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01.
arXiv (CS.CV) 2026-06-17

Future Dynamic 3D Reconstruction: A 3D World Model with Disentangled Ego-Motion

Forecasting the evolution of dynamic environments is crucial for autonomous agents. While generative world models have recently achieved high photorealism in 2D video synthesis by mixing ego-motion and environmental dynamics within the image plane, they exhibit physical inconsistencies, such as morphing or vanishing objects, especially over long time horizons. In this paper, we propose FR3D, a world model that predicts a persistent 3D latent representation for future dynamic 3D reconstruction. Unlike prior works that treat the world as a sequence of image-based features, FR3D explicitly decouples the 3D evolution of the scene from the agent's trajectory, treating the inferred ego-motion as a latent proxy for action. This disentanglement resolves the ambiguities between self-motion and world-motion, ensuring geometric consistency into the future. Furthermore, we introduce a teacher-student distillation strategy that leverages the spatial "common sense" of off-the-shelf foundation models, leading to robust zero-shot generalization. Extensive experiments demonstrate FR3D's strong performance for future dynamic 3D reconstruction from monocular observations across multiple datasets, even 2 seconds into the future. Project page: https://fr3d-wm.github.io.

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

NeRD: Neuro-Symbolic Rule Distillation for Efficient Ontology-Grounded Chain-of-Thought in Medical Image Diagnosis

Interpretability is essential for trustworthy medical image diagnosis. However, existing concept-driven interpretable methods have key limitations: Concept Bottleneck Models (CBMs) require scoring all predefined concepts at inference time and for manual intervention, imposing a substantial burden on clinicians, while rationale-based generative approaches often select concepts by class discriminability, which can drift from diagnostic ontologies. To address these issues, we propose Neuro-Symbolic Rule Distillation (NeRD), a framework that produces efficient, ontology-grounded reasoning chains that are sufficient yet non-redundant, without manually crafting diagnostic rules. Experiments on two skin datasets demonstrate strong diagnostic performance and interpretability, and blinded expert evaluation confirms the clinical plausibility of NeRD rationales. Our method further enables a first expert-in-the-loop study for Multimodal Chain-of-Thought-based diagnosis, achieving efficient and effective concept-level intervention.

03.
arXiv (CS.LG) 2026-06-18

Estimating carbon pools in the European Shelf sea environment: replacing reanalysis by model-informed machine learning?

arXiv:2508.10178v3 Announce Type: replace-cross Abstract: Shelf seas are important for the economy and the carbon cycle, but shelf sea observations for carbon pools are often sparse, or highly uncertain. An alternative can be provided by carbon reanalyses (whether assimilating proxy variables, such as chlorophyll-$a$, or directly carbon), but these are often expensive to run. We propose to use a computationally cheap ensemble of neural networks (i.e. deep ensemble) to learn the relationship between the directly observable (atmospheric, riverine and ocean) variables and marine carbon pools from a coupled physics-biogeochemistry model. The deep ensemble was trained on a North-West European Shelf (NWES) physical-biogeochemistry model free run simulation. After training, the deep ensemble was run using inputs from the NWES reanalysis instead of the free run, demonstrating that it can efficiently predict several NWES carbon pools (e.g., detritus, zooplankton, heterotrophic bacteria) in much better agreement with the reanalysis than the free run, while also providing uncertainty information. We further show that the deep ensemble performs similarly well when it is driven directly by the observations assimilated into the reanalysis, with the limitation that carbon pools can then be predicted only at the observed locations and times. We focus on explainability of the results and demonstrate potential use of the deep ensembles for future climate what-if scenarios. We suggest that model-informed machine learning presents a viable alternative to expensive reanalyses and could complement observations, wherever they are missing and/or highly uncertain.

04.
arXiv (CS.CL) 2026-06-17

Learning from the Self-future: On-policy Self-distillation for dLLMs

On-policy self-distillation (OPSD) has proven effective for post-training large language models (LLMs), yet its application to diffusion LLMs (dLLMs) remains unexplored. Existing OPSD methods are inherently autoregressive-centric. They inject privileged information via left-to-right prefix conditioning with token-level divergence supervision, a design that fundamentally conflicts with the arbitraryorder generation of dLLMs. We introduce d-OPSD, the first OPSD framework tailored for dLLMs. Our approach makes two core contributions. First, we reframe self-teacher construction by using self-generated answers as suffix conditioning, enabling the student model to learn from "self future-experience" rather than privileged prefixes. Second, we shift supervision from token-level to step-level, aligning training with the iterative denoising process of dLLMs. Experiments across four reasoning benchmarks show that d-OPSD consistently outperforms RLVR and SFT baselines with superior sample efficiency, requiring only around 10% of the optimization steps by RLVR and opening a promising pathway for dLLM posttraining. The code is available at https://github.com/xingzhejun/d-OPSD.

05.
arXiv (CS.AI) 2026-06-17

FllumaOne: A Code-Native Multimodal CAD Dataset with Executable Programs and Kernel-Validated Feature Histories

作者:

arXiv:2606.17696v1 Announce Type: new Abstract: Parametric computer-aided design records both final geometry and the ordered construction history that determines how a part can be edited. Datasets for editable CAD research should therefore expose modeling operations, parameters, and feature dependencies together with validated geometry. We introduce FllumaOne, a code-native multimodal CAD dataset whose models are generated by executable Python programs in Flluma, a Qt/C++ OpenCASCADE-based CAD system. Each sample aligns its program with a structured feature tree, a training-oriented intermediate representation, STEP geometry, a surface point cloud, natural-language descriptions, metadata, and eight canonical visible-edge renderings. The primary release, FllumaOne-100K, contains 100,000 accepted samples across four template-level complexity regimes. Programs are executed and retained only after kernel geometry, solid validity, and export checks; release reports also record modality completeness and split-level duplicate tests. A Qwen2.5-Coder-1.5B LoRA baseline trained on 80,000 samples achieves 99.98% Python syntax validity, 99.97% Flluma build success, and 99.14% STEP-export validity on the held-out 10,000-sample test split. For the 9,909 predictions converted to surface point clouds, the mean normalized Chamfer Distance is 0.002124. The dataset supports conditioned CAD reconstruction, executable program synthesis, feature-tree prediction, B-Rep analysis, retrieval, design completion, and editable reverse engineering.

06.
medRxiv (Medicine) 2026-06-17

Sao Tome and Principe on the verge of eliminating lymphatic filariasis as a public health problem: evidence from IDA impact assessment surveys

Background Accelerated efforts to eliminate lymphatic filariasis (LF) as a public health problem have been supported by the introduction of the triple-drug regimen of ivermectin, diethylcarbamazine and albendazole (IDA) in endemic settings. In Sao Tome and Principe, nationwide mass drug administration (MDA) with diethylcarbamazine and albendazole was implemented in 2018, followed by IDA in 2019 and 2020. This study assesses progress towards elimination using post-MDA impact assessment surveys conducted after cessation of treatment. Methods Cross-sectional surveys were conducted among adults aged 20 years and older in 2022 and again between December 2024 and January 2025. Circulating filarial antigen (CFA) was detected using the filarial test strip (FTS). Individuals who tested positive were examined for microfilaremia using nocturnal calibrated thick blood smear microscopy. Additionally, programme data on MDA coverage and morbidity were obtained from national surveillance records. Results Three rounds of nationwide MDA achieved high epidemiological coverage (86.4% in 2018, 74.2% in 2019 and 80.0% in 2020). The impact assessment surveys conducted in 2022 evaluated 14 132 adults, with 21 individuals (0.15%) testing positive for CFA, while the follow-up survey conducted between December 2024 and January 2025 assessed 14 653 adults and detected seven positive cases (0.05%). No microfilariae were detected among the 28 antigen-positive individuals examined using nocturnal calibrated thick blood smears. National morbidity records documented 190 cases of lymphoedema and nine cases of hydrocoele. Conclusions Infection indicators remain well below WHO decision thresholds, suggesting that LF transmission is unlikely to be sustained. Sao Tome and Principe appears to be close to eliminating LF as a public health problem. However, strengthening morbidity management services will be essential to support the preparation of the national elimination dossier.

07.
arXiv (CS.LG) 2026-06-15

Private Prediction via PAC Privacy

arXiv:2601.14033v2 Announce Type: replace Abstract: Machine learning models are increasingly served behind APIs. This renders private prediction, i.e., privatizing a model's outputs rather than its parameters, a natural privacy target: model outputs are lower-dimensional and far more stable to training-data changes than weights. While differential privacy (DP) cannot effectively exploit this as it calibrates noise to worst-case sensitivity that is intractable to bound for non-convex models, we argue that PAC privacy is a natural fit for private prediction. It is instance-based, and calibrates noise to a black-box function's empirical stability to control mutual-information (MI) leakage. The missing ingredient is efficient, adaptive composition. Serving predictions means answering a long stream of adaptively chosen queries from untrusted users; existing composition either fails under adaptivity, grows quadratically, or reverts to input-independent, DP-like noise. We close this gap with a new adversarial composition result via adaptive noise calibration and prove that MI accumulates only linearly under adaptive and adversarial querying. Experiments across modalities show that prediction stability enables high utility even at a tiny per-query budget: on CIFAR-10, we achieve 87.79% accuracy with a per-query MI budget of $2^{-32}$. This enables serving one million queries while provably bounding membership-inference success to 51.08% – the same guarantee as $(0.04, 10^{-5})$-DP. Further, in the presence of auxiliary public data, the large volume of PAC-private predictions enables us to distill a publishable model that can be queried without limit. Concretely, 210,000 private labels on an ImageNet subset distill into a student reaching 91.86% accuracy on CIFAR-10 with membership inference success bounded by 50.49%, comparable to $(0.02, 10^{-5})$-DP.

08.
arXiv (CS.AI) 2026-06-11

\texttt{Range-Arithmetic}: Verifiable Deep Learning Inference on an Untrusted Party

arXiv:2505.17623v2 Announce Type: replace-cross Abstract: Verifiable computing (VC) has gained prominence in decentralized machine learning systems, where resource-intensive tasks like deep neural network (DNN) inference are offloaded to external participants due to blockchain limitations. This creates a need to verify the correctness of outsourced computations without re-execution. We propose \texttt{Range-Arithmetic}, a novel framework for efficient and verifiable DNN inference that transforms non-arithmetic operations, such as rounding after fixed-point matrix multiplication and ReLU, into arithmetic steps verifiable using sum-check protocols and concatenated range proofs. Our approach avoids the complexity of Boolean encoding, high-degree polynomials, and large lookup tables while remaining compatible with finite-field-based proof systems. Experimental results show that our method not only matches the performance of existing approaches, but also reduces the computational cost of verifying the results, the computational effort required from the untrusted party performing the DNN inference, and the communication overhead between the two sides.

09.
arXiv (math.PR) 2026-06-16

Logarithmic Large Deviations for Heavy-Tailed Sums

arXiv:2606.16487v1 Announce Type: new Abstract: We establish logarithmic large-deviation bounds for sums of independent nonnegative random variables with regularly varying tails. The normalization is chosen at the extreme-value scale and the speed is $\log n$. In contrast with Cramér's theorem, the resulting rate function is determined only by the tail index. The proof transfers a maximum large-deviation principle to sums in the one-big-jump region.

10.
arXiv (CS.CV) 2026-06-17

Fluently Lying: Adversarial Robustness Can Be Substrate-Dependent

The primary tools used to monitor and defend object detectors under adversarial attack assume that when accuracy degrades, detection count drops in tandem. This coupling was assumed, not measured. We report a counterexample observed on a single model: under standard PGD, EMS-YOLO, a spiking neural network (SNN) object detector, retains more than 70% of its detections while mAP collapses from 0.528 to 0.042. We term this count-preserving accuracy collapse Quality Corruption (QC), to distinguish it from the suppression that dominates untargeted evaluation. Across four SNN architectures and two threat models (l-infinity and l-2), QC appears only in one of the four detectors tested (EMS-YOLO). On this model, all five standard defense components fail to detect or mitigate QC, suggesting the defense ecosystem may rely on a shared assumption calibrated on a single substrate. These results provide, to our knowledge, the first evidence that adversarial failure modes can be substrate-dependent.

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

Language-Instructed Vision Embeddings for Controllable and Generalizable Perception

Vision foundation models are typically trained as static feature extractors, placing the burden of task adaptation onto large downstream models. We propose an alternative paradigm: instead of solely feeding visual features into language models, we use language itself to dynamically guide the vision encoder. Our method, Language-Instructed Vision Embeddings (LIVE), leverages language as high-level guidance to produce task-centric embeddings at inference time, removing the need for task-specific retraining. This enables the encoder to focus on contextually relevant aspects of the input, yielding more controllable and generalizable representations. Empirically, LIVE reduces visual hallucinations (+34 points on MMVP), surpasses vision-language models with orders of magnitude more parameters on visual question answering, and generalizes to unseen instructions and tasks – offering a direct path toward adaptive, instruction-driven visual intelligence.

12.
bioRxiv (Bioinfo) 2026-06-19

Identification of Altered Potassium Channels for Drug Repurposing in Long COVID Patients

Long COVID (LC) is a complex condition characterized by persistent, chronic multisystem manifestations, with a significant proportion of patients exhibiting neurological symptoms. Human ion channels (HICs), particularly potassium channels, are abundantly expressed in the nervous system and linked to key metabolic processes, making them potential candidates for understanding LC pathophysiology and drug repurposing. Meta-analysis of RNA-Seq datasets from COVID-19 recovered and LC patients was performed to identify altered HICs in LC. Differential gene expression analysis, functional enrichment analysis, and weighted gene co-expression network analysis (WGCNA) were performed to uncover key genes, pathways, and co-expression modules consisting of HICs, lipid metabolism-, and immune signaling-related genes. Drug-gene interaction analysis was performed to identify approved drugs targeting potential HICs. A total of 715 dysregulated genes, including eighteen HICs were identified, among which seven were potassium channels. Three significant modules containing HICs, lipid metabolism-, and immune signaling-related genes were identified and found to be associated with antigen processing and presentation, complement and coagulation cascades, and cytokine-related pathways. Approved drugs targeting KCNA6, KCNJ10, KCNN3, and KCNH4 were identified. With further experimental validation, these dysregulated potassium channels, supported by their co-expression networks and pathway associations, may act as potential candidates for drug repurposing in LC patients.

13.
arXiv (CS.LG) 2026-06-19

Insulin4RL: Real-Time Insulin Management in the Intensive Care Unit for Offline Reinforcement Learning

arXiv:2606.19481v1 Announce Type: new Abstract: Offline reinforcement learning (ORL) offers the potential to improve the quality of clinical decision-making using historical electronic health record (EHR) data. Current training and evaluative practices in this field rely heavily on EHR datasets that have been temporally discretised into fixed, regular time intervals. Discretisation creates fictional representations of complex clinical scenarios and compromises the generalisability of retrospective model evaluations. In this paper, we introduce Insulin4RL, a healthcare ORL dataset featuring naturally irregular inputs and actions from real clinical trajectories. Derived from MIMIC-IV, Insulin4RL comprises over 375,000 labelled decisions across 12,209 patients requiring insulin infusion titration in the Intensive Care Unit. The dataset can thus be used for research into ORL model performance under realistic clinical sampling assumptions. We provide a description of the dataset's structure and characteristics, baseline performance metrics using model-free offline reinforcement learning, and a standardised evaluation protocol using fitted Q-evaluation. We conclude with suggested areas for future research that could be addressed using this resource.

14.
arXiv (CS.AI) 2026-06-11

Noise-Guided Transport for Imitation Learning

arXiv:2509.26294v2 Announce Type: replace-cross Abstract: We consider imitation learning in the low-data regime, where only a limited number of expert demonstrations are available. In this setting, methods that rely on large-scale pretraining or high-capacity architectures can be difficult to apply, and efficiency with respect to demonstration data becomes critical. We introduce Noise-Guided Transport (NGT), a lightweight off-policy method that casts imitation as an optimal transport problem solved via adversarial training. NGT requires no pretraining or specialized architectures, incorporates uncertainty estimation by design, and is easy to implement and tune. Despite its simplicity, NGT achieves strong performance on challenging continuous control tasks, including high-dimensional Humanoid tasks, under ultra-low data regimes with as few as 20 transitions.

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

Agents All the Way Down; A Methodology for Building Custom AI Agents from Substrate to Production

arXiv:2606.11869v1 Announce Type: cross Abstract: Custom AI agents areagents that live inside their own application, talk to their own data and tools, enforce their own security boundaries, and carry their own brand and audit trail. What separates them from the general-purpose tier is fit, not capability: each is built for one job, by the engineer who will maintain it. No published practice sets out how to build one end to end. The pieces are everywhere (function-calling APIs, the Model Context Protocol, code agents to pair with), but the practice that chains them lives in podcasts, blogs, and leaked system prompts. This paper writes that practice down as a methodology, Agents All the Way Down: two preconditions crossed once and kept, then three practices repeated for the agent's life. The preconditions are (P1) Substrate, the LLM as a software component, framed as tools, then system, then messages under prompt-caching; and (P2) Building blocks: function calling, MCP, CLI orchestration, the liteshell pattern, the agent loop, skills, characters, hooks, and scaffolding. The practices are (P3) prototype with a general-purpose agent; (P4) harvest, fold, and ship the result as a CLI, the Turtle pattern; and (P5) agent-tests-agent, in which a general-purpose agent drives it through behavioural scenarios, a complement to classical testing, not a replacement. The working loop is P3 to P4 to P5 and back, and one corollary falls out for free: multi-agent orchestration is just CLI composition. The methodology is framework-free by construction. It was distilled from the AAC, a custom agent for the open-source LAMB platform, built in about ten days by one developer with an AI pair-programmer and in production . We present it as a transferable practice, independent of any language or framework.

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

Operator Boosting Produces Pareto-Efficient PDE Surrogates

arXiv:2606.17460v1 Announce Type: new Abstract: Neural operators are widely used as surrogate solution maps for partial differential equations (PDEs), but full-size models can be costly to store, deploy, and evaluate in many-query scientific workflows. This work introduces Operator Boosting, a stagewise residual-learning framework for constructing compact neural-operator surrogates directly, rather than training a large model and compressing it afterward. Starting from the empirical mean predictor in normalized output coordinates, the method trains a sequence of tiny same-family neural operators on residual fields and incorporates each correction through validation-selected shrinkage. We instantiate the framework with Fourier neural operators (FNOs), DeepONets, and convolutional neural operators (CNOs), and compare boosted tiny stacks against full-size monolithic baselines across one-, two-, and three-dimensional PDE benchmarks from PDEBench, APEBench, and The Well. Across 30 dataset-architecture pairs, 21 show positive mean accuracy gains and 17 have positive confidence intervals, while all boosted stacks reduce trainable parameter count by approximately 72-95%. Best-model comparisons show empirical Pareto improvements on 7 of 10 completed PDE benchmarks, including two-dimensional Navier-Stokes, shallow-water dynamics, Darcy flow, one-dimensional transport and reaction systems, and three-dimensional compressible Navier-Stokes. These results show that Operator Boosting often improves the empirical accuracy-parameter Pareto frontier of neural PDE surrogates, while also exposing PDE- and architecture-dependent regimes where residual boosting fails to offset compression.

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

Provenance-Enhanced Statements in Knowledge Graphs

arXiv:2606.15246v1 Announce Type: cross Abstract: Provenance-enhanced statements of the form "according to $X$, $\varphi$" are pervasive in contemporary knowledge graphs, especially in domains where graph content primarily represents claims, interpretations, and hypotheses (capta) rather than observer-independent facts (data). Current provenance models can record who asserted what, but they typically treat provenance as semantically neutral, leaving underspecified how attributed claims relate to factual commitment, to one another, and to reasoning. In this paper we introduce DEC, a framework that interprets provenance predicates as indicators of epistemic stance and groups provenance-homogeneous sets of statements into cognitive worlds. Drawing on cognitive modal logics (doxastic, epistemic, and conjectural), DEC characterizes locality, rationality, and controlled permeation between cognitive worlds and a distinguished factual core ("reality"), thereby enabling principled reasoning over attributed content without collapsing disagreements into inconsistencies. We formalize a DEC interpretation for RDF datasets that is conservative over RDF~1.2 semantics, clarify the role of intensionality and identity (including the Superman paradox), and illustrate the approach on common Semantic Web representations (named graphs, quoted triples/RDF-star, and reification). Finally, we describe our prototype DEC reasoner implemented as a Fuseki dataset module, supporting controlled factualisation and explicit detection of disagreements and delusions.

18.
arXiv (CS.LG) 2026-06-17

On Surjectivity of Neural Networks: Can you elicit any behavior from your model?

arXiv:2508.19445v3 Announce Type: replace Abstract: Given a trained neural network, can any specified output be generated by some input? Equivalently, does the network correspond to a function that is surjective? In generative models, surjectivity implies that any output, including harmful or undesirable content, can in principle be generated by the networks, raising concerns about model safety and jailbreak vulnerabilities. In this paper, we prove that many fundamental building blocks of modern neural architectures, such as networks with pre-layer normalization and linear-attention modules, are almost always surjective. As corollaries, widely used generative frameworks, including GPT-style transformers and diffusion models with deterministic ODE solvers, admit inverse mappings for arbitrary outputs. By studying surjectivity of these modern and commonly used neural architectures, we contribute a formalism that sheds light on their unavoidable vulnerability to a broad class of adversarial attacks.

19.
arXiv (CS.LG) 2026-06-12

Central Limit Theorems for Stochastic Gradient Descent Quantile Estimators

arXiv:2503.02178v3 Announce Type: replace-cross Abstract: This paper develops asymptotic theory for quantile estimation via stochastic gradient descent (SGD) with a constant learning rate. The quantile loss function is neither smooth nor strongly convex. Beyond conventional perspectives and techniques, we view quantile SGD iteration as an irreducible, periodic, and positive recurrent Markov chain, which cyclically converges to its unique stationary distribution regardless of the arbitrarily fixed initialization. To derive the exact form of the stationary distribution, we analyze the structure of its characteristic function by exploiting the stationary equation. We also derive tight bounds for its moment generating function (MGF) and tail probabilities. Synthesizing the aforementioned approaches, we prove that the centered and standardized stationary distribution converges to a Gaussian distribution as the learning rate $\eta\rightarrow0$. This finding provides the first central limit theorem (CLT)-type theoretical guarantees for the quantile SGD estimator with constant learning rates. We further propose a recursive algorithm to construct confidence intervals of the estimators with statistical guarantees. Numerical studies demonstrate the effective finite-sample performance of the online estimator and inference procedure. The theoretical tools developed in this study are of independent interest for investigating general SGD algorithms formulated as Markov chains, particularly in non-strongly convex and non-smooth settings.

20.
arXiv (CS.CL) 2026-06-19

PASQA: Pitch-Accent-Focused Speech Quality Assessment Model Trained on Synthetic Speech with Accent Errors

Existing mean opinion score (MOS) prediction models typically predict utterance-level naturalness MOS and can be insensitive to localized pitch-accent errors. We propose Pitch-Accent-focused Speech Quality Assessment (PASQA), which explicitly targets pitch-accent correctness. To train our model, we construct a controlled Japanese accent-error dataset by changing accent patterns using an accent-controllable text-to-speech system, and compute a pseudo accent-quality score from the accent-error rate. PASQA builds on self-supervised representations and employs mora-conditioned fusion, ranking loss, an auxiliary accent-error localization task, and speaker-invariant training. Experiments show that conventional models fail to preserve the ordering by accent-error severity, whereas PASQA achieves high ordering accuracy on both seen and unseen speakers. Further, PASQA shows stronger agreement with human accent-correctness judgments. The code is available at https://github.com/lycorp-jp/PASQA.

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

Lost in a Single Vector: Improving Long-Document Retrieval with Chunk Evidence Aggregation

Dense retrieval ranks one query vector against one document vector. On long documents, this interface can fail when a short but decisive span is weakened during document encoding before ranking. We study this failure mode as document-side early compression and introduce the Evidence Dilution Index (EDI) to measure how far a document-level representation falls below the strongest chunk-level evidence within the same gold document. Guided by this view, we propose DICE (Document Inference via Chunk Evidence), a training-free document-side strategy that splits documents into chunks, encodes them independently with a frozen model, and aggregates them back into a single vector while preserving the standard one-query-one-document interface. On LongEmbed, DICE improves retrieval across four backbones, with the largest gains on slices beyond 4k tokens: for Dream, Passkey >4k rises from 30.0 to 90.0 and Needle >4k from 23.3 to 74.0. Across 12,779 filtered samples, DICE yields lower EDI than the single-vector baseline in 92.8% of cases. These results establish document-level encoding as a practical and underexplored lever for long-document retrieval.

22.
bioRxiv (Bioinfo) 2026-06-17

Beyond phylogeny: Genome-wide DNA sequence patterns suggest DNA physical properties associated with thermal adaptation in extremophile microbes

Temperature is a fundamental constraint on biological systems, yet how it is reflected in genome sequence organization remains unclear. Here, we show that genome-wide distributions of short DNA sequences contain a robust signal of thermal adaptation that is largely independent of phylogeny. Using Structural Topic Modelling (STM), a machine-learning approach for identifying groups of co-occurring sequence motifs, we analyze canonical 6-mer and 9-mer frequency profiles of bacterial and archaeal genome proxies (randomly sampled genomic regions) and identify motif families systematically associated with thermophiles and psychrophiles. In bacterial thermophiles, the identified motif families are dominated by highly specific, overrepresented and co-occurring C- and G-stacked hexamers, and a distinct family of CG-periodic hexamers recurring across multiple temperature comparisons. In contrast, bacterial psychrophile-associated motifs are dominated by low-complexity A-, T-, and AT-run hexamers. Thermophilic archaea generally exhibit a distinct CTAG-centred hexamer family, suggesting that different domains may adapt to similar environmental constraints through different sequence-level solutions. However, this domain-level contrast is not absolute: in a targeted analysis of two thermophilic bacterium–archaeon pairs, we find unusually similar frequencies of all the STM-identified thermophile-associated hexamer families, suggesting that shared high-temperature environments can, in specific cases, partially override phylogenetic divergence. Notably, the identified motif families constitute only a small and highly selective subset of the vast space of possible G+C-rich or A+T-rich sequences. This indicates that thermal adaptation is associated with specific sequence architectures rather than broad shifts in nucleotide composition. Accordingly, the observed signal cannot be explained by overall base composition alone, but instead arises from structured combinations and positional arrangements of nucleotides within short sequence contexts. Related motif families are recovered at both k=6 and k=9, indicating that the signal reflects systematic shifts in genome-wide sequence organization rather than isolated sequence motifs. These patterns are consistent with known sequence-dependent DNA physical properties documented in biochemical and biophysical studies, including differences in base-stacking interactions and conformational flexibility. Together, our results suggest that genome-wide sequence organization reflects sequence-dependent DNA physical properties associated with thermal adaptation, revealing a previously underappreciated physical layer of genomic information beyond phylogenetic history.

23.
arXiv (CS.CV) 2026-06-16

Mutual Distillation of Dual-Foundation Models for Semi-Supervised PET/CT Segmentation

Organ segmentation from PET/CT is critical for quantitative analysis and radiotherapy planning in oncology. To ease the high annotation cost of PET/CT segmentation, semi-supervised learning (SSL) provides a practical and effective solution for developing deep models with limited labeled data. Recent developments in visual foundation models have demonstrated remarkable adaptability with improved efficiency. In this work, we propose a mutual distillation framework that seamlessly exploits both structural and functional foundation models, which act as modality-specific generalists for distilling knowledge from structural CT and metabolic PET imaging. By bridging the gap between the task-specific precision of student models and the segmentation priors of generalist foundation models, we propose MuDuo, a mutual distillation framework that synergistically leverages SAM-Med3D for CT and SegAnyPET for PET to distill their knowledge into a lightweight student network. Our approach eliminates the need for manual prompts while maximizing the utility of unlabeled data for automatic segmentation, achieving state-of-the-art performance on the AutoPET dataset with only 5 labeled cases. Our source code is available at https://github.com/Wu-beining/MuDuo.

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

Morphology-Aware Sample Assignment: Overcoming IoU Insensitivity for Surface Defect Detection

Intersection-over-Union (IoU), as a pivotal metric for evaluating the spatial alignment between candidate proposals and ground-truth annotations, directly determines the quality of positive sample sets and the training efficacy of visual detection models. Through theoretical modeling and analysis, we uncover a non-sensitive region on the IoU response curve, within which samples yield nearly identical IoU scores despite distinct geometric overlaps. To overcome this limitation, we introduce a set of morphological similarity metrics covering area, shape, and aspect ratio, to refine the positive sample assignment process, thereby ensuring more discriminative and reliable matching. A supplementary matching score is derived via mean-based aggregation of these multidimensional similarities, compensating for the intrinsic limitation of IoU in representing structural correspondence. Theoretically, incorporating morphological similarity reshapes the response distribution of the matching function, yielding both effective directional gradients and polygon-like iso-response contours, which tightly confine high-response regions around each ground-truth instance and substantially enhance the precision of positive sample selection. Experiments based on the YOLOv9 framework demonstrate consistent performance gains on both NEUDET and GC10- DET datasets. Notably, the proposed approach is fully plug-and-play and incurs zero additional inference overhead, thereby ensuring deployment efficiency for industrial visual inspection.

25.
arXiv (CS.AI) 2026-06-11

Categorical Prior Lock-in: Why In-Context Learning Fails for Structured Data

arXiv:2606.11961v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used as conditional generators for structured data, relying on in-context learning (ICL) to adapt to new distributions without parameter updates. We investigate the limits of ICL for structured generation under distribution mismatch, using high-cardinality tabular data as a controlled test case, and identify a structural failure mode we term categorical prior lock-in: the inability of ICL to update the model's prior over token distributions inherited from pre-training. Across two 7B-parameter open-weight models, ICL improves numerical fidelity with additional examples but exhibits a sharp ceiling on categorical distributions, failing to reproduce rare classes entirely. Parameter-efficient fine-tuning (LoRA) overcomes these limitations but introduces measurable memorization risk and, in some cases, destabilizes structured output generation, highlighting a fundamental trade-off between adaptability and privacy.