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01.
arXiv (CS.CV) 2026-06-24

A Benchmark of State-Space Models vs. Transformers and BiLSTM-based Models for Historical Newspaper OCR

End-to-end OCR for historical newspapers remains challenging, as models must handle long text sequences, degraded print quality, and complex layouts. While Transformer-based recognizers dominate current research, their quadratic complexity limits efficient paragraph-level transcription and large-scale deployment. We investigate linear-time State-Space Models (SSMs), specifically Mamba, as a scalable alternative to Transformer-based sequence modeling for OCR. We present to our knowledge, the first OCR architecture based on SSMs, combining a CNN visual encoder with bi-directional and autoregressive Mamba sequence modeling, and conduct a large-scale benchmark comparing SSMs with Transformer- and BiLSTM-based recognizers. Multiple decoding strategies (CTC, autoregressive, and non-autoregressive) are evaluated under identical training conditions alongside strong neural baselines (VAN, DAN, DANIEL) and widely used off-the-shelf OCR engines (PERO-OCR, Tesseract OCR, TrOCR, Gemini). Experiments on historical newspapers from the Bibliotheque nationale du Luxembourg, with newly released >99% verified gold-standard annotations, and cross-dataset tests on Fraktur and Antiqua lines, show that all neural models achieve low error rates (~2% CER), making computational efficiency the main differentiator. Mamba-based models maintain competitive accuracy while halving inference time and exhibiting superior memory scaling (1.26x vs 2.30x growth at 1000 chars), reaching 6.07% CER at the severely degraded paragraph level compared to 5.24% for DAN, while remaining 2.05x faster. We release code, trained models, and standardized evaluation protocols to enable reproducible research and guide practitioners in large-scale cultural heritage OCR available at https://github.com/MarcoPerson/ssm-ocr-benchmark.

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

Progressive Pixel-Neighborhood Deformable Cross-Attention for Multispectral Object Detection

Effective cross-modal feature alignment and interaction are central challenges in multispectral object detection. Although global cross-attention provides strong long-range modeling ability, its quadratic complexity with respect to feature size limits deployment on resource-constrained platforms. We therefore propose Progressive Pixel-Neighborhood Deformable Cross-Attention for multispectral feature fusion, termed PNAFusion. The proposed framework is motivated by two observations: weak misalignment between visible and thermal images is usually concentrated around local neighborhoods, and semantic correspondence across modalities often follows non-linear spatial mappings that fixed receptive fields cannot model well. To address these issues, PNAFusion incorporates local spatial priors into its architectural design to concentrate feature interaction and alignment on the most relevant neighborhoods. Specifically, a Pixel-Neighborhood Cross-Attention (PNCA) module is introduced to avoid redundant global feature matching and suppress background noise. Meanwhile, an Adaptive Deformable Alignment (ADA) module captures non-linear spatial correspondences through learned pixel-wise offsets. These components are further integrated through an iterative feedback mechanism to progressively refine cross-modal feature alignment. Experiments on FLIR, M3FD, and DroneVehicle show that PNAFusion achieves 84.2, 90.5, and 85.5 mAP@0.5, respectively, under the YOLOv5 detector, and further reaches 86.8 mAP@0.5 on FLIR and 90.8 mAP@0.5 on M3FD when transferred to Co-DETR. Efficiency analysis indicates that PNAFusion reduces allocated GPU memory by 33.0\% compared with ICAFusion and reduces theoretical FLOPs from 194.8 G to 156.4 G, although the deformable sampling and iterative refinement introduce additional latency. Our code will be available at https://github.com/DanielQiuTian/PNAFusion.

03.
arXiv (CS.CV) 2026-06-24

ObsGraph: Hierarchical Observation Representation for Embodied Reasoning and Exploration

Embodied reasoning and exploration are increasingly considered crucial abilities for robots operating in complex and unfamiliar environments. To accomplish tasks in such settings, an agent must identify and acquire the information necessary for the task through exploration. We propose ObsGraph, an observation-centric hierarchical scene graph that unifies scene representation, retrieval, and exploration. It retains visual evidence and organizes it into room-view-object layers: rooms provide coarse semantic anchors, views preserve contextual object covisibility, and objects store fine-grained details. On top of this representation, we perform coarse-to-fine hierarchical retrieval under a bounded budget, and crucially use retrieval outcomes to structure the exploration candidate space–activating room-level exploration, view refinement, or frontier exploration–thereby tightly coupling representation, retrieval, and adaptive multi-scale exploration. Experiments across embodied reasoning and exploration benchmarks demonstrate improved success and efficiency, highlighting the benefits of structured scene representation and more targeted information gathering driven by identified evidence gaps.

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

Evaluation of Alternative-Based Information Systems for Deliberative Polling using an Agentic Simulator

arXiv:2606.11692v1 Announce Type: cross Abstract: Deliberative polling promises to improve collective decision-making by exposing shareholders to a broad range of arguments before they vote. Yet ensuring that every voter encounters a representative sample of the reason space, the coverage problem, remains an open challenge, particularly at scale and in adversarial or strategically motivated electorates. This paper introduces a way of evaluating solutions using the LLM-based Agentic Bipolar Argumentation Simulator, grounded in a framework which formalises a poll as a six-tuple of endorsing and opposing justifications, attack and enhance relations, and shareholder- and relation-weights. ABAS simulates N autonomous shareholder agents, each assigned a latent opinion according to desired distributions in [-1, 1], who sequentially vote, choose or author justifications, and optionally submit argumentation-graph links. The simulator implements recommendations that rank existing justifications by their observable endorsement mass. It evaluates the mechanism's success by coverage, namely the fraction of the corpus reason-tag set represented in the K recommendations presented to each shareholder, as a solution to the NP-hard Subsuming Justification Problem. Reported experiments characterise how creativity rate (pown), recommendation size (K), argumentation density (plinks), and population size (N) affect coverage and corpus diversity. In an authenticated electorate where Sybil attacks are impossible and only the relation graph is gameable, we stress-test the scoring with coordinated strategic voting attacks: a tag-flood attack collapses coverage, while author-count relation weighting through a reversed-PageRank rule resists the flood markedly better than uniform weights.

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

An Improved Generative Adversarial Network for Micro-Resistivity Imaging Logging Restoration

An improved GAN-based imaging logging image restoration method is presented in this paper for solving the problem of partially missing micro-resistivity imaging logging images. The method uses FCN as the generative network infrastructure and adds a depth-separable convolutional residual block to learn and retain more effective pixel and semantic information; an Inception module is added to increase the multi-scale perceptual field of the network and reduce the number of parameters in the network; and a multi-scale feature extraction module and a spatial attention residual block are added to combine the channel attention. The multi-scale module adds a multi-scale feature extraction module and a spatial attention residual block, which combine the channel attention mechanism and the residual block to achieve multi-scale feature extraction. The global discriminative network and the local discriminative network are designed to gradually improve the content and semantic structure coherence between the restored parts and the whole image by playing off each other and the generative network. According to the experimental results, the average structural similarity measure of the five sets of imaged logging images with different sizes of missing regions in the test set is 0.903, which is an improvement of about 0.3 compared with other similar methods. It is shown that the method in this study can be used for the restoration of micro-resistivity imaging log images with good improvement in semantic structural coherence and texture details, thus providing a new deep learning method to ensure the smooth advancement of the subsequent interpretation of micro-resistivity imaging log images.

06.
medRxiv (Medicine) 2026-06-10

Prediction of immunotherapy response using live tumor fragments from routine clinical biopsies

Functional ex vivo assays using live tumor tissues have demonstrated strong predictive accuracy for response to immune checkpoint inhibitors (ICIs) but are not scalable, requiring manual processing of large resections collected at academic centers. Here, an ex vivo live tumor fragment (LTF) platform was developed using standard-of-care biopsies from 228 patients with suspected malignancy collected across prospective, multicenter observational trials and biobanks. Hierarchical clustering of ICI-mediated changes in cytokine production identified two groups: responders and nonresponders. A binary classifier (elive index) using 8 cytokines achieved an AUC of 0.99 for cluster prediction. elive index correctly predicted clinical benefit in 93% (26/28) of patients (P = 3.2x10-5) and accurately identified 83% (10/12) of objective responders. Critically, elive responders were identified among biomarker-negative patients, highlighting the platform as a scalable approach that complements existing companion diagnostics and expands the population of patients identified to benefit from ICI therapy.

07.
arXiv (quant-ph) 2026-06-12

Symmetry and Topology of Monitored Quantum Dynamics

arXiv:2412.06133v4 Announce Type: replace-cross Abstract: The interplay between unitary dynamics and quantum measurements induces diverse phenomena in open quantum systems with no counterparts in closed quantum systems at equilibrium. Here, we generally classify Kraus operators and their effective non-Hermitian dynamical generators, thereby establishing the tenfold classification for symmetry and topology of monitored free fermions. Our classification elucidates the role of topology in measurement-induced phase transitions and identifies potential topological terms in the corresponding nonlinear sigma models. Furthermore, we establish the bulk-boundary correspondence in monitored quantum dynamics: nontrivial topology in spacetime manifests itself as topologically nontrivial steady states and gapless boundary states in Lyapunov spectra, such as Lyapunov zero modes and chiral edge modes, leading to the topologically protected slowdown of dynamical purification.

08.
bioRxiv (Bioinfo) 2026-06-18

Benchmarking gene expression reconstruction from single-cell latent representations

Single-cell transcriptomics is typically modeled in low-dimensional latent representations that improve the signal-to-noise ratio of the data. Such representations underpin data integration, cell state discovery, and perturbation prediction, with applications ranging from large-scale organ atlases to latent trajectory modeling. Recent virtual cell approaches further leverage these representations to predict cellular responses as distributional shifts in latent space. Each of these applications ultimately requires faithful gene expression reconstruction from latent spaces for biological interpretation, enabling gene-level analysis of predicted perturbed or batch-corrected cells. Yet representation choice is typically treated as an implementation detail rather than a primary modeling decision, with no systematic evaluation of how well latent representations support gene expression reconstruction. Here, we introduce ReconEval, a benchmark for evaluating gene expression reconstruction from single-cell latent spaces. We benchmark two classes of latent representations: end-to-end trained models such as PCA, autoencoders, and variational autoencoders, and pretrained single-cell foundation model embeddings coupled to newly trained decoders. Reconstruction is evaluated both directly and after latent-space perturbation prediction. Across perturbational and observational datasets totaling over 100 million cells, our metric suite quantifies statistical fidelity; biological signal preservation, including differential expression, coexpression, cell-cycle structure, cytokine response and pathway activity; and perturbation-specific effects. We find that autoencoders achieve the strongest stand-alone reconstruction at low dimensionality, while variational regularization does not improve generalization in reconstruction. Frozen foundation model embeddings retain recoverable gene-level information, with reconstruction quality depending strongly on decoder architecture and pretraining objective. In latent perturbation modeling, high-dimensional PCA matches foundation model embeddings, while low-dimensional AE embeddings are optimal for flow-based generative models. Overall, reconstruction depends critically on the interplay between representation and downstream model, and simpler representations can outperform complex alternatives given appropriate capacity. Our benchmark establishes reconstruction as a critical evaluation axis for single-cell foundation models. We envision it improving the biological interpretability of latent-space modeling, a prerequisite for future virtual cell models to be validated by domain experts and grounded in biology.

09.
arXiv (CS.CV) 2026-06-16

Scribby: A Multi-Level LLM Framework for Semantic Video Analysis

As video content continues to expand across educational platforms, recorded lectures, and live-streamed entertainment, the need for efficient and structured analysis of long-form footage has increased [1]. Although many existing AI programs provide high-level video summaries based on AI-generated transcripts [2,3,4,5], these approaches are often limited to coarse overviews and lack detailed analysis of a video's structure, thematic progression, and semantic relationships, all of which are required for comprehensive video analysis. This paper proposes an LLM-based video summarization framework that balances macro-level comprehension with micro-level semantic analysis [6,12,13]. The first stage of the process indexes the video at a micro level by (1) analyzing the full transcript, (2) analyzing individual transcript sentences, and (3) grouping these sentences by semantic similarity using an LLM as a judge [6,13]. Contextual continuity is retained during sentence-level processing by incorporating both the global transcript analysis and adjacent sentence information into each evaluation prompt. This framework establishes a foundation for video analysis tools that visualize semantic chunking and semantic matching through relevance-based heatmaps. Limitations and future expansions of the framework are also discussed.

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

Does VLA Even Know the Basics? Measuring Commonsense and World Knowledge Retention in Vision-Language-Action Models

arXiv:2606.19297v1 Announce Type: new Abstract: Embodied Vision-Language-Action (VLA) models are typically obtained by fine-tuning powerful pretrained VLMs on robotics data, yet it is unclear how much commonsense and factual knowledge they retain after adaptation. Failures on knowledge-sensitive tasks are ambiguous, conflating missing knowledge with poor generalization of low-level control. We introduce Act2Answer, a lightweight protocol that adapts VLM knowledge benchmarks to VLA evaluation by requiring agents to answer through action. Each question becomes a short tabletop episode where the agent performs a single object-placement action to select among candidate answers, yielding an action-grounded success rate with reduced control confounds. We curate a test suite of such environments across diverse commonsense and world-knowledge categories and introduce layerwise intent probing to localize answer-relevant information across the VLM backbone and action head. In a large-scale study of 7 VLA models and 9 VLM baselines, we systematically rank models across categories, finding that VLAs show solid performance on simple concepts while exhibiting larger gaps on richer semantic categories relative to their source VLMs, that VQA co-training is associated with better knowledge retention, and that answer-relevant signals peak in middle VLA layers but attenuate in upper layers. Act2Answer is available at https://tttonyalpha.github.io/act2answer/.

12.
arXiv (math.PR) 2026-06-16

Quantitative Oppenheim Conjecture for Random Quadratic Forms and Optimal Variance Bounds in Function Fields

arXiv:2606.16699v1 Announce Type: cross Abstract: We prove a quantitative version of Oppenheim's conjecture in the function field setting. In order to do so, we compute the higher moments of the Siegel transform. In particular, we find an optimal bound on the variance of the number of lattice points in a set. Moreover, we compute the exact variance of the number of lattice points in a ball, which is of independent interest.

13.
arXiv (CS.AI) 2026-06-24

Token Complexity of Certifying Stochastic-Oracle Reliability

Authors:

arXiv:2606.24074v1 Announce Type: cross Abstract: Wang[Wang2026] introduced the Stochastic-Oracle Turing Machine (SOTM) framework and defined token complexity as the minimum expected cost of interacting with a stochastic oracle needed to attain a specified solution quality for a task. This paper develops an analogous notion for certifying the reliability of a stochastic oracle on a given domain. Certification token complexity is the minimum expected token cost required, with controlled error probability, to distinguish oracles that meet a target reliability level from those that fall below a lower reliability threshold. We construct an SPRT-based certification SOTM that queries the oracle, computes binary correctness scores, and stops when the accumulated log-likelihood evidence crosses a decision threshold. The SOTM halts almost surely, satisfies the desired two-sided error guarantee over the reliability regions to be certified, and yields an explicit upper bound on certification token complexity in terms of the reliability thresholds, the error bound, and the expected per-turn token cost. We then establish a matching information-theoretic lower bound: even with adaptive queries, every error-bounded certification SOTM must incur the same leading-order expected token cost as the SPRT-based construction as the prescribed error bound tends to zero. Together, these bounds characterize the leading-order certification token complexity in the small-error regime.

14.
arXiv (math.PR) 2026-06-11

Construction of ergodic IDLA forests in $\mathbb{Z}^d$

arXiv:2506.10476v2 Announce Type: replace Abstract: We prove the existence of infinite-volume IDLA forests in $\mathbb{Z}^d$ , with $d \geq 2$, based on a multi-source IDLA protocol. Unlike IDLA aggregates, the laws of the IDLA forests studied here depend on the trajectories of particles, and then do not satisfy the famous Abelian property. Their existence is due to a stabilization result (Theorem 1.1, our main result) that we establish using percolation tools. Although the sources are infinitely many, we also prove that each of them play the same role in the building procedure, which results in an ergodicity property for the IDLA forests (Theorem 1.2).

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

Hierarchical Modeling of ICD Codes in EHR Foundation Models

arXiv:2606.15447v1 Announce Type: new Abstract: Electronic health record foundation models typically treat ICD diagnosis codes as flat tokens, overlooking the clinically meaningful hierarchical structure that captures disease families, subcategories, and fine-grained diagnostic detail. As a result, existing EHR representation learning methods do not explicitly exploit the hierarchical structure already present in the coding system. In this work, we study ICD-10-CM hierarchy as a general inductive bias for clinical representation learning. We investigate two complementary mechanisms for incorporating hierarchy: first, by augmenting diagnosis sequences in a BERT-style transformer with tokens corresponding to different levels of the ICD hierarchy, and second, by injecting hierarchy into graph-based code representations through hierarchy-aware edges combined with diagnosis co-occurrence structure. Across these settings, we evaluate whether explicit hierarchy improves downstream prediction, which levels of the hierarchy are most useful, whether hierarchy encoding improves transfer across datasets, and how hierarchy reshapes embedding similarity structure. We conduct experiments on two large-scale real-world clinical datasets: MIMIC-IV, used for pretraining and in-domain evaluation, and eICU, used to assess cross-dataset transfer via frozen encoder probing. Our findings show that explicitly encoding ICD hierarchy improves over flat code representations in both in-domain and cross-dataset settings, while revealing that the most useful level of hierarchy depends on both the task and the modeling approach. More broadly, we focus on hierarchy-aware EHR representation learning and show that the benefits of encoding hierarchy are generalizable across modeling settings and hierarchy levels.

16.
arXiv (quant-ph) 2026-06-17

Experimental Characterization and Modeling of Measurement-Induced State-Transitions in a Fluxonium Superconducting Qubit

arXiv:2606.17866v1 Announce Type: new Abstract: Superconducting qubits are most often measured using dispersive readout, which, ideally, implements a projective quantum non-demolition (QND) measurement. While a larger readout drive can increase the signal and, thus, reduce discrimination errors in the readout, strong microwave drives may also cause non-QND errors by driving the qubit to a state outside the computational subspace. In this work, we experimentally characterize measurement-induced state transitions (MIST) in a fluxonium qubit over its full external flux range. We further numerically calculate the MIST errors, and find that the theory accurately predicts eleven experimentally identified regions with increased MIST. In addition to transitions to higher fluxonium levels, we also find that, at certain flux points, MIST errors are dominated by transitions that include the transmission-line-like array modes of the fluxonium's superinductor. The excellent match between theory and experiment validates that the models accurately predict the occurrence of MIST in these systems, and further highlights the influence of array modes in fluxonium readout.

17.
medRxiv (Medicine) 2026-06-22

A Randomized, Controlled, Double Blind Clinical Study to Evaluate Use of Hydron Alkaline Ionised Water (HAIW) in Healthy Participants

Background and Objectives: Alkaline Ionized Water (AIW) is considered among the highest quality healthy drinking water worldwide and is widely discussed for its various health benefits. Hydron Alkaline Ionized Water (HAIW) is produced through electrolysis, resulting in a stable pH of approximately 9.5 with a negative Oxidation Reduction Potential (ORP), making it an antioxidant beverage. The objective of this study was to evaluate the safety of HAIW and its effects on digestion, sleep, energy, and overall quality of life in healthy participants compared to Packaged Drinking Water (PDW). Materials and Methods: A randomized, controlled, double blind, prospective clinical study was conducted in which a total of 24 healthy participants between the age group of 21 to 40 years were randomized in a 1:1 ratio to either HAIW Group or Packaged Drinking Water Group with equal gender distribution. Participants were hospitalized for 7 days and asked to consume at least 3 litres of the assigned water daily. Primary outcomes were safety-related laboratory parameters and adverse event monitoring. Secondary outcomes included assessment of digestion (appetite, digestion, bowel habits), urine parameters, sleep quality, freshness after waking, fatigue, energy/stamina/strength, quality of life, and global assessment Results: All 24 participants completed the study with no dropouts. Baseline demographics were comparable between the two groups. Assessment of primary safety-related laboratory parameters including Complete Blood count, liver function tests, renal function tests, blood sugar, Electrocardiogram and serum electrolytes showed non-significant change from baseline to 7 days and remained within normal limits in both groups, with non-significant difference between groups (p>0.05). HAIW showed significantly better improvement in appetite, digestion, and bowel habits from Day 2 onwards compared to Packaged drinking water. Sleep quality and freshness after waking up showed significant improvement from Day 3 and Day 2 respectively in the HAIW and PDW group, with significantly better improvement in HAIW group. Fatigue scores showed significant reduction at Day 6 and 7 in both groups with non-significant difference between groups. A total of 5 adverse events were reported (3 in HAIW, 2 in PDW), all unrelated to study products and were mild in nature. Global assessment showed excellent to good overall safety and tolerability in both groups. Conclusion: HAIW was well tolerated by all participants without any adverse effects. All laboratory safety parameters remained within normal range. HAIW demonstrated significant improvements in digestive function (appetite, digestion, bowel habits), sleep quality, and freshness after waking as compared to PDW. The study concludes that HAIW can be safely consumed. HAIW improves digestive and sleep-related functions.

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

Traditional machine learning vs. deep learning from dynamic graph representations of proteins' 3D folds in the task of protein structure classification

arXiv:2605.29228v2 Announce Type: replace Abstract: Protein structure classification (PSC) uses supervised learning to predict a protein's CATH/SCOP(e) class from the protein's sequence or 3D structural feature(s). We already modeled 3D structures as (static) protein structure networks (PSNs), demonstrating the competitiveness of PSN-based features to sequence or direct (i.e. non-network) 3D structural features in the PSC task. More recently, we demonstrated the power of features extracted from dynamic PSNs over features extracted from static PSNs (and thus by transitivity over sequence and direct 3D structural features) in the same task. That dynamic PSN approach used traditional machine learning (ML), combining manual (pre-engineered) features with an off-the-shelf classifier. Here, we evaluate whether automatic deep learning (DL) from the dynamic PSNs yields improvements. Our evaluation on 72 datasets spanning ~44,000 CATH- or SCOPe-labeled dynamic PSNs reveals that in terms of PSC accuracy, traditional ML and DL are (close to) tied for a large majority of the datasets, while DL is on average 10+ times slower. We are the first to evaluate traditional ML vs. DL in the dynamic PSN-based PSC task.

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

ADORE: Iterative Query Expansion with Retrieval-Grounded Relevance Feedback

LLM-based query expansion improves retrieval by enriching the original query with additional context. Yet most methods remain generation-driven, producing plausible pseudo-documents or expansions without checking how the target corpus responds. This can introduce retrieval drift, amplify misleading vocabulary, or miss terms that distinguish relevant from non-relevant documents. We argue that effective expansion requires retrieval-grounded feedback, not just single-pass generation or unverified iteration. We introduce ADORE (ADapt, Observe, Relevance Evaluate), an iterative framework that turns retrieval outcomes into feedback for the next expansion. At each round, an LLM generates pseudo-passages, a retriever exposes the corpus response, and a relevance assessor evaluates retrieved documents against the original query. These judgments identify what to reinforce, what remains undercovered, and what to suppress. Across TREC Deep Learning, BEIR, and BRIGHT, ADORE consistently outperforms strong query expansion baselines with notable improvements across nearly all evaluation settings, improving average nDCG@10 by 24.5% over BM25 and 3.6% over the strongest prior query expansion method on BEIR, and by 122.9% over BM25 and 9.2% over the best query expansion baseline on BRIGHT. Our code and data are publicly available.

20.
bioRxiv (Bioinfo) 2026-06-08

DipSkmer: Reference-free population genomics with diploid genome skims

Ecologists and conservation biologists rely on genetic diversity as a key essential biodiversity variable (EBV) used to track population health and dynamics, and utilize the population parameter {theta} (estimated by the average pairwise genomic distance) as a key metric of diversity. While whole-genome-sequencing (wgs) is increasingly affordable, it will be considerable time before the full diversity of life is represented by high-quality assembled genomes; even then, constant monitoring will still require repeated sampling of populations. In contrast, genome skimming (low-coverage, short-read wgs) is highly cost-effective but challenging to analyze because the coverage is too low for assembly and reliable error correction. Mature methods, such as Mash, exist for estimating pairwise genomic distances based on the Jaccard similarity of k-mer sets computed using sketching techniques. Some, such as Skmer, additionally model the impacts of low coverage. These methods have been successfully applied to assembly-free species identification and phylogenetics; however, their use in population genetics has been limited. This is because these methods implicitly treat genomes as haploid and heterozygosity confounds true estimates of genomic distance for diploid organisms. In this paper, we address this problem through a number of technical advances. First, we use coalescent theory to mathematically derive how the Jaccard index between two diploid samples changes with the scaled population size parameter ({theta}). Next, we derive an estimator that computes {theta} from the Jaccard index, in addition to several auxiliary variables, which we also estimate from the genome skims. The resulting method, DipSkmer, enables more accurate estimates of coverage, sequencing error, and pairwise nucleotide distance for diploid samples. Analyses of both simulated and empirical datasets show that for diploids and low distances (e.g.,

21.
arXiv (CS.LG) 2026-06-16

Greedy Coordinate Diffusion: Effective and Semantically Coherent Adversarial Attacks via Diffusion Guidance

arXiv:2606.15531v1 Announce Type: new Abstract: Fine-tuning aligned language models on benign tasks (e.g. math tutoring) systematically breaks safety guardrails, even when training data contains no harmful content. While mechanistic approaches have shed light on where alignment resides in model weights, they do not by provide a general formal framework for deriving guarantees about when fine-tuning degrades it – leaving the field without principled tools for predicting or preventing alignment collapse. We develop a local geometric framework through geometric analysis of parameter-space trajectories and apply it to understand the fragility of alignment in fine-tuning. While first-order analysis suggests orthogonal updates are safe, we prove this is illusory: the curvature of the fine-tuning loss induces second-order acceleration that can induce second-order drift into alignment-sensitive regions. We formalize a construct of our framework as the Alignment Instability Condition (AIC), three geometric properties that, when present, are sufficient to guarantee degradation. Our main result proves quartic onset of alignment degradation along gradient-flow trajectories, determined by how sharply alignment depends on specific parameters and how strongly tasks couple to these parameters. These findings yield formal sufficient conditions under which static first-order protection can fail under gradient descent. We further empirically validate the framework's foundations, showing that the Fisher Information Matrix provides a proxy for the degree of safety degradation across diverse fine-tuning.

22.
arXiv (CS.LG) 2026-06-11

Range-Aware Bayesian Optimization for Discovering Diverse Designs within Target Property Windows

arXiv:2606.11574v1 Announce Type: new Abstract: In many materials and product design problems, desirable candidates exhibit properties that fall within an acceptable range rather than achieve a single optimum. Recovering multiple, distinct solutions that satisfy such specifications is also practically valuable, as some candidates may be preferred for reasons of cost, processability, or robustness that are difficult to encode directly in an objective function. Here, we develop a range-aware Bayesian optimization (BO) framework in which the acquisition function directly scores the posterior probability that a candidate satisfies a target range. The framework naturally extends to parallel pursuit of multiple distinct specifications over a shared candidate space. Across benchmark tasks, range-aware acquisition consistently recovers larger and more diverse sets of valid designs than standard BO baselines and recent goal-seeking methods. Its utility is further demonstrated in two practically motivated design case studies involving optimizing reaction conditions for polymer synthesis and sequence-defined oligomer discovery for prescribed optical absorption bands, supported by quantum chemical calculations. These results suggest that range-aware BO can provide a practical and sample-efficient foundation for specification-driven design, particularly when design flexibility and solution diversity are important considerations.

23.
arXiv (CS.CL) 2026-06-11

Compatibility-Aware Dynamic Fine-Tuning for Large Language Models

Supervised Fine-Tuning (SFT) is the predominant paradigm for aligning large language models (LLMs), yet it suffers from optimization instability and limited generalization. Recent work attributes this issue to pathological gradient scaling and proposes Dynamic Fine-Tuning (DFT) to correct it at the token level. However, DFT assumes all demonstrations are equally suitable learning targets, an assumption violated by the strong heterogeneity of large-scale instruction data, where demonstration-policy mismatch induces high-variance updates at the sample level. We introduce Compatibility-Aware Dynamic Fine-Tuning (CADFT), a principled extension of DFT that controls sample-level optimization variance. CADFT derives a dynamic, policy-dependent compatibility signal from model likelihoods to modulate supervised updates, suppressing high-variance gradients from incompatible demonstrations. We further propose a delayed, low-frequency compatibility-guided rewriting strategy to transform persistently incompatible demonstrations into learnable targets. We show that CADFT can be interpreted as a variance-controlled estimator that generalizes token-level stabilization in DFT to the sample level. Extensive experiments demonstrate improved stability, generalization, and cold-start reinforcement learning initialization, while remaining fully supervised and independent of explicit reward modeling.

24.
arXiv (CS.LG) 2026-06-15

Graph Structured Combinatorial Semi-Bandit with Nonlinear Reward Associations through Separable Signals

arXiv:2606.14650v1 Announce Type: new Abstract: The identification of optimal structures within vast arrays of interconnected data necessitates significant sampling- and computational effort. Learning and leveraging underlying signal dependencies can improve efficiency and predictive capabilities considerably, but the ubiquity of nonlinear statistical relations amplifies the complexity of such undertakings. In this paper, we develop novel generic and adaptive strategies equipped with routines for graph-based causal reward modeling, analytic reproducing kernel methods, and Taylor approximation of functional processes. We establish theoretical performance guarantees sublinear in time and linear in data volume over time. Our analyses cover robustness to a multitude of uncertainties arising from noise interference, gradual model convergence, and solution space mismatch. The framework's general appeal is substantiated by a minimalistic set of conditions or reliance on prior estimates, while various outlined modifications address specific or extended settings. To demonstrate practical effectiveness, we conduct numerical experiments using both benchmarked synthetic and real-world transportation datasets.

25.
arXiv (CS.AI) 2026-06-18

Enhancing Fatigue Detection through Heterogeneous Multi-Source Data Integration and Cross-Domain Modality Imputation

arXiv:2507.16859v5 Announce Type: replace-cross Abstract: Fatigue detection for human operators is important in safety-related applications such as aviation, mining, and long-haul transport. Reliable estimation of operator fatigue can support timely warnings, adaptive task scheduling, takeover reminders, and other safety-management decisions in human-machine systems. However, the effectiveness of these functions depends on whether fatigue-related signals can be reliably captured in the deployment environment. While many studies have shown the value of high-fidelity sensors in controlled laboratory environments, their performance often degrades when used in real-world settings because of noise, lighting conditions, and field-of-view constraints, thereby limiting their practical use. This paper formalizes a deployment-oriented setting for real-world fatigue detection, where high-quality sensors are often unavailable in practical applications. To address this issue, we use knowledge from heterogeneous source domains, including high-fidelity sensors that are difficult to deploy in the field but commonly used in controlled environments, to assist fatigue detection in the real-world target domain. Based on this idea, we design a heterogeneous and multi-source fatigue-detection framework that uses the available modalities in the target domain while leveraging diverse configurations in the source domains through cross-domain modality imputation based on shared modalities.