; -), IL12p70 (-, Cluster of Differentiation 30 (sCD30;-), Interferon alpha 2a (IFN2a;+), and Leukemia Inhibitory Factor (LIF;+). Unique associations with pain interference ERD included Lipopolysaccharide (LPS;-), Activin A (-), IL8 (-), Serum Amyloid A (SAA;-), and IL7 (+). Protein-protein interaction analyses and topology motifs suggest a centralized network with higher-than-expected connectivity, involving IL5, IL7, IL8, MIP1{beta}, and IFN2a, among others. This study proposes rigorous yet feasible approaches to expedite pain biomarker research, and introduces presurgical biomarkers t0 consider in future TKA-CPSP biosignature derivation.

22.
arXiv (CS.CV) 2026-06-19

Contour-Constrained Deformable Registration with Parameter Characterization for Head and Neck Surgical Guidance

With 890,000 annual new cases globally, head and neck squamous cell carcinoma has one of the highest recurrence rates among solid malignancies. Although frozen section analysis is the standard of care for intraoperative margin assessment, accurately relocating detected positive margins on the resection bed remains challenging due to imprecise alignment between resected specimens and their resection bed, compounded by post-resection mucosal tissue shrinkage. We present a biomechanics-driven deformable registration framework that corrects post-resection tissue deformation to provide intraoperative guidance. Our approach registers 3D specimen meshes to intraoperative resection bed point clouds using a deformable registration approach based on regularized Kelvinlet basis functions. The registration matches surface point clouds, fiducial landmarks, and boundary contour constraints that directly penalize perpendicular distance-to-agreement between specimen and resection bed boundaries. Across nine specimens from skin, buccal mucosa, and tongue sites, the overall mean target registration error was $11.11 \pm 4.07$ mm using rigid registration, which decreased to $8.20 \pm 2.68$ mm (26.19\% reduction) using deformable registration without contour constraint. The proposed contour-constrained deformable registration further reduced the error to $5.62 \pm 2.28$ mm, a 49.41\% reduction relative to rigid registration. We observed the largest reduction in the most clinically challenging tongue specimens. We also performed a systematic two-stage parameter search to characterize the relative importance of surface alignment, fiducial correspondences, contour constraint, and strain energy regularization. This search revealed that contour weighting dominates registration accuracy for tissue types with large lateral deformation, while the algorithm operates over a broad range of parameter combinations.

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.CV) 2026-06-11

BiWM: Advancing Open-Source Interactive Video World Models with Bidirectional Autoregression

Transitioning bidirectional video diffusion models into an autoregressive paradigm improves the interactivity of video world models, but existing causal pipelines need many stages (control fine-tuning, autoregressive training, causal initialization, few-step distillation) and still trail bidirectional models in quality due to error accumulation. Recent world models such as Yume-1.5 and Matrix-Game-3.0 instead adopt a bidirectional autoregressive approach, gaining fidelity and stable long-horizon rollout from self-correcting error propagation, yet open-source frameworks (e.g., minWM) support only causal models. We present BiWM, the first full-stack framework for interactive video world models under the bidirectional autoregressive paradigm, jointly optimizing generation quality and inference speed. From a pretrained video backbone, BiWM injects camera control by fine-tuning, then runs a few-step Distribution Matching Distillation (DMD) stage that turns the backbone into an action/camera-controllable world model: just two training stages instead of four in minWM, converging in a few hundred steps on 8xH200 GPUs. A single recipe spans Wan2.1-1.3B, Wan2.2-5B, HunyuanVideo-1.5-8B, and LTX-2.3-22B, and also supports secondary fine-tuning of existing bidirectional models. BiWM enables real-world camera control where minWM loses controllability, integrates pluggable history compression (FramePack-style and PackForcing-style) for long rollouts, and offers an optional NVFP4 4-bit training/inference pipeline. To counter DMD's mode-seeking degradation, we add GAN and mass-covering forward-KL objectives that preserve scene dynamics. We open-source BiWM for resource-constrained research and high-fidelity environment simulation.

25.
arXiv (CS.CL) 2026-06-19

CombEval: A Framework for Evaluating Combinatorial Counting in Large Language Models

We present CombEval, a dynamic benchmark for evaluating combinatorial counting in large language models. CombEval represents each problem as a typed Cofola specification over entities, combinatorial objects, object dependencies, and constraints, enabling controlled generation of natural-language counting problems with exact solver-verified answers. Unlike static collections, CombEval supports systematic variation of object type, entity scale, constraint count, and reasoning depth. We evaluate 11 LLMs under direct and code-augmented settings and find that models remain brittle on ordered objects, indistinguishable elements, relatively positional constraints, and nested object dependencies. Error analysis further identifies failures in constraint interpretation and counting principles. CombEval provides a diagnostic testbed for studying when and why LLMs fail at combinatorial reasoning. The code and generated benchmark suites are publicly available at \url{https://github.com/YuxuZhou-CN/combination-problem-generation}.