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01.
arXiv (CS.AI) 2026-06-18

What Must Generalist Agents Remember?

arXiv:2606.18746v1 Announce Type: new Abstract: This paper develops a formal account of what generalist agents must store in memory in order to act near-optimally across multiple environments and goals. It shows that when two domains share an observational bottleneck but require incompatible optimal actions, any uniformly near-optimal policy must induce distinct memory distributions at that bottleneck. The result yields a separation theorem: sufficiently successful agents cannot rely only on current state observations, but must preserve domain-relevant information in memory. The paper further shows that if an agent's memory contains enough information to estimate values for related goals, then that memory can be used to approximately reconstruct the agent's local transition dynamics. Together, these results characterize memory as the substrate that supports domain disambiguation, transition-model reconstruction, and planning for generalist agents.

02.
arXiv (CS.AI) 2026-06-19

Analyzing Defensive Misdirection Against Model-Guided Automated Attacks on Agentic AI Systems

arXiv:2606.20470v1 Announce Type: cross Abstract: Agentic AI systems increasingly rely on language-model components to interpret instructions, process external data, invoke tools, and coordinate with other agents. These capabilities make prompt-injection and jailbreak attacks more consequential, especially as attackers adopt model-guided automation to scale probing, prompt refinement, and response evaluation. This work analyzes the resulting attack-defense setting through a probabilistic model of a target system, its defense mechanism, and the attacker's automated judge. Our analysis shows that conventional detect-and-block defenses can allow attacker success rate (ASR) to approach one as the query budget grows, since predictable refusals provide useful feedback to automated search. We then examine detect-and-misdirect, where detected malicious interactions receive controlled, non-operational responses designed to induce false-positive errors in the attacker's judge. This strategy reduces the positive predictive value of attacker-selected candidates and yields a bounded asymptotic ASR. We evaluate a proof-of-concept realization of this strategy through Contextual Misdirection via Progressive Engagement (CMPE), a lightweight conversational misdirection method designed to replace predictable refusal text with safe but strategically misleading responses in automated jailbreak settings. On jailbreak benchmarks, CMPE reduces estimated ASR upper bounds by up to two orders of magnitude and nearly eliminates verified attack success in end-to-end PAIR and GPTFuzz attack runs.

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

Integrating national forest inventory, airborne lidar, and satellite imagery for wall-to-wall mapping of forest structure with computer vision

arXiv:2606.20291v1 Announce Type: new Abstract: Remote sensing is increasingly relied upon to deliver actionable science for forest and wildfire risk management across large landscapes. Wall-to-wall, annually updated maps are a persistent need for effective forest management. Many planning systems and data collections combine disparate data sources with different purposes, vintages, and prediction quality, which leads to confounding behavior in operational planning systems. We introduce the VibrantForests framework, developed and applied to map forest attributes and provide a coherent foundation for effective forest and wildfire planning. VibrantForests includes a satellite-based forest structure model trained on lidar-derived samples and applied across the contiguous United States to concurrently generate estimates of canopy cover, canopy height, aboveground live tree biomass, basal area, and quadratic mean diameter at 10-meter resolution. We demonstrate predictive capability spanning the full spectrum of forest conditions ranging from sparse-canopy/low-biomass to dense-canopy/high-biomass. Results show that our model extends the range at which saturation is commonly encountered in comparable passive-sensor models, and reduces regression-to-mean behavior that commonly produces overestimation of forest attributes in small/sparse conditions and underestimation in large/dense conditions. The VibrantForests framework addresses a key limitation in large-area forest and wildfire planning by delivering coherent wall-to-wall estimates of management-relevant attributes at annual cadence and 10m resolution.

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

Quantizing Time-Series Models As Dynamical Systems: Trajectory-Based Quantization Sensitivity Score

arXiv:2606.13300v1 Announce Type: new Abstract: We introduce the Trajectory-based Quantization Sensitivity Score (TQS), a metric that reframes post-training quantization (PTQ) through the lens of dynamical-systems stability. By modeling the network's rollout as a discrete-time dynamical system, TQS characterizes how quantization-induced errors propagate and amplify over the rollout horizon. Unlike conventional PTQ methods, where sensitivity analysis is often coupled to the quantization procedure, TQS enables a priori sensitivity estimation decoupled from quantizer selection and bit-width assignment. This separation allows for quantization budget planning even for black-box or compiled networks with fused operators. Building on this, we present TQS-PTQ, a flexible mixed-precision framework that requires no calibration data or costly second-order approximations. Our experiments show that a dynamical-systems perspective provides a robust, high-performing pathway for low-precision deployment in resource-constrained settings.

05.
arXiv (math.PR) 2026-06-17

Absolute continuity, supports and idempotent splitting in categorical probability

arXiv:2308.00651v5 Announce Type: replace Abstract: Markov categories have recently turned out to be a powerful high-level framework for probability and statistics. They accommodate purely categorical definitions of notions like conditional probability and almost sure equality, as well as proofs of fundamental results such as the Hewitt–Savage 0/1 Law, the de Finetti Theorem and the Ergodic Decomposition Theorem. In this work, we develop additional relevant notions from probability theory in the setting of Markov categories. This comprises improved versions of previously introduced definitions of absolute continuity and supports, as well as a detailed study of idempotents and idempotent splitting in Markov categories. Our main result on idempotent splitting is that every idempotent measurable Markov kernel between standard Borel spaces splits across another standard Borel space, and we derive this as an instance of a general categorical criterion for idempotent splitting in Markov categories.

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

daVinci-kernel: Co-Evolving Skill Selection, Summarization, and Utilization via RL for GPU Kernel Optimization

GPU kernel optimization represents a paradigm where functional correctness is assumed and execution efficiency is the objective. We present daVinci-kernel, a reinforcement learning framework that couples skill discovery with skill exploitation through a dynamically evolving skill library. daVinci-kernel jointly trains three agents sharing one LLM backbone: a Skill Selection Agent that retrieves relevant techniques via BM25 and LLM reranking, a Policy Agent that generates multi-turn CUDA/Triton kernels conditioned on selected skills, and a Skill Summary Agent that distills successful rollouts into reusable skills. Candidate skills are added only after execution-based verification confirms reproducible speedups. All three agents share a single LLM backbone, are initialized via a structured SFT cold start on diversity-filtered data, and are then jointly optimized end-to-end with multi-turn REINFORCE and per-agent advantage estimation. On KernelBench, daVinci-kernel-14B achieves 37.2%, 70.6%, and 32.2% on Level 1, Level 2, and Level 3 under the Fast$_1$ threshold, outperforming the strongest prior RL-trained model, Dr.Kernel-14B.

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

Learning Survival Models with Right-Censored Reporting Delays

arXiv:2510.04421v3 Announce Type: replace-cross Abstract: Survival analysis provides statistical methods to model the time until an event occurs. Reporting delays arise when event times are not observed at their occurrence but are only revealed upon reporting. This issue is particularly critical for timely risk evaluation when the observation window is short due to administrative censoring. In this study, we incorporate right-censored reporting delays by jointly modeling parametric hazards for the event and reporting processes. We then construct a consistent estimator for the model parameters and develop a Monte Carlo expectation-maximization algorithm to compute it. To address the challenges posed by administrative censoring, we leverage these findings and propose a transfer-learning procedure. Experimental results demonstrate that our method improves the accuracy of timely risk evaluation under administrative censoring.

08.
arXiv (CS.AI) 2026-06-15

AudioDER: A Deduplication-Enhanced Reasoning Dataset for Post-Training Large Audio-Language Models

arXiv:2606.14591v1 Announce Type: cross Abstract: Large Audio-Language Models (LALMs) have shown strong performance on a wide range of audio understanding tasks, yet they still struggle with complex audio reasoning. A practical way to improve such capabilities is post-training, whose effectiveness critically depends on the quality and diversity of training data. However, existing audio-language datasets often contain substantial redundancy, where many samples are highly similar in acoustic content and thus provide overlapping supervisory signals. Such redundancy not only increases annotation cost, but also limits corpus diversity and reduces the effectiveness of post-training. To address this issue, we propose a redundancy-aware data construction pipeline for building reasoning-oriented supervision for LALMs. Specifically, we first perform acoustic similarity-based deduplication across raw audio datasets to improve corpus diversity. We then integrate existing audio captions and question-answer pairs into a unified multiple-choice format. Based on these unified annotations, we leverage Qwen3-30B to generate chain-of-thought (CoT) rationales for reasoning-oriented supervision. Based on this pipeline, we construct AudioDER, a reasoning-oriented post-training dataset containing approximately 191k samples spanning sound, speech, and music. Each sample consists of an audio clip, a multiple-choice question, four answer candidates, an audio caption, and a CoT rationale. Extensive experiments show that post-training on AudioDER consistently improves the performance of Qwen2-Audio-7B-Instruct on multiple audio reasoning benchmarks, including MMAU-mini, MMSU, and MMAR. We hope AudioDER can serve as a valuable resource for advancing audio reasoning research and the development of more capable LALMs.

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

Reframing AI Loss of Control: What It Is, How to Have It, How to Lose It

arXiv:2606.12442v1 Announce Type: cross Abstract: At present, loss of control risks have gained much prominence in public discussion, particularly in relation to AI, with extensive discourse present among academics, frontier labs, and even governments. However, in the existing literature, the concept seems to rest on surprisingly weak foundations, where even those that discuss loss of control extensively do not first establish what control is and what exactly is being lost. Our paper aims to address these gaps. We establish a working definition of control by anchoring it to the "setting and getting of goals". Then, we discuss various aspects of control, built on foundational concepts from related fields like cybernetics, management control, and control theory. This includes who (or what) can be in control, and the things they require to be in control, such as the ability to set goals, having a functional control loop, having requisite variety, and having sufficient goal alignment. Once a framework for control is established, we then discuss how control can be lost, how AIs can contribute to such loss of control, and offer relevant recommendations for how one can maintain control. One interesting consequence of our work is that humanity, as individuals and as groups, can lose varying degrees of control as a result of AI behaviour that is far below the level of superintelligence; the potential for loss of control scenarios (as we define them) already exist, and have existed for a long time.

10.
arXiv (CS.CL) 2026-06-12

From Tokens to Faces: Investigating Discrete Speech Representations for 3D Facial Animation

The choice of speech representation is critical in speech-driven 3D facial animation. Representations differ in what they encode: SSL features emphasize segmental and semantic cues, neural codecs yield latents optimized for acoustic reconstruction, and ASR-style objectives produce label-based spaces. We evaluate four speech representation families for 3D facial synthesis, comparing their facial reconstruction quality across two facial decoders using objective metrics and a perceptual evaluation. We additionally conduct probing analyses that relate tokenized representations to phonetic units and to articulatory deformations. We found that encoding phonetic classes is beneficial for accurate facial animation prediction on both semantic and label-based representations with comparable facial animation quality. From the latter, we introduce an Audio Visual Text-to-Speech (AVTTS) pipeline that leverages, as a shared space, discrete representations to decode speech and 3D facial motion.

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

Confidence Calibration for Multimodal LLMs: An Empirical Study through Medical VQA

arXiv:2606.19950v1 Announce Type: cross Abstract: Multimodal Large Language Models (MLLMs) show great potential in medical tasks, but their elicited confidence often misaligns with actual accuracy, potentially leading to misdiagnosis or overlooking correct advice. This study presents the first comprehensive analysis of the relationship between accuracy and confidence in medical MLLMs. It proposes a novel method that combines Multi-Strategy Fusion-Based Interrogation (MS-FBI) with auxiliary expert LLM assessment, aiming to improve confidence calibration in Medical Visual Question Answering (VQA). Experiments demonstrate that our method reduces the Expected Calibration Error (ECE) by an average of 40\% across three Medical VQA datasets, significantly enhancing MLLMs' reliability. The findings highlight the importance of domain-specific calibration for MLLMs in healthcare, offering a more trustworthy solution for AI-assisted diagnosis.

12.
arXiv (quant-ph) 2026-06-15

Quantum codes and optimal pure quantum $(r,\delta)$-LRCs via the MP construction

arXiv:2606.14253v1 Announce Type: new Abstract: In this paper, we employ MP codes whose defining matrices are $\tau$-optimal defining ($\tau$-OD) matrices to construct new quantum codes and quantum $(r,\delta)$-LRCs. Specifically, we report the following results: We establish a unified $\tau$-monomial decomposition theorem for invertible self-adjoint matrices over finite fields of arbitrary characteristic, which generalizes the result in "Quantum codes using the $\tau$-OD MP construction" where the characteristic was required to be odd. Based on this theorem, we prove the existence of $\tau$-OD matrices over $\mathbb{F}_{q^2}$ for any characteristic and demonstrate that there exist several new infinite families of $\tau$-OD matrices over $\mathbb{F}_{q^2}$ of characteristic $2$. As an application of MP codes involving $\tau$-OD matrices, we construct several infinite families of quantum codes with flexible parameters. Within this framework, we present $222$ record-breaking quantum codes that surpass the best-known records maintained in Grassl's database. We propose two effective schemes for constructing optimal pure quantum $(r,\delta)$-LRCs via MP codes. Accordingly, we construct four new infinite families of optimal pure quantum $(r,\delta)$-LRCs with flexible parameters. Notably, we report an interesting phenomenon by exhibiting $30$ optimal pure quantum $(r,\delta)$-LRCs derived from our framework; that is, there exist quantum codes that are not only optimal pure quantum $(r,\delta)$-LRCs but also, according to Grassl's database, best-known, optimal, or record-breaking quantum codes. To the best of our knowledge, the new discovery that quantum codes are simultaneously optimal pure quantum $(r,\delta)$-LRCs and record-breaking quantum codes has not been previously reported in the literature.

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

Learn-to-learn on Arbitrary Textual Conditioning: A Hypernetwork-Driven Meta-Gated LLM

Conventional LLMs may suffer from corpus heterogeneity and subtle condition changes. While finetuning can create the catastrophe forgetting issue, application of meta-learning on LLMs is also limited due to its complexity and scalability. In this paper, we activate the meta-signal of $\beta$ within the SwiGLU blocks, resulting in a meta-gating mechanism that adaptively adjusts the nonlinearity of FFN. A hypernetwork is employed which dynamically produces $\beta$ on textual conditions, providing meta-controllability on LLMs. By testing on different condition types such as task, domain, persona, and style, our method outperforms finetuning and meta-learning baselines, and can generalize reasonably on unseen tasks, condition types, or instructions. Our code can be found in https://github.com/AaronJi/MeGan.

14.
arXiv (quant-ph) 2026-06-19

Quantum deformations of $\mathcal{U}(\mathfrak{sl}(2, \mathbb{R}))$. Part I: Fidelity and experimental benchmarking

arXiv:2606.19462v1 Announce Type: new Abstract: This work explores the effects of both the standard quantum $q$-deformation and the non-standard $h$-deformation of the Hopf algebra $\mathcal{U}(\mathfrak{sl}(2, \mathbb{R}))$ on multi-qubit systems. By constructing the states of a Hilbert space of $N$ qubits through the Clebsch-Gordan coefficients associated with the deformed algebras, we show that these states naturally coincide with the eigenstates of the Hamiltonian of the $q$- and $h$-deformed Kittel-Shore models. We compare the resulting deformed states with those typically targeted in quantum information experiments, providing a bridge between algebraic constructions and experimentally relevant quantum resources. Fidelities with respect to the undeformed states are computed to establish how the quantum correlations are affected, both for few-qubit systems (including Dicke and non-Dicke states), and in the macroscopic limit ($N \to \infty$) through closed-form formulas derived for arbitrary Dicke states. The results reveal different behaviors between the two deformations. The $q$-deformation smoothly modifies the states and maintains a residual overlap with the original configurations, while the $h$-deformation rapidly makes the states orthogonal to their undeformed counterparts. Both models demand a standard $N^{-1}$ rescaling to preserve fidelity stability in the macroscopic limit.

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

TopoCap: Learning Topology-Agnostic Motion Priors for Monocular Video-to-Animation

The explosion of generative 3D assets has created a massive demand for animation, yet current motion capture methods remain brittle, restricted to species-specific templates (e.g., SMPL) or requiring labor-intensive manual rigging. We introduce TopoCap, the first unified framework capable of extracting motion from monocular video and retargeting it onto characters with arbitrary, unseen skeletal topologies, i.e., from bipeds to hexapods and inanimate objects, without test-time optimization. Our key insight is that while skeletal structures are combinatorial and discrete, the underlying physics of motion occupy a continuous, low-dimensional manifold. We materialize this insight via a two-stage generative pipeline. First, we learn a Universal Motion Manifold using a Graph CVAE that compresses heterogeneous kinematic chains into a shared, fixed-length latent code. By explicitly conditioning the decoder on a structural embedding of the target rig, we disentangle motion dynamics from skeletal topology. Second, we treat video-to-animation as a conditional flow matching problem, predicting these topology-agnostic codes from visual features. To learn this generalized prior, we introduce Mobjaverse, a massive-scale dataset curated from Objaverse-XL. Comprising over 5,000 unique skeletal topologies and 2 million frames, it exceeds the structural diversity of existing datasets by two orders of magnitude. Extensive experiments demonstrate that \MethodMotion outperforms specialist models on human and quadruped benchmarks while enabling zero-shot retargeting for the long tail of 3D creatures. Dataset is publicly available at https://huggingface.co/datasets/duckduckplz/Mobjaverse.

16.
bioRxiv (Bioinfo) 2026-06-15

SMS: Symmetric Mediation Statistics for Powerful High-Dimensional Mediation Analysis

Background: Mediation analysis of high-dimensional features, particularly molecular-level omics features, provides important opportunities to uncover biological mechanisms underlying human health and disease. However, two central statistical challenges remain: testing the composite-null hypothesis and maintaining power when the exposure-mediator and mediator-outcome associations differ substantially in statistical significance. Existing methods typically rely on accurate estimation of the proportions of the three null types or on the maximum of the two association p-values, and may not always control the FDR well and may have limited power under imbalanced significance. Methods: We propose SMS, a new statistical framework based on symmetric mediation statistics. By exploiting symmetry, SMS calibrates the composite null distribution as a whole for FDR control. It also allows flexible combinations of the two association p-values, including the maximum, and then enables construction of an omnibus test. Moreover, it permits direct use of effect-size estimates, bypassing the need to compute p-values. Results: SMS controlled the FDR across a wide range of simulation scenarios while achieving a substantial sensitivity gain, often around 20 percentage points, over existing methods including HDMT, DACT, and DEI-B. Applications to a metabolomics dataset and a DNA methylation dataset further corroborated these findings. Notably, SMS discovered five plausible mediators in the metabolomics dataset that were missed by all existing methods considered.

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

Self-Guidance: Enhancing Neural Codecs via Decoder Manifold Alignment

arXiv:2606.12940v1 Announce Type: cross Abstract: Neural speech codecs based on Vector-Quantized VAEs (VQ-VAEs) are core audio tokenizers for speech LLMs, yet their reconstruction fidelity is bottlenecked by quantization error. Modifying the quantizer or increasing model capacity are common fixes, but they complicate downstream language modeling. Our core idea is to align the decoder's internal feature manifolds when processing both the quantized tokens and their original continuous embeddings, using a lightweight feature-mapping loss. This requires minimal training overhead and no inference-time changes. Applied to XCodec2, self-guidance improves all reconstruction metrics, achieving state-of-the-art low-bitrate performance. Notably, it enables a 4x codebook reduction without fidelity loss, which downstream TTS experiments show significantly improves LLM-based synthesis by simplifying the token modeling space. Multiple statistical observations and visualizations corroborate the enhanced internal manifold alignment in the decoder. Extensive experiments confirm its generality across various inductive biases. Self-guidance thus establishes an efficient, broadly applicable method for high-fidelity neural audio coding.

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

On the Limits of LLM-as-Judge for Scientific Novelty Assessment

arXiv:2606.12071v1 Announce Type: cross Abstract: LLMs are increasingly used to generate and judge scientific ideas. This makes novelty evaluation a central problem. Full idea evaluation is difficult because it often requires judging a method, its feasibility, and its empirical promise. We therefore study a cleaner upstream object: the research question (RQ). RQ generation is a prerequisite for scientific ideation, and RQs can be compared against questions pursued in real papers. We introduce RQ-Bench, a benchmark built from recent arXiv papers. For each paper, we reconstruct author-anchored RQs from its cited background, gaps, and contributions. These RQs are not the only valid questions for the same background. They are author-anchored reference points for testing novelty judgments. We evaluate model-generated RQs with standalone LLM judging, comparative LLM judging, and human expert evaluation. LLM judges consistently rate model-generated RQs as highly novel, producing a novelty mirage; in comparative evaluations, this preference becomes even stronger. Domain experts, however, reach the opposite conclusion and prefer the author-anchored reference questions. We further find that many generated RQs are narrow or source-bound, a dimension that LLM judges often miss unless explicitly tested. Overall, the contradictory novelty evaluations between LLM judges and human experts raise a serious concern about the reliability of using LLMs to assess the scientific novelty of research questions.

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

Cross-lingual Embedding Clustering for Hierarchical Softmax in Low-Resource Multilingual Speech Recognition

We present a novel approach centered on the decoding stage of Automatic Speech Recognition (ASR) that enhances multilingual performance, especially for low-resource languages. It utilizes a cross-lingual embedding clustering method to construct a hierarchical Softmax (H-Softmax) decoder, which enables similar tokens across different languages to share similar decoder representations. It addresses the limitations of the previous Huffman-based H-Softmax method, which relied on shallow features in token similarity assessments. Through experiments on a downsampled dataset of 15 languages, we demonstrate the effectiveness of our approach in improving low-resource multilingual ASR accuracy.

20.
bioRxiv (Bioinfo) 2026-06-22

PhaseWY: A pipeline for haplotype phasing, sex chromosome identification and extraction of sex-limited sequences

Sex chromosomes are central to many ecological and evolutionary processes. Evidence has accumulated that sex chromosome systems vary extensively in age, turnover and transitions, motivating renewed efforts to study the diversity of sex chromosome systems across the tree of life. However, successful genomic detection of sex chromosomes depends on several factors, including the size and divergence time, background genetic diversity, and the number of sequenced females and males. In addition, technical challenges associated with sequencing and analysing the sex-limited Y/W chromosome remain. Here, we present PhaseWY, an automated Snakemake pipeline that uses whole-genome sequencing data from multiple female and male individuals to identify sex-chromosomal regions and extract the corresponding Y/W sequences. PhaseWY (i) detects sex differences in alignment depth, (ii) applies read-based and statistical haplotype phasing, (iii) identifies sex-linked regions using haplotype clustering, and (iv) subsets autosomal, X/Z- and Y/W-linked variants for downstream analyses. We applied PhaseWY to simulated data to benchmark factors influencing sex-linkage detection and successful extraction of Y/W-linked variants. To demonstrate its practical utility, we further applied PhaseWY to the neo-sex chromosome system in Alauda larks (Alaudidae) and performed a range of downstream analyses demonstrating the scope of applications of the PhaseWY output. We conclude that PhaseWY provides an easy-to-use and reproducible tool for population-genomic analyses in non-model organisms, with particular importance for advancing our understanding of sex-chromosome evolution.

21.
arXiv (CS.AI) 2026-06-18

Deep-Learning-Based Pixelated Microwave Filter Design and Characterization using Electro-Optical Electric-Field Measurements

arXiv:2606.18402v1 Announce Type: cross Abstract: Traditional microwave filter design typically relies on iterative parameter tuning and predefined topologies, which limits design space and increases development time. This study uses a deep learning approach combining convolutional neural networks with genetic algorithms to automate pixelated microwave filter synthesis. To validate the approach experimentally, both S-parameter and spatial electric-field measurements were analyzed. The synthesized low-pass filter demonstrated excellent agreement between simulated and measured performance, achieving a 7 GHz passband with over 20 dB suppression beyond 9.5 GHz. Electro-optical measurements, for the first time, revealed electric field patterns that resemble coupled transmission-lines or stub structures, providing insight into the emergent characteristics of AI-generated designs.

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

HierSVA: A Data Synthesis Pipeline, Dataset, and Benchmark for LLM-Driven Hierarchical Hardware Formal Verification

arXiv:2606.13706v1 Announce Type: cross Abstract: We present HierSVA, an integrated suite that combines a pipeline, dataset, and benchmark for LLM-driven hierarchical hardware formal verification. HierSVA-SP pairs an RTL preprocessing toolchain with an LLM-in-the-loop formal verification flow to produce reference SystemVerilog Assertions (SVA) on hierarchical RTL. Applying it to BaseJump STL yields HierSVA-DS, a dataset of 342 modules, with hierarchy metadata and depths 0–9, accompanied by a deep subset of 28 module-bug pairs with natural-language specifications and bug variants. HierSVA-B decomposes assertion quality into six metric axes: syntax correctness, assertion proof success rate, vacuity, specification faithfulness, mutation coverage, and formal core coverage. Applying HierSVA-B to twelve recent LLMs reveals three findings. First, the module-level compile rate is 67.1\%; among generated assertions in evaluable runs, 82.1\% prove non-vacuously, but the corresponding assertion sets detect only 70.2\% of eligible injected faults and cover 36.2\% of the formal core. Second, on 211 evaluable model–module entries in the deep subset, assertion sets flag buggy RTL with 0.87 recall, but 40\% of predicted-buggy outcomes are false positives on correct RTL, limiting precision to 0.60. Third, agentic mode improves S1-style provability and strength metrics, but gains plateau and oscillate. Codes and artifacts are available at \href{https://github.com/HierSVAAnon/HierSVACodeAndArtifacts}{https://github.com/HierSVAAnon/HierSVACodeAndArtifacts}. Dataset is available at \href{https://huggingface.co/datasets/AnonymousHierSVA/HierSVA}{https://huggingface.co/datasets/AnonymousHierSVA/HierSVA}.

23.
medRxiv (Medicine) 2026-06-16

AI-assisted continuous-time modelling of metastatic breast cancer reveals subtype-specific spatiotemporal organ interactions

Metastatic breast cancer is one of the leading causes of premature mortality among women worldwide. A major barrier to optimal care is the marked heterogeneity in both the temporal dynamics of metastatic spread and the organ-specific spatial distribution of metastases. Existing analyses do not adequately capture this complexity, as they either neglect temporal dependencies or assume independence between metastasic sites. As a result, it remains unclear how established metastases influence subsequent organ-specific dissemination. We address this question using patient-level longitudinal trajectories from a large multicentre real-world metastatic breast cancer registry, combined with an AI-assisted disease-progression modelling framework based on continuous-time Markov chains that represent combinations of metastatic sites and the non-uniform and practice-driven timing of radiologic response assessments, as encountered in routine clinical care. We present a stochastic model determined by progression rates, which are parameterised to capture baseline organ-specific transition risks, patient-level covariates, and pairwise inter-organ interaction effects. High-dimensional treatment information is incorporated using an large language model based encoding. We find that metastatic spread follows non-independent, subtype-specific spatiotemporal patterns, with subtype-specific inter-organ interaction patterns that shape progression. Visceral metastases, particularly lung and liver metastasis, are associated with an increased hazard of subsequent brain metastasis, with effects varying across hormone receptor-positive, HER2-positive, and triple-negative subtypes. Together, these findings define a clinically relevant spatiotemporal architecture of metastatic progression in breast cancer. This framework enables refined mechanism-informed risk stratification and provides a data-driven rationale for targeted and risk-adapted – rather than symptom-triggered – surveillance strategies.

24.
arXiv (CS.CL) 2026-06-16

PVminerLLM2: Improving Structured Extraction of Patient Voice via Preference Optimization

Motivation: Patient-generated text contains critical information on patients' lived experiences, social context, and care engagement, but remains largely unstructured, limiting its use in patient-centered outcomes research. Prior work introduced the PV-Miner benchmark and PVMinerLLM models for structured extraction. However, supervised fine-tuning (SFT) alone struggles with rare, fine-grained, and unevenly distributed errors, particularly in token-critical structured outputs. Results: We present PVminerLLM2, an improved set of LLMs for structured patient voice extraction that applies preference optimization to address token-critical errors beyond the reach of supervised fine-tuning. Our method introduces (i) a preference objective with token-level gated stabilization term that prevents degradation of absolute token likelihood under preference optimization, and (ii) confusion-aware preference pair construction to better capture low-separation distinctions. We further incorporate token-importance weighting and inverse-frequency reweighing to address token imbalance and class skew. Across multiple model sizes, PVMinerLLM2 consistently outperforms strong baselines, achieving gains of up to 4.43% (Code), 3.50% (Sub-code), and 1.55% (Span), and outperforms baseline LLM trained with existing preference optimization methods. Availability and Implementation: The supplementary material, code, evaluation scripts, and trained models for PVminerLLM2 are publicly available at: https://github.com/Data-Mining-Lab-Yale/PVminerLLM2

25.
arXiv (CS.CV) 2026-06-17

Structure-Aware Text Recognition for Ancient Greek Critical Editions

Recent advances in visual language models (VLMs) have transformed end-to-end document understanding. However, their ability to interpret the complex layout semantics of historical scholarly texts remains limited. This paper investigates structure-aware text recognition for Ancient Greek critical editions, which have dense reference hierarchies and extensive marginal annotations. We introduce two novel resources: (i) a large-scale synthetic corpus of 185,000 page images generated from TEI/XML sources with controlled typographic and layout variation, and (ii) a curated benchmark of real scanned editions spanning more than a century of editorial and typographic practices. Using these datasets, we evaluate three state-of-the-art VLMs under both zero-shot and fine-tuning regimes. Our experiments reveal substantial limitations in current VLM architectures when confronted with highly structured historical documents. In zero-shot settings, most models significantly underperform compared to established off-the-shelf software. Nevertheless, the Qwen3VL-8B model achieves state-of-the-art performance, reaching a median Character Error Rate of 1.0\% on real scans. These results highlight both the current shortcomings and the future potential of VLMs for structure-aware recognition of complex scholarly documents.