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

Unifying Post-hoc Explanations of Knowledge Graph Completions

arXiv:2507.22951v2 Announce Type: replace Abstract: Knowledge Graphs organize information as entity-relation-entity triples, enabling machine learning models to predict plausible missing triples in a task known as Knowledge Graph Completion (KGC). Post-hoc explainability for KGC addresses the problem of identifying which triples most influence the predictions of machine learning models. Currently, the field lacks formalization and consistent evaluations, hindering reproducibility and cross-study comparisons. This paper argues for a unified taxonomy for post-hoc explainability in KGC. First, we propose a characterization of post-hoc explanations via multi-objective optimization that unifies existing post-hoc explainability algorithms in KGC and the explanations they produce, balancing explanation effectiveness and conciseness. Next, we examine improved evaluation protocols based on popular metrics, such as Mean Reciprocal Rank and Hits@k, through illustrative experiments. Finally, we stress the importance of interpretability as the ability of explanations to address queries meaningful to end users. By unifying methods and discussing evaluation standards, this work puts forward a case for more reproducible and impactful research in KGC explainability.

02.
arXiv (CS.AI) 2026-06-17

PearlVLA: Progressive Embodied Action-Plan Refinement in Latent Space

arXiv:2606.17924v1 Announce Type: cross Abstract: Current Vision-Language-Action (VLA) models face a trade-off between efficient action generation and explicit deliberation. Directly decoding actions from vision-language backbone representations enables low-latency control, whereas explicit reasoning through textual chains, pixel-level subgoals, or action search can improve planning but incurs substantial latency and computational cost. We propose PearlVLA, a VLA framework that moves deliberation into the latent space of a vision-language model (VLM). PearlVLA separates VLM meta-query representations into a fixed visual grounding branch and an iterative latent plan branch. At each refinement round, a plan-conditioned world query probes a lightweight frozen latent world model for an action-free future observation latent, which is fed back to guide plan refinement. A future-guided RefineNet then applies scheduled residual updates to progressively refine a coarse semantic draft into a fine-grained latent action plan. The refined plan after K rounds is then decoded in parallel into an action chunk for low-latency execution. We further introduce Causal Refinement-Grouped Process-Reward RL to optimize the latent refinement process with rewards from longer-horizon imagined futures induced by latent plan edits. Empirical evaluations on the LIBERO benchmark demonstrate that PearlVLA achieves state-of-the-art performance among existing methods.

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

RoSE: Round-robin Synthetic Data Evaluation for Selecting LLM Generators without Human Test Sets

LLMs are powerful generators of synthetic data, which are used for training smaller, specific models. This is especially valuable for low-resource languages, where human-labelled data is scarce but LLMs can still produce high-quality text. However, LLMs differ in how useful their outputs are for training. Selecting the best LLM as a generator is challenging because extrinsic evaluation requires costly human annotations (which are often unavailable for low-resource languages), while intrinsic metrics correlate poorly with downstream performance. We introduce Round robin Synthetic data Evaluation (RoSE), a proxy metric for selecting the best LLM generator without human test sets. RoSE trains a small model on the outputs of a candidate generator (LLM) and then evaluates it on generated synthetic examples from all other candidate LLMs. The final RoSE score is the mean performance of this small model. Across six LLMs, eleven languages, and three tasks (sentiment, topic, intent), RoSE identifies the optimal generator more often than any other intrinsic heuristics. RoSE outperforms intrinsic heuristics and comes within 0.76 percentage points of the optimal generator baseline. This result is measured in terms of downstream performance, obtained by training a small model on the chosen generator's outputs (optimal vs. proxy metric selected) and evaluating it on human-labelled test data. Additionally, RoSE is the only metric to achieve a positive correlation with performance on human test data.

04.
bioRxiv (Bioinfo) 2026-06-16

Phylogenetic tree inference using generative models

Accurate inference of phylogenetic trees is fundamental to evolutionary biology, yet existing methods rely on complex pipelines involving multiple sequence alignment, explicit evolutionary models, and computationally intensive tree search procedures. Here, we present BetaInfer, a generative framework that reformulates phylogenetic tree inference as a sequence transduction problem. BetaInfer leverages hybrid transformer-based architectures to directly map sets of unaligned sequences to phylogenetic trees represented in Newick format. Trained on large-scale simulated evolutionary data with known ground truth, BetaInfer learns to capture complex evolutionary signals directly from sequence data. Ensemble-based generation of multiple candidate trees further improves robustness, reducing reconstruction error by over 30% relative to single predictions. Across extensive evaluations on both simulated and empirical datasets, BetaInfer achieves competitive performance relative to state-of-the-art phylogenetic pipelines, matching, and in some cases exceeding, the accuracy of established likelihood-based and distance-based methods under a wide range of conditions. Interpretability analyses reveal that BetaInfer leverages internal pairwise-distance computations to synthesize evolutionary relationships into an integrated, global representation that supports direct tree generation. Together, these results demonstrate that generative models can serve as a viable and scalable alternative to standard phylogenetic pipelines.

05.
arXiv (CS.CL) 2026-06-12

InnoEval: On Research Idea Evaluation as a Knowledge-Grounded, Multi-Perspective Reasoning Problem

The rapid evolution of Large Language Models has catalyzed a surge in scientific idea production, yet this leap has not been accompanied by a matching advance in idea evaluation. The fundamental nature of scientific evaluation needs knowledgeable grounding, collective deliberation, and multi-criteria decision-making. However, existing idea evaluation methods often suffer from narrow knowledge horizons, flattened evaluation dimensions, and the inherent bias in LLM-as-a-Judge. To address these, we regard idea evaluation as a knowledge-grounded, multi-perspective reasoning problem and introduce InnoEval, a deep innovation evaluation framework designed to emulate human-level idea assessment. We apply a heterogeneous deep knowledge search engine that retrieves and grounds dynamic evidence from diverse online sources. We further achieve review consensus with an innovation review board containing reviewers with distinct academic backgrounds, enabling a multi-dimensional decoupled evaluation across multiple metrics. We construct comprehensive datasets derived from authoritative peer-reviewed submissions to benchmark InnoEval. Experiments demonstrate that InnoEval can consistently outperform baselines in point-wise, pair-wise, and group-wise evaluation tasks, exhibiting judgment patterns and consensus highly aligned with human experts.

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

DeMix: Debugging Training Data with Mixed Data Error Types by Investigating Influence Vectors

arXiv:2606.11616v1 Announce Type: new Abstract: High-quality training data is essential for the success of machine learning models. However, real-world datasets often contain mixed types of errors arising from systematic flaws in data preparation pipelines, including label errors, feature errors, and spurious correlations. Effective debugging of training data requires both detecting erroneous samples and identifying their specific error types to enable targeted repair, yet existing data cleaning and attribution methods fail to adequately address this dual requirement. In this paper, we propose DeMix, a novel framework that simultaneously diagnoses erroneous samples and their error types. Our key insight is that different error types produce distinct patterns on model behavior. DeMix captures such error-specific patterns by influence vectors that characterize how each training sample affects model predictions across all validation samples. We formulate training data debugging as a multi-label classification problem where a classifier is developed to predict error types directly from influence vectors. We further introduce an intervention-based learning strategy that guides the classifier to capture invariant rationales specific to each error type, ensuring the learned classifier generalizes effectively. Empirical evaluations on 11 tasks across tabular data prediction, recommendation systems, and LLM alignment demonstrate that DeMix significantly outperforms state-of-the-art approaches, achieving a 22.61% improvement in data debugging F1-score and a 9.32% gain in task model performance after data repair. Code is available at: https://github.com/SJTU-DMTai/DeMix.

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

HyperTool: Beyond Step-Wise Tool Calls for Tool-Augmented Agents

Tool-augmented LLM agents commonly rely on step-wise atomic tool calls, where each invocation, observation, and value transfer is exposed in the main reasoning trace. This creates an execution-granularity mismatch: locally deterministic tool workflows are unfolded into repeated model-visible decisions, consuming context and forcing the model to manage low-level dataflow in the trace. We introduce HyperTool, a unified executable MCP-style tool interface that changes the model-visible unit of tool execution. A model invokes HyperTool with a code block that can call existing tools through their original schemas, manipulate returned values, and pass intermediate results locally, folding deterministic tool subroutines into a single outer call. To train models to use this interface, we synthesize HyperTool-format trajectories from cross-tool compositional tasks and verify them in real MCP environments. On MCP-Universe, HyperTool improves average accuracy from 15.69\% to 35.29\% on Qwen3-32B and from 9.93\% to 33.33\% on Qwen3-8B, and surpass GPT-OSS and Kimi-k2.5 on average accuracy, showing that our HyperTool can substantially improve multi-step tool use.

08.
medRxiv (Medicine) 2026-06-10

Resolving Diagnostic Discordance in Group 2 Pulmonary Hypertension Through Staged Physiologic Testing: Insights From PVDOMICS

Background World Symposium on Pulmonary Hypertension (WSPH) Group 2 pulmonary hypertension (PH) is a clinically integrated phenotype attributed to left heart disease, whereas pre- versus post-capillary classification is operationalized primarily by pulmonary capillary wedge pressure (PCWP). Although current recommendations emphasize contextual interpretation and provocative testing for intermediate PCWP values, the relationship between PCWP-based classification and underlying phenotype has not been systematically evaluated. We aim to quantify phenotype-hemodynamic discordance across the PCWP spectrum and evaluate a staged physiology-guided framework incorporating inhaled nitric oxide (iNO), ventricular geometry, and provocative testing. Methods We studied 1,032 participants from the NHLBI-sponsored PVDOMICS cohort with multidisciplinary adjudicated phenotypes integrating clinical, imaging, physiologic, and hemodynamic data. Stage-specific PCWP thresholds classified pre- versus post-capillary physiology at rest, during iNO, and during provocation (fluid challenge or invasive cardiopulmonary exercise testing [iCPET]). Echocardiographic right ventricular-to-left ventricular (RV/LV) ratio was evaluated as a marker of ventricular interdependence. Restricted cubic spline and staged concordance analyses defined certainty-based PCWP ranges and incremental diagnostic yield. Results Adjudicated Group 2 phenotype was present in 37.0% of participants. Resting PCWP demonstrated good discrimination (AUC 0.86), but substantial bidirectional phenotype-hemodynamic discordance persisted across intermediate PCWP ranges. At a resting PCWP of 12 mmHg, 25% of participants classified as pre-capillary had adjudicated Group 2 PH, whereas at 18 mmHg, 35% classified as post-capillary remained discordant non-Group 2. Concordance did not approach 90% until PCWP values were 24 mmHg. Dynamic testing incrementally improved concordance within these overlap zones. Nearly half of adjudicated Group 2 PH participants (46.5%) were not identified by resting PCWP alone; incorporation of iNO and provocative testing increased cumulative Group 2 identification by 63.4% and improved sensitivity from 79.9% to 83.7%. Model discrimination improved from an AUC of 0.863 to 0.908 (likelihood-ratio P

09.
arXiv (CS.AI) 2026-06-17

BadScientist: Can a Research Agent Write Convincing but Unsound Papers that Fool LLM Reviewers?

arXiv:2510.18003v2 Announce Type: replace-cross Abstract: The convergence of LLM-powered research assistants and AI-based peer review systems creates a critical vulnerability: fully automated publication loops where AI-generated research is evaluated by AI reviewers without human oversight. We investigate this through BadScientist, a framework that evaluates whether fabrication-oriented paper generation agents can deceive multi-model LLM review systems. Our generator employs presentation-manipulation strategies requiring no real experiments. We develop a rigorous evaluation framework with formal error guarantees (concentration bounds and calibration analysis), calibrated on real data. Our results reveal systematic vulnerabilities: fabricated papers achieve acceptance rates up to . Critically, we identify concern-acceptance conflict – reviewers frequently flag integrity issues yet assign acceptance-level scores. Our mitigation strategies show only marginal improvements, with detection accuracy barely exceeding random chance. Despite provably sound aggregation mathematics, integrity checking systematically fails, exposing fundamental limitations in current AI-driven review systems and underscoring the urgent need for defense-in-depth safeguards in scientific publishing.

10.
arXiv (math.PR) 2026-06-19

Hermite trace polynomials and chaos decompositions for the Hermitian Brownian motion

arXiv:2207.13180v4 Announce Type: replace Abstract: For a non-zero parameter $q$, we define Hermite trace polynomials, which are multivariate polynomials indexed by permutations. We prove several combinatorial properties for them, such as expansions and product formulas. The linear functional determined by these trace polynomials is a state for $q = \frac{1}{N}$ for $N$ a non-zero integer. For such $q$, Hermite trace polynomials of different degrees are orthogonal. The product formulas extend to the closure with respect to the state. The state can be identified with the expectation induced by the $N \times N$ Hermitian Brownian motion. Hermite trace polynomials are martingales for this Brownian motion, while the elements in the closure can be interpreted as stochastic integrals with respect to it. Using the grading on the algebra, we prove several chaos decompositions for such integrals, as well as analyze corresponding creation and annihilation operators. In the univariate, pure trace polynomial case, trace Hermite polynomials can be identified with the Hermite polynomials of matrix argument.

11.
arXiv (CS.LG) 2026-06-12

ShapeBench: A Scalable Benchmark and Diagnostic Suite for Standardized Evaluation in Aerodynamic Shape Optimization

arXiv:2605.20763v2 Announce Type: replace Abstract: Rapid progress in aerodynamic shape optimization (ASO) has outpaced currently-available standardized evaluation frameworks. Fair comparison requires a unified benchmark spanning diverse shape classes, objective formulations, and matched-budget state-of-the-art baselines. We introduce ShapeBench, an open-source ASO benchmark with a unified API spanning 103 tasks across eight shape categories and multiple optimization regimes. Each ShapeBench task includes a validated surrogate for fast search; when feasible, a high-fidelity Computational Fluid Dynamics (CFD) pipeline for final verification is available, enabling systematic fidelity-gap analysis. ShapeBench provides a reproducible protocol with well-configured baselines to compare fairly using a consistent budget metric, allowing for comparison among both classical and LLM-driven methods, including general-purpose optimizers and a new domain-specialized evolutionary LLM baseline, ShapeEvolve. Results on ShapeBench demonstrate substantial variance in optimizer rankings across shape categories and problem formulations, with mean pairwise Spearman $\rho = 0.013$, so single-task conclusions do not reliably generalize across problem classes. The benchmark is also far from saturation; classical methods are rarely applicable across all shape categories and tasks, further highlighting the need for more general-purpose approaches.

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

Persona-Pruner: Sculpting Lightweight Models for Role-Playing

Language Models (LMs) have shown remarkable potential as role-playing chatbots, delivering consistent, stylized interactions when given a specification of a character or user persona. However, applying these capabilities to real-world applications (e.g., ecosystems with numerous NPCs interacting simultaneously) exposes a critical inefficiency due to the excessive computational cost. In this paper, we question the necessity of dedicating a full, generalist model to a single persona, hypothesizing that a specific character identity relies on only a fraction of the model's total capacity. We observe that naively pruning LMs often severely degrades the role-playing performance for a specific persona; it does not distinguish between redundant knowledge and essential character traits. We propose Persona-Pruner, a framework that sculpts a lightweight role-playing model by isolating persona-specific sub-networks from a single description. Our experiments consistently show that Persona-Pruner preserves role-playing performance substantially more effectively than existing state-of-the-art LLM pruning techniques, reducing the performance drop from the dense model by up to 93.8% over the strongest baseline on RoleBench in LLM-as-a-judge score, while still maintaining general LLM capabilities. Code is available at https://github.com/jsu-kim/Persona-Pruner.

13.
arXiv (CS.CL) 2026-06-18

DSB: Dynamic Sliding Block Scheduling for Diffusion LLMs

Diffusion large language models (dLLMs) have emerged as a promising alternative for text generation, distinguished by their native support for parallel decoding. In practice, block inference is crucial for avoiding order misalignment in global bidirectional decoding and improving output quality. However, the widely-used fixed, predefined block (naive) schedule is agnostic to semantic difficulty, making it a suboptimal strategy for both quality and efficiency: it can force premature commitments to uncertain positions while delaying easy positions near block boundaries. In this work, we analyze the limitations of naive block scheduling and disclose the importance of dynamically adapting the schedule to semantic difficulty for reliable and efficient inference. Motivated by this, we propose Dynamic Sliding Block (DSB), a training-free block scheduling method that uses a sliding block with a dynamic size to overcome the rigidity of the naive block. To further improve efficiency, we introduce DSB Cache, a training-free KV-cache mechanism tailored to DSB. Extensive experiments across multiple models and benchmarks demonstrate that DSB, together with DSB Cache, consistently improves both generation quality and inference efficiency for dLLMs. Code is released at https://github.com/lizhuo-luo/DSB.

14.
arXiv (CS.LG) 2026-06-18

Self-attention-based non-linear basis transformations for compact latent space modelling of dynamic optical fibre transmission matrices

arXiv:2406.07775v2 Announce Type: replace Abstract: Multimode optical fibres are hair-thin strands of glass that efficiently transport light. They promise next-generation medical endoscopes that provide unprecedented sub-cellular image resolution deep inside the body. However, confining light to such fibres means that images are inherently scrambled in transit. Conventionally, this scrambling has been compensated by pre-calibrating how a specific fibre scrambles light and solving a stationary linear matrix equation that represents a physical model of the fibre. However, as the technology develops towards real-world deployment, the unscrambling process must account for dynamic changes in the matrix representing the fibre's effect on light, due to factors such as movement and temperature shifts, and non-linearities resulting from the inaccessibility of the fibre tip when inside the body. Such complex, dynamic and nonlinear behaviour is well-suited to approximation by neural networks, but most leading image reconstruction networks rely on convolutional layers, which assume strong correlations between adjacent pixels, a strong inductive bias that is inappropriate for fibre matrices which may be expressed in a range of arbitrary coordinate representations with long-range correlations. We introduce a new concept that uses self-attention layers to dynamically transform the coordinate representations of varying fibre matrices to a basis that admits compact, low-dimensional representations suitable for further processing. We demonstrate the effectiveness of this approach on diverse fibre matrix datasets. We show our models significantly improve the sparsity of fibre bases in their transformed bases with a participation ratio, p, as a measure of sparsity, of between 0.01 and 0.11. Further, we show that these transformed representations admit reconstruction of the original matrices with < 10% reconstruction error, demonstrating the invertibility.

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

SMEPilot: Characterizing and Optimizing LLM Inference with Scalable Matrix Extensions

arXiv:2606.16332v1 Announce Type: cross Abstract: Modern CPUs increasingly integrate matrix extensions, such as Arm Scalable Matrix Extension (SME), that provide high-throughput matrix execution within the CPU. For LLM inference, however, these units are not a universal replacement for conventional CPU cores: prefill, decode, attention, and KV-cache operations expose different arithmetic intensities, vector behavior, and layout requirements, while SME units and CPU cores still compete for shared memory bandwidth. This paper studies this mismatch through a roofline-based characterization of SME-enabled CPUs and uses the resulting model to guide operator-level execution choices. We present SMEPilot, an LLM inference engine that selects CPU-only, SME-only, or cooperative SME+CPU execution for each operator shape. SMEPilot partitions matrix work across SME and CPU cores at tile granularity, overlaps SME-suitable matrix stages with CPU-suitable vector stages in attention, and maintains layout state so packed tensor representations are reused rather than repeatedly rebuilt on critical paths. Across Llama-3.2-3B, Qwen3-4B, and Qwen3-30BA3B on phone, PC, and server platforms, SMEPilot improves end-to-end inference performance by up to 3.94$\times$.

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

Learning from Your Own Mistakes: Constructing Learnable Micro-Reflective Trajectories for Self-Distillation

arXiv:2606.18844v1 Announce Type: new Abstract: Self-distillation improves reasoning in large language models by using the model's own rollouts as training signal, typically through implicit logit-level alignment that minimizes KL divergence toward a privileged target distribution. However, because this supervision is generated via uncontrolled sampling, it provides no diagnostic insight into the model's specific errors or corrective guidance for its individual failure patterns. Consequently, the model learns to imitate a privileged distribution rather than receiving fine-grained corrections that pinpoint where and why its reasoning fails. In this paper, we propose Trajectory-Augmented Policy Optimization (TAPO), which advances self-distillation from implicit distributional alignment to explicit trajectory construction. During RL training, the model produces both correct and incorrect rollouts to the same query, and TAPO leverages this contrastive structure to construct micro-reflective corrections, new training trajectories that retain the model's erroneous reasoning up to the point of failure, then insert a natural-language diagnosis and corrected reasoning guided by a correct reference from the same sampling group. Since each trajectory is anchored in the learner's own prefix and solutions, the corrective signal preserves the model's on-policy distribution to a greater extent than the position-wise alignment imposed by KL-based methods. To integrate these trajectories, TAPO introduces difficulty-aware candidate selection at the model's capability boundary and decoupled advantage estimation to prevent gradient contamination. Experiments on AIME 2024, AIME 2025, and HMMT 2025 show that TAPO achieves consistent improvements over GRPO under the same number of training steps. Further analysis demonstrates that TAPO strengthens both first-pass reasoning and error-correction effectiveness.

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

Learning Topology-Aware Implicit Field for Unified Pulmonary Tree Modeling with Incomplete Topological Supervision

Pulmonary trees extracted from CT images frequently exhibit topological incompleteness, such as missing or disconnected branches, which substantially degrades downstream anatomical analysis and limits the applicability of existing pulmonary tree modeling pipelines. Current approaches typically rely on dense volumetric processing, explicit graph reasoning, or generic point cloud completion priors, leading to limited efficiency, weak structural awareness, and reduced robustness under realistic structural corruption. We propose TopoField, a topology-aware implicit modeling framework that treats topology repair as a first-class modeling problem and enables unified multi-task inference for pulmonary tree analysis. TopoField represents pulmonary anatomy using sparse surface and skeleton point clouds and learns a continuous implicit field that supports topology repair without relying on complete or explicit disconnection annotations, by training on synthetically introduced structural disruptions over already incomplete trees. Building upon the repaired implicit representation, anatomical labeling and lung segment reconstruction are jointly inferred through task-specific implicit functions within a single forward pass. Extensive experiments on the Lung3D+ dataset demonstrate that TopoField consistently improves topological completeness and achieves accurate anatomical labeling and lung segment reconstruction under challenging incomplete scenarios. We further validate TopoField on real incomplete outputs from an external segmentation model, demonstrating its applicability to realistic segmentation pipelines. Owing to its implicit formulation, TopoField attains high computational efficiency, completing all tasks in just over one second per case, highlighting its practicality for large-scale and time-sensitive clinical applications.

18.
arXiv (CS.AI) 2026-06-11

GEAR-VLA: Learning Geometry-Aware Action Representations for Generalizable Robotic Manipulation

arXiv:2606.08530v2 Announce Type: replace-cross Abstract: Vision-Language-Action (VLA) models achieve strong benchmark performance but still struggle in real-world deployment with unseen objects, background shifts, and different robot embodiments. We argue that this stems from the lack of a unified geometry-aware manipulation representation, leaving existing VLAs vulnerable to low-level trajectory supervision, misaligned 3D features, and embodiment differences. To address this, we propose GEAR-VLA, a VLA framework for learning unified geometry-aware action representations for generalizable robotic manipulation. GEAR-VLA adopts coarse-to-fine action learning, where multi-source embodied pretraining equips the VLM with embodied reasoning and discrete action understanding before latent action tokens connect action semantics to a gradient-decoupled DiT continuous action expert. It further performs semantic-aligned 3D integration by aligning a trainable 3D spatial backbone with the VLA representation while freezing the original VLM-aligned visual pathway. To share this representation across robots, GEAR-VLA uses embodiment canonicalization, where embodiment-aware states and embodiment-invariant actions confine robot differences to the low-level interface. Extensive simulation and real-world experiments demonstrate strong generalization: GEAR-VLA achieves state-of-the-art performance on LIBERO, zero-shot LIBERO-Plus, and RoboTwin 2.0, reaches 85.9% success on AgileX and 81.0% on the pretraining-unseen LDT-01 embodiment, and obtains 90.1% success on a 6,360-trial universal grasping benchmark with 212 unseen objects. Code and models will be released at https://github.com/babynabeauty/GEAR-VLA.

19.
medRxiv (Medicine) 2026-06-17

LLM-Driven Extraction of NI-RADS and Imaging Tumor Characteristics to Enhance Oropharyngeal Cancer Survivorship Surveillance

Abstract Purpose Radiologic surveillance is essential for oropharyngeal cancer (OPC) survivors, guiding recurrence detection and follow-up strategies. The Neck Imaging Reporting and Data System provides a standardized framework for post-treatment risk reporting at both the primary tumor site (pNI-RADs) and cervical lymph nodes (nNI-RADS). Comprehensive surveillance additionally requires assessment of disease status, including the primary tumor, nodal involvement, and distant metastases. These clinical results are often embedded as unstructured data within free-text radiology reports. We hypothesized that a large language model (LLM) can reliably extract NI-RADS score criteria and summarize key imaging features from unstructured radiology text, achieving high concordance with expert review. Methods Previously untreated OPC patients who received definitive cancer therapy were identified. Eligible imaging reports included post-treatment head and neck CT, MRI, or FDG PET/CT scans containing narrative and impression text. Examinations lacking narrative or impression text, containing pre-existing NI-RADS annotations, or involving non-surveillance imaging modalities were excluded. A total of 200 reports were randomly selected from 7,076 eligible examinations for manual abstraction using a three-reviewer consensus framework to establish a reference dataset. Using the Palantir Foundry Pipeline Builder, a GPT-5-based LLM was deployed to extract pNI-RADS and nNI-RADS scores, and key imaging features of disease status from these reports. Performance was evaluated using exact agreement and F1-based metrics. Results Agreement for no evidence of disease (score of 1) was 93.3% (126/135; F1 = 0.94) and 90.3% (130/144; F1 = 0.93) for pNI-RADS and nNI-RADS, respectively. For NI-RADS [&ge;]2, exact category agreement was 73.1% (38/52; macro-F1 = 0.75) for pNI-RADS and 64.3% (27/42; macro-F1 = 0.56) for nNI-RADS. Quadratic weighted {kappa} was 0.81 and 0.59, respectively. For post-treatment disease surveillance variables, agreement was 94.9% (149/157; F1 = 0.87) for primary tumor presence, 89.1% (164/184; F1 = 0.87) for nodal disease presence, and 94.7% (126/133; F1 = 0.70) for distant metastasis detection. Specificity was high across disease-status variables (0.95-0.99), with negative predictive values of 0.95 for primary tumor, 0.87 for nodal disease, and 0.99 for distant metastasis. Conclusions Our LLM-based information retrieval and classification approach for radiographic treatment response from unstructured, multidimensional imaging reports achieved high performance for disease exclusion and moderate performance for detecting suspected residual and/or new disease. This pipeline supports scalable and standardized surveillance data capture for longitudinal monitoring, clinical analytics, and survivorship research in head and neck oncology.

20.
arXiv (CS.CL) 2026-06-15

Residual Context Diffusion Language Models

Diffusion Large Language Models (dLLMs) have emerged as a promising alternative to purely autoregressive language models because they can decode multiple tokens in parallel. However, state-of-the-art block-wise dLLMs rely on a "remasking" mechanism that decodes only the most confident tokens and discards the rest, effectively wasting computation. We demonstrate that recycling computation from the discarded tokens is beneficial, as these tokens retain contextual information useful for subsequent decoding iterations. In light of this, we propose Residual Context Diffusion (RCD), a module that converts these discarded token representations into contextual residuals and injects them back for the next denoising step. RCD uses a decoupled two-stage training pipeline to bypass the memory bottlenecks associated with backpropagation. We validate our method on both long CoT reasoning (SDAR) and short CoT instruction following (LLaDA) models. We demonstrate that a standard dLLM can be efficiently converted to the RCD paradigm with merely ~300 million tokens. RCD consistently improves frontier dLLMs by 4-11 percentage points in accuracy with minimal extra computation overhead across a wide range of benchmarks. Notably, on the most challenging AIME tasks, RCD nearly doubles baseline accuracy and attains up to 4-5x fewer denoising steps at baseline's peak accuracy.

21.
arXiv (CS.CV) 2026-06-17

Visuals Lie, Consistency Speaks: Disentangling Spatial Attention from Reliability in Vision-Language Models

Multimodal Foundation Models are increasingly used as reasoning agents, making reliability, knowing when a model may hallucinate, critical. A common intuition, which we call the Attention-Confidence Assumption, holds that reliability follows from "structural" visual perception: tight attention on relevant regions should signal a trustworthy answer, while scattered attention signals confusion. We challenge this through the VLM Reliability Probe (VRP), a systematic cross-family study of reliability signals in contemporary Vision-Language Models (VLMs). We introduce structural-attention metrics, cluster counts (C_k) and spatial entropy (H_s), to quantify the visual encoder's gaze, and track its evolution (Delta H_s) across layers. This reveals a "Symbolic Detachment": models often "Early Lock" visual features only to diffuse attention later, severing early perception from final generation. Contrary to the grounding hypothesis, we find a "Cluster Failure": spatial attention has near-zero correlation (R approx 0.001) with accuracy. Instead, reliability is a phenomenon of generation dynamics and internal-state distributions. Self-Consistency, the agreement rate across sampled reasoning paths, is the dominant predictor of truth (R = 0.429). Scaling causal interventions exposes a sharp architectural divergence: LLaVA locks its prediction in a fragile late-stage bottleneck, whereas PaliGemma and Qwen2-VL distribute reliability globally, staying resilient even when ~50% or more of their most predictive layer is destroyed. For current VLMs, reliability signals are detached from visual grounding maps and are best inferred from generation-time dynamics and hidden-state probes.

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

Quantum-classical physics-informed Kolmogorov-Arnold networks for PDEs

arXiv:2606.20326v1 Announce Type: new Abstract: We develop QCPIKAN, the first quantum-classical physics-informed Kolmogorov-Arnold network designed to solve partial differential equations (PDEs). Built upon Chebyshev-polynomial KAN layers and parameterized quantum circuits, this hybrid framework embeds physical constraints into the training loss to enforce physical consistency. Our theoretical investigations grounded in approximation theory prove that this design accelerates high-frequency error convergence to an exponential rate and effectively mitigates numerical dispersion. We validate the framework across three typical seepage scenarios in porous media, including single-phase flow, component transport and two-phase flow. Compared with existing quantum-classical physics-informed neural networks, QCPIKAN achieves superior performance in global prediction accuracy, local error control, dynamic evolution tracking and displacement front localization. This work provides a robust and efficient alternative for solving complex PDEs.

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

Impact of Hand Impairment and Occlusions on Hand Pose Estimation Accuracy in Augmented Reality Applications

Mixed reality applications can be designed for hand rehabilitation. Augmented reality (AR) head mounted displays (HMDs) specifically allow for ecologically valid tasks because individuals can see their real environment and interact with real objects while receiving additional cues on the HMD. While these applications rely on accurate hand pose estimation, there is a gap in investigating the influence of hand impairment or occlusion from real-object interactions on pose estimation accuracy. Further, comparisons between AR HMD predictions and state-of-the-art pose estimation methods have not been established. The current study assessed pose estimation accuracy of the HoloLens 2 HMD and state-of-the-art pose estimation algorithms (WiLoR, HaMeR, WildHands, and MediaPipe) while individuals with cervical spinal cord injury (cSCI; n = 13, Neurological Level of Injury: C3-C6; American Spinal Injury Association Impairment Scale: A-D) and 15 uninjured controls interacted with clear and opaque objects. Ground truth estimates of 3D joint positions were generated via triangulation from a multi-camera setup. Pose estimation accuracy did not differ between the cSCI and uninjured control groups suggesting that 3D joint predictions from the HoloLens 2 and pose estimation algorithms can generalize to populations with hand impairment. Further, clear objects provided a small accuracy advantage over opaque objects (0.1 mm) and predictions from both WiLoR and HaMeR were slightly more accurate than the HoloLens 2 (2 mm). Overall, these results suggest that the HoloLens 2 may be viable for hand rehabilitation applications and the dataset generated can be used to refine pose estimation methods for hand-impaired populations.

24.
arXiv (CS.CL) 2026-06-11

Pre-AF 13: An Interpretable Atrial Fibrillation Risk Score Mined from Discharge Reports

Background. Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia and a major determinant of prognosis. Established AF risk scores rely on factors (older age, hypertension) nearly ubiquitous among patients with cardiovascular disease (CVD), offering limited stratification in this high-risk group. Most target long-term (5-10 year) rather than medium-term prediction. We developed interpretable ML models predicting AF risk over a 24-month and entire follow-up horizon in CVD patients using routinely collected hospital data. Methods. Single-center retrospective study of electronic health records from the National Research Cardiology Center (Russia) for patients aged >=18 with CVD but without pre-existing AF, hospitalized more than once between January 2012 and May 2019. A custom NLP pipeline transformed unstructured discharge reports into 73 structured features, combining a rule-based parser with transformer-based NER. Using LightAutoML we built a full model (73 features), a simple model (reduced subset), and a linear model for a bedside risk score. Performance was assessed by ROC AUC, compared with CHARGE-AF, C2HEST, MHS, and HAVOC, and interpreted via SHAP. Results. Of 80,576 records from 45,000 patients, 17,562 met inclusion criteria; 1,438 (8.19%) developed AF. The full model reached ROC AUC 0.735 (24-month) and 0.696 (entire follow-up); the simple model was nearly identical (0.725, 0.696). All non-linear models outperformed the four clinical risk scores (ROC AUC 0.53-0.64). The simple model uses 13 features and is named Pre-AF 13. SHAP identified age and left atrial volume as dominant predictors. A linear risk score (Pre-AF 9) stratified observed 24-month AF incidence from ~7% to 36%. Conclusion. Interpretable ML models built from routinely collected EHR data identify high-AF-risk CVD patients, outperforming established clinical risk scores.

25.
medRxiv (Medicine) 2026-06-11

Population-scale detection of methylation outliers from long-read genome sequencing

Background: Aberrant DNA methylation can mediate the functional effects of rare genetic variation and contribute to imprinting disorders, repeat expansion diseases, and other pathogenic regulatory mechanisms. Long-read sequencing technologies now enable genome-wide detection of CpG methylation alongside genetic variation from a single assay. However, methods for systematic identification and interpretation of methylation outliers from long-read sequencing data remain limited. Methods: We developed METAFORA, a computational workflow for detecting methylation outlier regions from PacBio and Oxford Nanopore long-read sequencing data. METAFORA constructs population-level methylation references, segments the genome into correlated CpG blocks, infers technical and biological sources of variation through hidden factor estimation, models uncertainty due to variable depth sequencing, and computes covariate-adjusted methylation outlier scores for individual samples. We applied METAFORA across large long-read sequencing cohorts and integrated methylation outliers with multi-omic data. METAFORA is implemented as a snakemake workflow available at https://github.com/tjense25/METAFORA. Results: METAFORA identified methylation outlier regions associated with rare structural variants, tandem repeat expansions, and imprinting abnormalities. We found outlier regions were enriched for molecular outliers across transcriptomic and chromatin accessibility datasets, supporting their functional relevance in gene regulation. In a representative case, METAFORA identified an imprinting defect affecting the GNAS locus associated with an STX16 deletion. Conclusions: METAFORA enables scalable detection and interpretation of methylation outliers from long-read sequencing data and provides a framework for integrating epigenetic outliers with genomic and multi-omic analyses. These approaches may improve interpretation of rare regulatory variation and support discovery of clinically relevant epigenetic abnormalities in genomic medicine.