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

Learning Directional Semantic Transitions for Longitudinal Chest X-ray Analysis

Chest X-ray (CXR) interpretation often requires longitudinal comparison to assess disease progression. Existing approaches typically rely on temporal feature fusion or inter-study discrepancy modeling, yet remain limited in capturing subtle progression semantics and overlook the inherently directional nature of disease trajectories. In this paper, we propose ProTrans, a novel vision-language pretraining framework that formulates disease progression as a directional semantic transition between paired CXR studies. ProTrans leverages radiology reports to anchor individual CXR representations within interpretable disease states, and introduces a learnable progression feature map to explicitly encode semantic shifts between states, aligned with report-derived progression descriptions. To enforce direction-aware perception, ProTrans incorporates a reversed temporal modeling process and imposes bidirectional reconstruction consistency across states and transitions, thereby disentangling directional semantics and promoting coherent trajectory modeling. Extensive experiments on longitudinal downstream tasks, including disease progression classification and progression captioning, demonstrate that ProTrans consistently outperforms existing methods, establishing a unified pretraining framework for longitudinal CXR understanding. https://github.com/RPIDIAL/ProTrans

02.
arXiv (quant-ph) 2026-06-17

Response kinetic uncertainty relation for Markovian open quantum systems

arXiv:2501.04895v2 Announce Type: replace Abstract: Response uncertainty relations in stochastic thermodynamics extend precision bounds to the sensitivity of observables under external perturbations. Here we derive a quantum response kinetic uncertainty relation for continuously monitored Markovian open quantum systems in the steady state of the Lindblad master equation. The response precision of a measured trajectory observable is bounded by two contributions: the conventional quantum dynamical activity and a perturbation-induced intersubspace transition term. The latter is absent in the classical limit and captures a genuinely quantum part of the response cost. We identify simple conditions under which either contribution vanishes, and we further clarify the structure of the intersubspace term through a symmetry-resolved decomposition and exact sector-selection rules. The bound and its structure are illustrated in a driven two-level atom.

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

Learning Policy from a Single Trajectory in Average-Reward Markov Decision Process

arXiv:2606.16729v1 Announce Type: new Abstract: While there is an extensive body of work characterizing the sample complexity of discounted cumulative-reward MDPs, finite sample analyses for average-reward MDPs have been limited, and most existing works rely on restrictive assumptions such as ergodicity or access to a generative model. In this work, we establish the first finite sample complexity guarantees from a single trajectory for weakly communicating average-reward MDPs. To this end, we study the dynamics of a single trajectory in weakly communicating MDPs and based on this analysis, we develop novel model-free methods. Notably, our value-based and policy-based methods provide finite sample complexity guarantees of $\widetilde{O}(1/\varepsilon^2)$ and $\widetilde{O}(1/\varepsilon^4)$ from a single trajectory in weakly communicating MDPs, respectively. Furthermore, we introduce the first model-free method that requires no prior knowledge of problem-dependent quantities for communicating MDPs.

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

Nemotron 3 Ultra: Open, Efficient Mixture-of-Experts Hybrid Mamba-Transformer Model for Agentic Reasoning

We introduce Nemotron 3 Ultra, a 550 billion total and 55 billion active parameter Mixture-of-Experts Hybrid Mamba-Attention language model. We pre-trained Nemotron 3 Ultra on 20 trillion text tokens, then extended the context length to 1M tokens, and post-trained using Supervised Fine Tuning (SFT), Reinforcement Learning (RL), and Multi-teacher On-Policy Distillation (MOPD). Nemotron 3 Ultra is our most capable model yet, employing multiple key technologies - LatentMoE, Multi Token Prediction (MTP), NVFP4 pre-training, multi-environment RLVR, MOPD, and reasoning budget control. Nemotron 3 Ultra achieves up to ~6x higher inference throughput as compared to state-of-the-art publicly available LLMs while attaining on-par accuracy. The state-of-the-art accuracy, high inference throughput, and 1M token context length make Nemotron 3 Ultra ideal for long-running autonomous agentic tasks. We open-source the base, post-trained, and quantized checkpoints, along with the training data and recipe on HuggingFace.

05.
arXiv (CS.AI) 2026-06-24

Learning to Trigger: Reinforcement Learning at the Large Hadron Collider

arXiv:2606.23993v1 Announce Type: cross Abstract: High-throughput scientific facilities such as the Large Hadron Collider depend on real-time event filtering (triggering) under tight constraints on bandwidth, latency, and storage. In practice, trigger menus are largely static and hand-tuned and can become suboptimal as detector conditions, pileup, and background composition drift over time. We cast online threshold tuning as a sequential decision-making problem: a reinforcement learning agent ingests streaming summaries of recent rates and signal-sensitive features and updates trigger thresholds to maximize signal efficiency while tracking a target background rate within a tolerance band. We adapt Group-Filtered Policy Optimization (GFPO) to streaming control and introduce two variants (GFPO-F, GFPO-FR) that enforce background rate feasibility during training. On a benchmark that emulates realistic collider operation, we study two representative triggers: a total transverse energy ($H_{T}$) trigger sensitive to pileup variation, and an anomaly-detection (AD) trigger based on reconstruction loss for rare or non-standard signatures. On Monte Carlo streams, our agent increases the fraction of in-tolerance time intervals by 48\% ($H_T$) and 28\% (AD), with a cumulative gain of up to 2\% in signal efficiency on those in-tolerance intervals. Transferring from simulation to real collision data (CMS Run 283408), the same agent, without fine-tuning, achieves a 56\% ($H_T$) and 28\% (AD) in-tolerance improvement over baselines, with further signal-efficiency gain on both triggers. To our knowledge, this is the first demonstration of RL-based trigger control on real Large Hadron Collider collision data. Code is available at https://github.com/Zixind/GFPO\_LHC.

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

Generalised Eigenvalue Geometry of Semantic Adversarial Attacks

arXiv:2606.19212v1 Announce Type: cross Abstract: Recent empirical work shows that semantically equivalent paraphrases can fool financial sentiment classifiers: although a paraphrase remains close to the original under a strong reference embedding, it may shift the target model's representation enough to change the predicted class. Existing robustness theory either assumes a single-model threat model or focuses mainly on empirical attack algorithms. We develop a continuous local model of semantic paraphrase perturbations that captures this two-model structure. We show that the worst-case local displacement of the target representation, subject to a proxy-model budget, is governed by the largest generalised eigenvalue of a matrix pencil $(A,B)$ constructed from the Jacobians of the two embedding maps. The resulting attackability index $\lambda^*(x)$ is intrinsic to the local paraphrase geometry and the chosen embedders, yields a closed-form prediction-flip condition for affine readouts, and supports conservative population and finite-sample attackability certificates. For uniform control over classes of affine readouts, we derive a distribution-free VC bound for binary attackability indicators and a scale-sensitive margin bound based on an attackability-adjusted margin that subtracts a local geometric penalty from the standard classifier margin. We also connect the continuous theory to discrete paraphrase search, identify an asymmetry between successful and unsuccessful finite searches, and give a covering condition under which the discrete and continuous settings agree. Finally, we propose an empirical verification framework using soft-token relaxations and generated paraphrase sets to assess the local eigenvalue geometry, prediction-flip condition, and finite-search approximation on a deployed financial-text classifier.

07.
arXiv (CS.AI) 2026-06-19

BrainG3N: A Dual-Purpose Tokenizer for Controllable 3D Brain MRI Generation

arXiv:2606.19651v1 Announce Type: new Abstract: Three-dimensional (3D) brain MRI is central to clinical neurology and neuro-oncology, where generative models could augment under-represented cohorts, simulate disease trajectories, and support privacy-preserving data sharing. Latent diffusion has been the go-to solution for modeling imaging data, but it places two competing demands on the tokenizer: encoder embeddings must retain the clinical information that downstream tasks act on, and the decoder must reconstruct anatomically faithful volumes. Existing reconstruction-driven tokenizers achieve the second at the expense of the first. To address this, we introduce a fully volumetric masked-autoencoder (MAE) based tokenizer for 3D brain MRI latent diffusion, decoupling encoder and decoder: a frozen 3D MAE encoder produces clinically informative embeddings, while a dedicated CNN decoder reconstructs voxels from a linear projection of those embeddings. We pretrain the encoder on 35,309 volumes from 18 public cohorts spanning four modalities, ten disease categories, and 200+ acquisition sites, and demonstrate its dual utility in two settings. First, on a 23-task linear-probing benchmark, the encoder outperforms or matches SOTA models (i.e., BrainIAC, BrainSegFounder, and MedicalNet) on 21 of 23 tasks. Second, a conditional diffusion transformer (DiT) trained on these clinically informative embeddings supports both conditional generation across six variables and patient-specific longitudinal forecasting. Together these results establish a single 3D brain-MRI embedding space capable of both downstream clinical tasks and controllable generation.

08.
arXiv (CS.AI) 2026-06-24

FlowR2A: Learning Reward-to-Action Distribution for Multimodal Driving Planning

arXiv:2606.24231v1 Announce Type: new Abstract: Multimodal driving planning faces a long-standing tension between two paradigms: scoring-based methods benefit from dense reward supervision but are confined to a fixed action vocabulary, while anchor-based methods generate proposals dynamically yet suffer from sparse supervision constrained to a single ground-truth trajectory. In this work, we propose FlowR2A, which resolves this tension by reframing simulation-based rewards from discriminative targets into generative conditions. By learning the reward-conditioned action distribution from dense trajectory-reward pairs with a flow-matching decoder, FlowR2A unifies the dense supervision of scoring-based methods with the proposal generation of anchor-based methods in a single generative model, forcing the model to internalize the correlation between an action and its outcomes in safety, progress, comfort, and rule compliance. To balance hard safety constraints against soft progress objectives, we introduce fine-grained per-timestep reward conditioning and reward noise augmentation. The generative formulation naturally supports controllable test-time sampling via reward guidance and anchored sampling, producing high-quality proposals. FlowR2A achieves state-of-the-art results on the NAVSIM v1 and v2 benchmarks, with multimodal proposals of substantially higher quality than prior methods.

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

PCR-CA: Parallel Codebook Representations with Contrastive Alignment for Multiple-Category App Recommendation

arXiv:2508.18166v5 Announce Type: replace-cross Abstract: Modern app store recommender systems struggle with multiple-category apps, as traditional taxonomies fail to capture overlapping semantics, leading to suboptimal personalization. We propose PCR-CA (Parallel Codebook Representations with Contrastive Alignment), an end-to-end framework for improved CTR prediction. PCR-CA first extracts compact multimodal embeddings from app text, then introduces a Parallel Codebook VQ-AE module that learns discrete semantic representations across multiple codebooks in parallel – unlike hierarchical residual quantization (RQ-VAE). This design enables independent encoding of diverse aspects (e.g., gameplay, art style), better modeling multiple-category semantics. To bridge semantic and collaborative signals, we employ a contrastive alignment loss at both the user and item levels, enhancing representation learning for long-tail items. Additionally, a dual-attention fusion mechanism combines ID-based and semantic features to capture user interests, especially for long-tail apps. Experiments on a large-scale dataset show PCR-CA achieves a +0.76% AUC improvement over strong baselines, with +2.15% AUC gains for long-tail apps. Online A/B testing further validates our approach, showing a +10.52% lift in CTR and a +16.30% improvement in CVR, demonstrating PCR-CA's effectiveness in real-world deployment. The new framework has now been fully deployed on the Microsoft Store.

10.
arXiv (CS.CV) 2026-06-16

The Importance of Phase in Neural Representations: An Internal Oppenheim-Lim Test of Image Classifiers

Oppenheim and Lim (1981) showed that natural images stay recognizable when reconstructed from their Fourier phase alone, while the magnitude carries little of their identity. We ask whether trained image classifiers reproduce this asymmetry inside their hidden layers, and we test it causally: given two images, we transplant the phase of one onto the magnitude of the other at a chosen layer and record which image the prediction follows. In PRISM2D, GFNet, and ViT-B/16 the prediction follows the phase or sign donor, and deleting all image-specific magnitude barely moves accuracy, so identity rides on phase while image-specific magnitude is largely dispensable to the readout. ResNet-50 at first seems to break the pattern, because transplanting sign after its ReLUs does nothing; a fair intervention before the ReLU reveals a strong latent sign code in the late blocks, and a DC-only control shows the readout consumes a channel-wise spatial average. Controls rule out the trivial case in which magnitude simply stops depending on the image. The architectures therefore share a phase/sign identity code but expose it in different bases, set by rectification and readout geometry, which gives a mechanistic account of the texture–shape gap between CNNs and attention models.

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

ASTER: Latent Pseudo-Anomaly Generation for Unsupervised Time-Series Anomaly Detection

Time-series anomaly detection (TSAD) is critical in domains such as industrial monitoring, healthcare, and cybersecurity, but it remains challenging due to rare and heterogeneous anomalies and the scarcity of labelled data. This scarcity makes unsupervised approaches predominant, yet existing methods often rely on reconstruction or forecasting, which struggle with complex data, or on embedding-based approaches that require domain-specific anomaly synthesis and fixed distance metrics. We propose ASTER, a framework that generates pseudo-anomalies directly in the latent space, avoiding handcrafted anomaly injections and the need for domain expertise. A latent-space decoder produces tailored pseudo-anomalies to train a Transformer-based anomaly classifier, while a pre-trained LLM enriches the temporal and contextual representations of this space. Experiments on three benchmark datasets show that ASTER achieves state-of-the-art performance and sets a new standard for LLM-based TSAD.

12.
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.

13.
medRxiv (Medicine) 2026-06-22

Toward less intrusive pubertal assessment: longitudinal evaluation of tanner and non-tanner metrics in East African adolescents

Background: Accurate pubertal assessment is essential in pediatric endocrinology and adolescent health research. While Tanner staging remains the gold standard, its subjective nature and invasive genital examination limit feasibility and acceptability, especially in longitudinal studies and culturally sensitive settings. This study evaluated less intrusive pubertal assessment combinations that maintain discriminative accuracy. Methods: We conducted a longitudinal study among 200 uncircumcised, sexually naive males aged 15-17 years in Southwestern Uganda, with quarterly follow-up over three years. Clinicians assessed Tanner staging metrics (pubic hair, testicular volume, penile length, scrotal color), axillary hair, and serum testosterone. Markov transition models estimated Tanner stage progression. Ordinal logistic regression and area under the receiver operating characteristic curve (AUC) analyses quantified discriminative performance of individual and combined metrics. Results: At baseline, participants were distributed across Tanner stages II (6.0%), III (13.5%), IV (55.0%), and V (25.5%). Among individual metrics, pubic hair distribution best predicted overall Tanner stage (AUC=0.867), while penile length was least predictive (AUC=0.833). The full four-metric Tanner model achieved high discrimination (AUC=0.993). However, a less intrusive combination of pubic hair and scrotal color achieved comparable discrimination (AUC=0.942), improving to AUC=0.953 with axillary hair and age. Markov modeling demonstrated frequent bidirectional transitions between Tanner stages IV and V, reflecting variability in longitudinal staging. Conclusions: A minimally intrusive assessment combining pubic hair, scrotal color, axillary hair, and age reliably predicts pubertal stage, offering an acceptable alternative to traditional Tanner staging for research and surveillance contexts where genital manipulation is impractical or unethical.

14.
Nature (Science) 2026-06-24

GW250114 reveals signatures of post-merger black-hole horizon

作者:

The horizon of a black hole, the ‘surface of no return’, is characterized by its rotation frequency ΩH and surface gravity κ. A striking signature is that any infalling object appears to orbit at ΩH owing to frame dragging, while its emitted signals decay exponentially at a rate set by κ as a consequence of gravitational redshift. Recent theoretical work1 predicts that gravitational waves from binary black-hole mergers carry direct imprints of the properties of the merger remnant in the form of a ‘direct wave’. This gravitational-wave component oscillates near 2ΩH, reflecting the horizon’s frame dragging, and decays at an increasing rate characterized by κ, with additional screening from the black hole’s spacetime. Here we report observational evidence of a direct wave in GW2501142, with a 90% credible matched-filter signal-to-noise ratio of $${15.8}_{-0.5}^{+0.1}$$ ( $${17.1}_{-0.4}^{+0.1}$$ ) in the LIGO Hanford (Livingston) detector. The measured properties are in full agreement with theoretical predictions for a Kerr black hole. These findings establish an observational channel to directly measure frame-dragging effects in black-hole ergospheres and explore (near-)horizon physics in dynamical, strong-gravity regimes. The observation of a direct wave after the merger of two black holes reveals signatures associated with the remnant black-hole horizon, establishing an observational channel to directly measure frame-dragging effects in black-hole ergospheres and probe the horizon surface gravity.

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

Reference-Driven Multi-Speaker Audio Scene Generation from In-the-Wild Priors

Existing multi-speaker dialogue systems bind speakers to utterances through structured supervision: per-turn tags, multi-stream transcriptions, or learnable speaker embeddings. These systems operate within speech-only pipelines that produce clean vocal sequences without the ambient texture of real conversations. We take a different approach. Our method, ScenA, conditions a text-to-audio flow-matching foundation model, pretrained on large-scale in-the-wild data, directly on multiple reference voices and a free-form natural language prompt that describes an entire multi-speaker audio scene. Leveraging such a foundational model allows us to inherit its capacity for natural, non-studio audio: background noise, room acoustics, overlapping dialogue, and spontaneous paralinguistic events, while adding multi-speaker control without any per-turn structure. Concretely, reference latents are concatenated into the model's token sequence and distinguished by lightweight identity-aware positional encodings. However, we identify a critical obstacle to this approach: the Reference Shortcut. During training under standard noise schedules, the model can identify the matching reference by acoustic similarity to the noisy target, bypassing the text prompt entirely. We address this with a high-noise-biased timestep distribution that forces the model to rely on the text prompt for speaker assignment. We evaluate ScenA on the CoVoMix2-Dialogue benchmark, showing that it outperforms existing multi-speaker systems on speaker-binding metrics while generating rich conversational audio with overlapping speech, emotional vocalizations, and ambient sound. Our results demonstrate the advantage of using a general-purpose audio model conditioned on a free-form scene description, rather than passing structured dialog scripts through a speech-only pipeline.

16.
arXiv (CS.CV) 2026-06-11

Weakly Supervised Segmentation as Semantic-Based Regularization

Weakly supervised semantic segmentation (WSSS) trains dense pixel-level segmentation models from partial or coarse annotations such as bounding boxes, scribbles, or image-level tags. While recent work leverages foundation models such as the Segment Anything Model (SAM) to generate pseudo-labels, these approaches typically depend on heuristic prompt choices and offer limited ways to incorporate prior knowledge or heterogeneous labels. We address this gap by taking a neurosymbolic perspective: integrating differentiable fuzzy logic with deep segmentation models. Weak annotations and domain-specific priors are unified as continuous logical constraints that fine-tune SAM under weak supervision. The refined foundation model then produces improved pseudo-labels, from which we train a second-stage prompt-free segmentation model. Experiments on Pascal VOC 2012 and the REFUGE2 optic disc/cup segmentation dataset show that our logic-guided fine-tuning yields higher-quality pseudo-labels, leading to state-of-the-art segmentation accuracy that often exceeds densely supervised baselines.

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

SurroundNEXO: Ego-Centric Metric Bridging for Spatially Consistent Geometry in Autonomous Driving

Modern autonomous driving depends on accurate metric 3D understanding for perception, reconstruction, and planning, which in turn requires reliable multi-camera depth prediction. However, the outward-facing nature of vehicle-mounted surround-view camera rigs inherently limits visual overlap across views, challenging the correspondence-based assumptions that underpin conventional multi-view geometry. To bridge this gap, we present SurroundNEXO, named after the Spanish word nexo for a geometric link, a low-overlap multi-camera metric depth framework that grounds cross-view reasoning in ego-centric geometry rather than dense visual correspondences. Instead of directly enforcing early global fusion, SurroundNEXO first assigns image tokens globally comparable ego-frame viewing directions through Ego-Ray Positional Encoding, then uses sparse LiDAR measurements as metric anchors to propagate absolute scale cues, and finally expands feature interaction progressively from view-local modeling to decomposed spatio-temporal reasoning and global integration. This design enables metric-scale depth prediction with improved spatial consistency across weakly overlapping cameras. Across low-overlap autonomous driving benchmarks, including NuScenes, Waymo and DDAD, SurroundNEXO reduces single-view error by 33.2%, improves cross-view consistency by 10.5%, and enhances metric reconstruction quality by 25.6% compared with SOTA methods. It further remains robust under extremely sparse depth prompts and exhibits strong zero-shot generalization to unseen camera layouts.

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

JailbreakOPT: Tool-Assisted Iterative Jailbreak Prompt Optimization

arXiv:2606.11425v1 Announce Type: cross Abstract: Jailbreak attacks expose persistent safety weaknesses in large language models (LLMs), but existing stateless single-turn methods face a trade-off: hand-crafted prompts are expressive but static, while iterative prompt optimization can adapt but often relies on low-level mutations that require many target queries. We propose JailbreakOPT, a tool-assisted framework for improving iterative single-turn jailbreak prompt optimization. JailbreakOPT organizes diverse atomic jailbreak prompts into an attack tool library and composes them through a unified intra-episode optimization abstraction to generate stronger standalone attack prompts. To reuse experience across attack episodes, JailbreakOPT further frames tool selection as a contextual bandit problem and applies contextual Thompson sampling to guide exploration and exploitation based on past outcomes. Experiments across multiple target LLMs and attack goals show that JailbreakOPT improves attack success rate (ASR) while reducing the number of attacks until success (No.A) compared with atomic single-turn attacks and existing iterative optimization baselines. This paper may contain offensive or harmful content.

19.
arXiv (CS.LG) 2026-06-24

Predictive variational inference: Learn the predictively optimal posterior distribution

arXiv:2410.14843v4 Announce Type: replace-cross Abstract: Vanilla variational inference finds an optimal approximation to the Bayesian posterior distribution, but even the exact Bayesian posterior is often not meaningful under model misspecification. We propose predictive variational inference (PVI): a general inference framework that seeks and samples from an optimal posterior density such that the resulting posterior predictive distribution is as close to the true data generating process as possible, while this closeness is measured by multiple scoring rules. By optimizing the objective, the predictive variational inference is generally not the same as, or even attempting to approximate, the Bayesian posterior, even asymptotically. Rather, we interpret it as implicit hierarchical expansion. Further, the learned posterior uncertainty detects heterogeneity of parameters among the population, enabling automatic model diagnosis. This framework applies to both likelihood-exact and likelihood-free models. We demonstrate its application in real data examples.

20.
arXiv (CS.LG) 2026-06-24

Stochastic Dimension Implicit Functional Projections for Global Integral Conservation in High-Dimensional PINNs

arXiv:2603.29237v3 Announce Type: replace Abstract: Enforcing prescribed global integral constraints in mesh-free neural PDE solvers is challenging in high-dimensional domains. Existing projection methods for spatial integrals are often tied to fixed grids or uniform quadrature, which can conflict with randomly sampled physics-informed neural networks (PINNs) and scale poorly with dimension. High-order differential operators also increase reverse-mode automatic differentiation memory costs. We propose Stochastic Dimension Implicit Functional Projection (SDIFP), a quadrature-level framework for enforcing prescribed first and second spatial moments. SDIFP replaces tensor-product nodal projection by a global affine correction of the neural-network output, with two scalar coefficients determined from a weighted quadrature rule. Under positive target variance and nonzero empirical raw variance, this correction is the nearest-point projection, in the weighted quadrature norm, onto the empirical two-moment constraint set. Thus, the prescribed moments are exact for the selected quadrature rule, while continuum errors are quadrature errors of the corrected field. For decomposable high-dimensional linear operators, SDIFP combines affine moment correction with stochastic operator-subset sampling. With independent residual and derivative sampling and conditionally unbiased coefficient-gradient estimation, the resulting estimator is unbiased for the specified quadrature-based residual objective; the shared-subset fast mode is biased in general. SDIFP avoids tensor-product quadrature for moment enforcement, separates forward quadrature evaluation from the reverse-mode graph, and retains pointwise inference efficiency once the affine coefficients are fixed or precomputed.

21.
medRxiv (Medicine) 2026-06-12

Deconvolution-based cell-type specific DNA methylation-wide and transcriptome-wide association studies identify risk CpG sites and genes associated with colorectal cancer risk

Bulk tissue-based DNA methylation-wide (MWAS) and transcriptome-wide association studies (TWAS) have identified CpG sites and genes associated with colorectal cancer (CRC) risk, but do not account for cellular heterogeneity. To address this, we developed a deconvolution-informed framework to infer cell-type specific DNA methylation and gene expression profiles from bulk normal colon tissues using reference single-cell epigenomic and transcriptomic datasets. We performed cell-type specific MWAS (ctMWAS) using deconvoluted DNA methylation data from 293 normal colon samples and conducted cell-type specific TWAS (ctTWAS) using deconvoluted gene expression data from 707 normal colon samples. Genetically predicted methylation and expression models were integrated with CRC GWAS summary statistics (78,473 cases and 107,143 controls) to identify risk-associated CpG sites and genes. Through ctMWAS, ctTWAS, and colocalization analyses, we identified 178 significant cell-type-specific CpG sites in 106 loci and 68 risk genes in 40 loci, including 26 previously unreported loci. Through additional integrative methylation-gene analysis, we prioritized 132 candidate risk genes, the majority of which were supported by multi-omics evidence and stage-specific dysregulation across the adenoma-carcinoma and serrated-carcinoma progression pathways. Pathway enrichment analyses implicated pathways involved in DNA double-strand break repair, TP53 regulation, TGF-{beta} signaling, and innate immune responses. Among prioritized genes, 14 were identified as putative druggable targets linked to 90 FDA-approved or clinical-stage drugs. Experimental validation supports an oncogenic role for SF3A3. These findings demonstrate that deconvolution-informed integrative analyses enable cell-type-resolved identification of epigenetic and transcriptional mechanisms underlying CRC susceptibility and provide insights into disease biology, prevention, and therapeutic target discovery.

22.
bioRxiv (Bioinfo) 2026-06-16

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets

作者:

Large-scale clinical and biomedical datasets increasingly contain both diverse subgroup attributes (e.g., demographic or clinical subgroups) and multiple prediction targets. Although various machine learning approaches can address subgroup differences or multi-target prediction, they often consider these aspects independently rather than jointly. To more effectively capture the shared and subgroup-specific information in such complex datasets, we propose the Integrative Transfer Network (ITN), a deep neural network designed to leverage data across subgroups and multiple related outcomes simultaneously. In extensive experiments, including time-to-event and classification tasks where demographic subgroups and multiple disease endpoints are prevalent, ITN demonstrates consistent improvements in subgroup-specific prediction by borrowing strength from other subgroups and outcomes. We envision ITN as a unified framework for learning from heterogeneous datasets where subgroup-specific insights are critical.

23.
Nature (Science) 2026-06-24

Genetic technologies to enhance crop nutritional value under climate change

At present, more than 700 million people live with caloric hunger, and more than two billion suffer from micronutrient deficiencies, known as ‘hidden hunger’. From an agricultural viewpoint, three major objectives need to be worked towards simultaneously to achieve zero hunger (the United Nations Sustainable Development Goal 2): (1) enhanced yield; (2) higher vitamin and mineral density to sustain recommended daily intake (multi-biofortification); and (3) enhanced climate-change resilience. Although the Green Revolution increased global calorie production, it exacerbated hidden hunger by prioritizing high yield over nutritional quality. Stress from global climate change has been shown to reduce the densities of several micronutrients. CRISPR–Cas, which allows genome editing with extremely high precision, has emerged as a groundbreaking breeding technology that has already been adopted by many countries. Here we examine how CRISPR–Cas-based approaches could be used to achieve biofortification targets by enhancing micronutrient densities to the levels necessary to alleviate dietary vitamin and mineral deficiencies. Given the limited time frame available to achieve zero hunger, we argue that CRISPR–Cas technologies should be combined with metabolic engineering based on transformation and other technologies. We also consider untapped resources beyond metabolic pathways and current CRISPR–Cas methodologies to address one of the most important societal issues of the twenty-first century. This Review reflects on the joint power of genetic technologies, including untapped CRISPR–Cas techniques to combat hidden hunger and improve crop resilience, and argues in favour of their combined use to overcome these societal challenges.

24.
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/.

25.
arXiv (CS.CV) 2026-06-24

Training-free Cross-domain Few-shot Segmentation via Robust Semantic Representation and Matching

Cross-domain Few-shot Segmentation (CD-FSS) aims to transfer knowledge learned from source domain to distinct target domains, segmenting unseen target classes with only a few annotated samples. Although existing methods have made significant progress, they still rely on training or fine-tuning processes, which incur high computational costs and risk overfitting. We observe that when powerful and general-purpose vision foundation models are incorporated into these methods, their performance shows only marginal improvement or even degrades due to overfitting. To address this, we eliminate trainable parameters and propose a training-free framework to avoid both training overhead and overfitting. Built upon the self-supervised vision encoder DINOv3, our framework addresses cross-domain challenges through three core modules. First, the Semantic-aware Feature Re-fusion (SAFR) module identifies and re-fuses features that emphasize semantic patterns, generating representations with enhanced semantic discriminability. Additionally, the Adaptive Support Enhancement (ASE) module narrows semantic gaps between support and query through robust query information aggregation. Finally, the Hybrid Prototype Matching (HPM) module integrates matching results from diverse prototypes to adapt to varying semantic complexity across domains. Extensive experiments on four target domain datasets demonstrate that our method achieves state-of-the-art performance in CD-FSS without any training.