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01.
arXiv (quant-ph) 2026-06-12

Coupling-Grouped XY-QAOA for Joint Anomaly-Feature Selection

arXiv:2606.13244v1 Announce Type: new Abstract: Selecting anomalous samples and explanatory features under fixed budgets defines a coupled constrained-optimization problem. Sequential feature-first selection ranks features before choosing samples, which can overlook features whose utility depends on which samples are selected, especially when scores are calibrated from reference data that may be limited, noisy, or drifting. We instead formulate the task as joint sample-feature selection under the same fixed counts. In the analyzed formal model, calibration-error sensitivity grows linearly with the number of samples for feature-first ordering but stays constant for joint selection. We introduce Coupling-Grouped XY-QAOA, a constraint-preserving grouped-angle variant for the resulting optimization problem. On matched sparse IBM Heron R3 benchmarks, a hardware-aware implementation reduces circuit depth by 45.9%-61.3% and two-qubit gates by 2.6%-5.2% relative to Qiskit optimization level 3 on the CZ-basis target. It enables, to our knowledge, the largest reported width-depth configurations for constraint-preserving bipartite-selection QAOA hardware executions with feasible-sector retention: 64 qubits at p=2 and 36 qubits at p=3. The 20-qubit p=5 runs retain 63% valid samples. Across 36-64 qubits, fixed-angle runs yield lower-energy feasible samples than matched random-feasible sampling. Warm starts reduce the gap to strict-feasible classical references by 57.5%-80.5%, and near-budget repair matches the sparse classical reference at 36 qubits. Benchmarks show gains in balanced fixed-budget regimes, and noiseless simulations show that problem-structured angle grouping improves over same-depth XY-QAOA and matched-parameter, type-preserving randomization controls. Overall, the results support calibrated joint selection and hardware-realizable constrained-mixer execution in the tested regimes.

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

DiT-JSCC: Rethinking Deep JSCC with Diffusion Transformers and Semantic Representations

Generative joint source-channel coding (GJSCC) has emerged as a new Deep JSCC paradigm for achieving high-fidelity and robust image transmission under extreme wireless channel conditions, such as ultra-low bandwidth and low signal-to-noise ratio. Recent studies commonly adopt diffusion models as generative decoders, but they frequently produce visually realistic results with limited semantic consistency. This limitation stems from a fundamental mismatch between reconstruction-oriented JSCC encoders and generative decoders, as the former lack explicit semantic discriminability and fail to provide reliable conditional cues. In this paper, we propose DiT-JSCC, a novel GJSCC backbone that can jointly learn a semantics-prioritized representation encoder and a diffusion transformer (DiT) based generative decoder, our open-source project aims to promote the future research in GJSCC. Specifically, we design a semantics-detail dual-branch encoder that aligns naturally with a coarse-to-fine conditional DiT decoder, prioritizing semantic consistency under extreme channel conditions. Moreover, a training-free adaptive bandwidth allocation strategy inspired by Kolmogorov complexity is introduced to further improve the transmission efficiency, thereby indeed redefining the notion of information value in the era of generative decoding. Extensive experiments demonstrate that DiT-JSCC consistently outperforms existing JSCC methods in both semantic consistency and visual quality, particularly in extreme regimes.

03.
Nature (Science) 2026-06-17

The EU needs to back its ambition to end animal testing with cash

作者: 未知作者

The European Union has declared that it wants to stop using animals in chemical safety testing. Its goal will need a timeline and a serious funding commitment. The European Union has declared that it wants to stop using animals in chemical safety testing. Its goal will need a timeline and a serious funding commitment.

04.
arXiv (CS.AI) 2026-06-18

UBP2: Uncertainty-Balanced Preference Planning for Efficient Preference-based Reinforcement Learning

arXiv:2606.19328v1 Announce Type: cross Abstract: Preference-based RL provides an approach to learning reward models from pairwise comparisons of behaviors, bypassing the need for explicit reward design. However, existing methods typically rely on passive data collection and suffer from poor sample efficiency, especially during the early stages of learning. We introduce a model-based approach that actively directs exploration by jointly reasoning over uncertainties in the reward, dynamics, and value functions. Our method, Uncertainty-Balanced Preference Planning (UBP2), uses ensembles of reward, dynamics, and value function models to evaluate candidate trajectories according to a unified score that combines expected reward, terminal value, and epistemic uncertainty. Planning under this objective yields an explicit tradeoff between exploitation and information acquisition without requiring ad hoc exploration heuristics. Under standard regularity assumptions, we establish sublinear regret guarantees for both finite-horizon and infinite-horizon settings. Empirically, experiments on the Meta-World benchmark show UBP2 achieves substantially higher sample efficiency than model-free preference-based methods and non-optimistic model-based baselines.

05.
arXiv (CS.AI) 2026-06-15

CoRe-MoE: Contrastive Reweighted Mixture of Experts for Multi-Terrain Humanoid Locomotion with Gait Adaptation

arXiv:2606.04718v3 Announce Type: replace-cross Abstract: Humans primarily rely on walking and running to traverse complex terrains. Similarly, humanoid robots should be able to smoothly transition between walking and running while maintaining natural and stable locomotion. However, unifying gait transition and multi-terrain adaptation within a single policy remains challenging due to gradient interference between tasks and the distribution shift caused by terrain variations. Although Mixture-of-Experts (MoE) architectures can mitigate multi-skill interference, direct joint training often fails to achieve clear expert specialization. To address these challenges, we propose CoRe-MoE, a two-stage reinforcement learning framework that decouples gait generation from terrain adaptation. In the first stage, a stable locomotion policy is learned to produce natural walking and running behaviors with smooth transitions. In the second stage, a terrain-aware MoE branch is introduced, and the gating network is trained with a contrastive objective to learn structured terrain representations and promote expert specialization. The final action is obtained through weighted fusion of the base gait policy and the terrain-aware branch, enabling the policy to preserve stable locomotion while adapting to complex terrains. Extensive simulation results demonstrate that the proposed method outperforms baseline approaches in terms of success rate, locomotion stability, and multi-terrain adaptability. Furthermore, zero-shot deployment on a Unitree G1 humanoid robot validates the effectiveness of our framework, achieving robust walking and running across stairs, slopes, steps, obstacles, and unstructured outdoor terrains while maintaining accurate foothold control and dynamic stability.

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

The $K$-th nearest neighbor random walk on a Poisson point process gets trapped

arXiv:2606.11271v1 Announce Type: new Abstract: The $K$-th nearest neighbor random walk $(X_n)_{n \geq 0}$ on a homogeneous Poisson point process $\chi$ on $\R^d$ ($d\geq 1$), starts at the origin and at each step picks its next Poisson point among its closest neighbors according to i.i.d. labels having the same distribution as $K$. Our main result (Theorem 1) states that the number of Poisson points visited by $(X_n)_{n \geq 0}$ admits an exponential decay whenever the random variable $K$ has a bounded support (BS). In particular, the $K$-th nearest neighbor random walk visits finitely many Poisson points if and only if $K$ satisfies Assumption (BS). To prove it, we introduce the key notion of pioneer point which allows us to deal with the region of $\R^d$ already explored by $(X_n)_{n \geq 0}$. Still under Assumption (BS), we also prove an exponential decay for the Euclidean length of the trajectory performed by $(X_n)_{n \geq 0}$ (Theorem 2). Finally, and quite surprisingly, we exhibit an example of label distribution with bounded support for which the $K$-th nearest neighbor random walk discovers new Poisson points after a number of steps whose tail distribution is at least polynomial (Theorem 3).

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

Can LLMs Be CEOs? Benchmarking Strategic Resource Reallocation with Multi-Role Agent Simulation

arXiv:2606.17459v1 Announce Type: new Abstract: Evaluating the decision-making capabilities of large language models (LLMs) is a growing research priority, yet existing benchmarks focus on isolated cognitive tasks such as reasoning, knowledge retrieval, and economic rationality in stylized settings. These evaluations overlook the defining challenge of real executive decision-making: integrating conflicting recommendations from specialized stakeholders under information asymmetry, organizational constraints, and temporal dependencies. We introduce \textsc{CEO-Bench}, a multi-agent benchmark that evaluates LLMs on CEO-level strategic resource reallocation – the process of redirecting capital across business units in a multi-round, constraint-rich organizational environment. In \textsc{CEO-Bench}, LLM agents receive conflicting advice from four role-conditioned C-suite advisors (CFO, CTO, COO, CMO), each with private signals and distinct priorities, and must synthesize these into a concrete allocation plan evaluated along four dimensions: role integration, conditional boldness, history-sensitive judgment, and plan validity. Experiments across five frontier models on 13 scenarios reveal that all models achieve high structural validity but diverge sharply on strategic calibration – the hardest capability layer. We identify systematic failure modes including single-advisor capture, conservative default under ambiguity, and historical amnesia, and uncover a structural integration-boldness tradeoff: models that engage more deeply with conflicting perspectives tend to produce less decisive action. These findings delineate the current capability boundary of LLMs as organizational decision-makers and inform the design of future AI-assisted executive systems.

08.
arXiv (CS.CV) 2026-06-19

Current World Models Lack a Persistent State Core

World models are increasingly regarded as a decisive step toward artificial general intelligence, yet modeling the physical world demands more than rendering convincing frames on demand: it requires an internal world state that keeps evolving over time, decoupled from observation, so that objects endure and events run to their conclusions whether or not a camera is watching, much as the moon holds to its orbit when no one is looking. This requirement is a blind spot of existing benchmarks, which reward surface properties such as fidelity, motion, and camera controllability while never asking whether a generated world keeps evolving once it is unobserved. We introduce WRBench, the first systematic diagnostic benchmark that treats camera motion as an intervention on observability and resolves evaluation into a human-calibrated chain that asks whether the camera executes the requested interaction, whether the scene stays continuous and identifiable while in view, and whether a returning target remains consistent with the event that was set in motion. Across 9{,}600 videos from 23 models spanning four control paradigms, one finding proves stubborn: current systems maintain the observed world as a tracking shot, resuming a returning target in the state at which it was abandoned rather than advancing the event while it went unseen. Because this failure recurs across control paradigms, model families, and increments of scale, robust world-state evolution does not follow from cleaner imagery, tighter control, richer geometric priors, or sheer parameter count We therefore argue that the stability of the physical state kernel and the consistency of worldlines under viewpoint intervention should become first-class objectives of world-model design, so that a world model captures how the world will unfold rather than how the next frame appears.

09.
arXiv (CS.CV) 2026-06-11

Exploring Adaptive Masked Reconstruction for Self-Supervised Skeleton-Based Action Recognition

Recently, masked skeleton reconstruction models have emerged as strong action representation learners, driving significant progress in self-supervised skeleton-based action recognition. However, existing state-of-the-art methods must predict an exceedingly large number of spatiotemporal patches, significantly prolonging training time. Besides, by treating all spatiotemporal regions equally during reconstruction, these models are distracted from learning the critical motion patterns that underlie action semantics. To address these challenges, we propose Adaptive Masked Reconstruction (AMR), a faster and stronger pre-training framework. We first decouple the decoder from the encoder, enabling flexible prediction of larger spatiotemporal patches and dramatically reducing reconstruction complexity. Given that larger patches contain more complex information, which is challenging to predict and consequently degrades performance, we accordingly introduce an adaptive guidance module. This module identifies regions of high motion informativeness, guiding the model to focus on the most discriminative parts of each patch and alleviating reconstruction difficulty. Experiments on NTU RGB+D 60, NTU RGB+D 120, and PKU-MMD datasets demonstrate that AMR not only accelerates pre-training substantially but also improves downstream recognition accuracy, surpassing current state-of-the-art approaches.

10.
Nature (Science) 2026-06-17

Confined migration induces non-lethal DNA damage in developing neurons

Migratory cells tend to have soft nuclei that deform and penetrate narrow spaces1,2. Extensive nuclear deformation during migration can cause nuclear-envelope rupture and DNA damage in cancer cells, which may contribute to malignant transformation during tumour progression3–6. However, the importance of DNA damage in physiological migration is less well understood. Here we demonstrate that the migration of neurons in developing cerebral and cerebellar cortices is accompanied by massive DNA double-stranded breaks (DSBs) due to mechanostress during passage through narrow interstitial spaces. In contrast to many other migratory cells, these DSBs occur without detectable nuclear envelope rupture. Confined migration increases topoisomerase-IIβ covalently bound DSBs, and these lesions are repaired through non-homologous end-joining during brain development without causing cell death. Genome sequencing revealed that DSBs tend to occur at transcriptionally inactive regions. The deletion of ligase IV at the onset of neuronal migration leads to persistent DSB accumulation in cerebellar neurons with moderate transcriptional changes in genes related to synaptic function, neuronal development and stress and immune responses. The mutant mouse develops mild motor deficits in later life, suggesting that the DNA damage generated during normal brain development poses a potential disease risk if left unrepaired. The migration of neurons in developing cerebral and cerebellar cortices is accompanied by massive DNA double-strand breaks due to mechanostress during passage through narrow interstitial spaces.

11.
medRxiv (Medicine) 2026-06-17

Perceptions of aging well among older adults with heart failure: insights from a qualitative study

Background: Heart failure (HF) is a prevalent and often debilitating cardiovascular condition among older adults, frequently accompanied by multimorbidity, functional limitations, and the need to age in place. Traditional models of successful aging emphasize disease absence and preserved function, yet most individuals with HF live with ongoing symptoms and chronic health challenges. How older adults with HF define aging well, particularly across different socioeconomic contexts, remains underexplored. Objectives: To explore how older adults with HF conceptualize aging well and to identify perceived facilitators and barriers across more and less resourced New York City neighborhoods. Methods: We conducted semi-structured interviews with 20 adults diagnosed with HF residing in Manhattan and Brooklyn neighborhoods classified by 2019 United States Census data. Interviews were guided by Rowe and Kahn's model. Transcripts were analyzed using an inductive-deductive thematic approach and interpreted in alignment with the Healthy People 2030 framework. Results: Participants had a mean age of 69 years; 50% identified as Black and 50% were women. Despite functional limitations, 65% reported aging well. Five themes emerged: maintaining physical function, maintaining cognitive function, sustaining social relationships, avoiding pain, and promoting overall well-being. Avoiding pain and promoting well-being extended beyond traditional models. Neighborhood context shaped priorities, with financial stability emphasized in more affluent areas and social cohesion prioritized in less affluent communities. Conclusions: Older adults with HF frequently perceive themselves as aging well despite chronic illness, reframing successful aging beyond disease avoidance. These findings support a patient-centered, place-informed model of aging well with implications for healthcare delivery and policy.

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

SpikeTAD: Spiking Neural Networks for End-to-End Temporal Action Detection

Video understanding is a crucial part of computer vision, with numerous application scenarios. With the increasing popularity of mobile devices, an increasing number of efforts are trying to deploy video understanding models on them. However, existing video understanding models are difficult to deploy due to their large size and prohibitive power consumption. Spiking Neural Networks (SNNs) have shown bioplausibility and low power advantages over Artificial Neural Networks (ANNs), especially on neuromorphic chips which are regarded as essential components of future mobile devices. However, excessively long conversion time-steps and severe performance degradation problems limit their application. To solve the problems above, we explore the application of SNNs on temporal action detection (TAD), which is an important task in video understanding, and propose the first SNN-based end-to-end TAD architecture coined as SpikeTAD. While maintaining extremely low power consumption, SpikeTAD achieves an average mAP of 67.2% in THUMOS14 and 37.42% in ActivityNet-1.3, demonstrating the feasibility of a low-power TAD model. Our code is available at https://github.com/MCG-NJU/SpikeTAD.

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

Contaminated Collaboration: Measuring Gender Bias Transfer in LLM-Assisted Student Writing

Gender bias in LLMs has been studied extensively in model outputs, with biased prompts shown to amplify stereotyped generations. Whether such bias propagates into text produced by humans who use these systems, however, remains underexplored. We investigate whether gender bias in an LLM writing assistant transfers into career plan essays written by students. We first verify that a gender-biased prompt induces gender-differentiated language in LLM-generated essays, while a neutral prompt does not. We then recruited participants (N = 123) in a controlled environment to write career plan essays for paired biographical profiles differing only in gender under three conditions: no AI assistance, neutral LLM assistance, or gender-biased LLM assistance. Students in the biased condition produced essays with a significantly larger agentic gap and more gender-stereotypic occupation suggestions than those in the control and neutral conditions. Our results also reveal that this bias transfer is asymmetric: agency is suppressed in female-target essays while male-target writing remains largely unaffected. Our findings highlight the risk of bias propagation in AI-assisted writing, calling for fairness-aware design in educational AI tools.

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

How Auxiliary Reasoning Unleashes GUI Grounding in VLMs

Graphical user interface (GUI) grounding is a fundamental task for building GUI agents. However, general vision-language models (VLMs) struggle with this task due to a lack of specific optimization. We identify a key gap in this paper: while VLMs exhibit significant latent grounding potential, as demonstrated by their performance measured by Pointing Game, they underperform when tasked with outputting explicit coordinates. To address this discrepancy and bypass the high data and annotation costs of current fine-tuning approaches, we propose three zero-shot auxiliary reasoning methods. By providing explicit spatial cues such as axes, grids and labeled intersections as part of the input image, these methods enable VLMs to better articulate their implicit spatial understanding capabilities. We evaluate these methods on four GUI grounding benchmarks across seven open-source and proprietary VLMs. Experimental results show substantial gains from auxiliary reasoning. Mark-Grid Scaffold boosts Gemini-3.1-Pro from 11.72\% under direct inference to 95.20\% on ScreenSpot-v2, achieves state-of-the-art performance on ScreenSpot, and approaches the strongest fine-tuned methods on ScreenSpot-v2 and UI-I2E-Bench. Our code is available at https://github.com/liweim/AuxiliaryReasoning.

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

Modeling light-matter coupled systems with neural quantum states

arXiv:2606.14352v1 Announce Type: cross Abstract: Recent advances in cold atom manipulation enable the study of many-body systems where short-range interactions between neighboring atoms coexist with long-range interactions mediated by photons. Such a combination of interactions makes a theoretical approach challenging beyond mean-field methods. In this work, we develop a neural quantum state based approach to study these systems numerically. We introduce a neural-network architecture capable of handling hybrid Hilbert spaces with large local bosonic dimensions in strongly interacting spin-photon systems. We benchmark this approach on a model of a two-dimensional lattice of Rydberg atoms coupled to a photon mode. The superradiant ground states found in the large spin-photon coupling regime allow us to demonstrate the efficiency of the method in the presence of high photon occupation. Furthermore, the ability to capture spin-spin and spin-photon correlations leads us to observe quantitative deviations in the ground state phase boundaries with respect to mean-field theory. The method extends to other systems with a similar hybrid Hilbert space structure, such as spin-phonon systems, and provides a scalable framework for investigating their ground state properties.

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

Optimizing Agentic Reasoning with Retrieval via Synthetic Semantic Information Gain Reward

arXiv:2602.00845v3 Announce Type: replace Abstract: Agentic reasoning enables large reasoning models (LRMs) to dynamically acquire external knowledge, but yet optimizing the retrieval process remains challenging due to the lack of dense, principled reward signals. In this paper, we introduce InfoReasoner, a unified framework that incentivizes effective information seeking via a synthetic semantic information gain reward. Theoretically, we redefine information gain as uncertainty reduction over the model's belief states, establishing guarantees, including non-negativity, telescoping additivity, and channel monotonicity. Practically, to enable scalable optimization without manual retrieval annotations, we propose an output-aware intrinsic estimator that computes information gain directly from the model's output distributions using semantic clustering via bidirectional textual entailment. This intrinsic reward guides the policy to maximize epistemic progress, enabling efficient training via Group Relative Policy Optimization (GRPO). Experiments across seven question-answering benchmarks demonstrate that InfoReasoner consistently outperforms strong retrieval-augmented baselines, achieving up to 5.4% average accuracy improvement. Our work provides a theoretically grounded and scalable path toward agentic reasoning with retrieval. The code is available at https://github.com/dl-m9/InfoReasoner

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

Rethinking Text-to-Image as Semantic-Aware Data Augmentation for Indoor Scene Recognition

In the realm of computer vision, indoor image recognition presents challenges due to the intricate interplay of lighting conditions, occlusions, and diverse object arrangements within confined spaces. To address the lacks of training indoor images, we introduce a novel approach leveraging Stable Diffusion (SD) for the generation of synthetic images, which serve as a powerful data augmentation tool. The utilization of SD offers a principled framework for synthesizing diverse and realistic indoor scenes, thereby enriching the training data pool for robust indoor image recognition models. Experimental findings on the MIT Indoor Scene dataset reveal the potential of our proposed approach in enhancing the training of deep models when authentic data is limited. Furthermore, to prevent the misuse of SD synthetic images, we introduce a counter measure based on DIffusion Reconstruction Error (DIRE). The powerful DIRE presentation enables training robust classifiers only using lightweight deep models. Experiments show that our approach can perfectly recognize SD generated images with the accuracy of 100% using MobilenetV3.

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

Discrete optimal transport is a strong audio adversarial attack

arXiv:2509.14959v3 Announce Type: replace-cross Abstract: In this paper, we investigate discrete optimal transport (DOT) as a black-box attack against modern automatic speaker verification (ASV) and anti-spoofing countermeasure (CM) systems. Our attack operates as a post-processing distribution-alignment step. Frame-level WavLM embeddings of generated speech (or another person speech) are aligned to an unpaired bona fide speech pool using entropic optimal transport and a top-k barycentric projection, followed by neural vocoding. Unlike gradient-based attacks, the proposed method requires no access to model parameters, gradients, or training data. Experiments on ASVspoof2019 and ASVspoof5 demonstrate that DOT attack substantially increases CM EER and substantially degrades ASV performance across multiple spoofing attacks. The attack transfers across datasets and remains effective after CM fine-tuning. Analysis using speaker similarity, Fréchet Audio Distance, and visualization of embedding distributions suggests that DOT succeeds by shifting source speech toward bona fide regions of the representation space rather than by maximizing speaker similarity. These results indicate that optimal-transport-based distribution alignment represents a previously underexplored attack vector for contemporary ASV and anti-spoofing systems.

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

Minimal Filling Architectures of Polynomial Neural Networks: Counterexamples, Frontier Search, and Defects

arXiv:2605.09609v2 Announce Type: replace Abstract: We provide counterexamples to the unimodal minimal filling architecture conjecture for polynomial neural networks (PNNs) with power activation functions. Fixing the input and output widths, the conjecture states that any minimal filling architecture has unimodal widths for the hidden layers. We found counterexamples via a frontier search, recursive dimension bounds on neurovarieties, and symbolic computation. Notably, several subarchitectures of our main example exhibit large defect, in contrast with the predominantly small-defect behavior observed in prior literature.

20.
arXiv (CS.CL) 2026-06-18

Beyond Tokenization: Direct Timestep Embedding and Contrastive Alignment for Time-Series Question Answering

Recent advances in large language models (LLMs) have given rise to time-series question answering (TSQA), which formulates time-series analysis as natural-language question answering. However, directly feeding raw numerical series into LLMs suffers from a tokenization bottleneck: Byte Pair Encoding fragments continuous values into unstable tokens whose embeddings lack meaningful metric structure, resulting in the loss of magnitude, scale, and trend information. Prior methods use patch-based encoders that split the series into fixed windows, locking in one granularity that breaks patterns and hides exact timesteps, through a separate module that rarely transfers across datasets with different lengths or sampling rates. To address this challenge, we propose CADE (Contrastive Alignment with Direct Embedding), a novel framework for TSQA built upon two key components: direct timestep embedding and semantic alignment. The proposed framework maps each timestep directly into the LLM embedding space through a point-wise linear encoder and MLP projector, preserving exact index-level access while eliminating the need for patching and padding. To further bridge the semantic gap between time-series and language representations, we introduce a novel one-directional supervised contrastive loss that aligns time-series embeddings with frozen class-name text anchors. Experimental results on the public Time-MQA benchmark demonstrate that our framework consistently improves performance across six TSQA tasks, outperforming both open-source and proprietary LLM baselines.

21.
bioRxiv (Bioinfo) 2026-06-11

DModE: An end-to-end framework for Differential Modification and Expression Analysis of Nanopore direct RNA sequencing data

Summary: Nanopore direct RNA sequencing (DRS) enables simultaneous quantification of transcript abundance and RNA modifications from native RNA molecules, providing a unique opportunity to study transcriptional and epitranscriptomic regulation within a single experiment. However, comprehensive analysis of DRS data remains challenging, as existing workflows typically focus on individual processing steps and often require manual integration of multiple software packages for expression analysis, modification detection, statistical testing, and visualization. Furthermore, integrated differential expression and differential RNA modification analysis at both gene and isoform resolution remains poorly supported by current workflows. Here, we present DModE (Differential Modification and Expression Analysis), an end-to-end framework for integrated analysis of Nanopore DRS data. DModE combines an Epi2ME-compatible Nextflow preprocessing workflow with a dedicated Python package for downstream statistical analysis, visualization, and reporting. The framework supports differential gene and isoform expression analysis, differential RNA modification analysis at genome and transcript level, metagene profiling, exploratory epitranscriptomic analyses, and integrated assessment of relationships between expression and modification dynamics. Results are automatically summarized in interactive HTML reports, facilitating reproducible and accessible data interpretation. By integrating transcriptomic and epitranscriptomic analyses within a single framework, DModE substantially simplifies comprehensive DRS data analysis and lowers the barrier for studying RNA modification biology using Nanopore sequencing.

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

When Does Language Matter? Multilingual Instructions Reveal Step-wise Language Sensitivity in Vision-Language-Action Models

Vision-Language-Action (VLA) models have shown strong performance in language-conditioned robotic manipulation, yet their robustness to linguistic variation remains poorly understood. In this work, we present the first systematic multilingual evaluation of VLA models by translating the LIBERO benchmark into ten languages, revealing severe performance degradation under non-English instructions, with success rates dropping by 30-50%. Through fine-grained analysis of task executions, we find that language influence is highly non-uniform across steps: certain steps exhibit strong language dependence and dominate overall task failure, while others are largely language-agnostic. Based on this insight, we propose a step-wise inference-time intervention that aligns representations according to step language sensitivity, substantially improving performance under linguistic variation. Our results indicate that language robustness in VLA models is fundamentally a step-wise control problem, highlighting the importance of temporally structured analysis for reliable embodied agents.

23.
medRxiv (Medicine) 2026-06-18

Plasma proteomics reveals clinical and mechanistic heterogeneity among individuals who develop coronary artery disease

BACKGROUND: Individuals who develop coronary artery disease (CAD) are clinically and mechanistically heterogeneous, and understanding this variation is crucial for precise risk stratification and tailored interventions. However, the molecular mechanisms that connect these two kinds of heterogeneity remain unclear, limiting progress toward biologically grounded risk stratification and targeted interventions. Here, we investigated the heterogeneity of individuals who develop CAD by leveraging plasma proteomic signatures, placed individuals along continuous metabolic gradients and revealed the molecular programs underlying these patterns, thereby linking mechanistic variation to clinical heterogeneity. METHODS AND RESULTS: From 42,803 UK Biobank participants, including 3,713 individuals who developed CAD within 10 years (incident CAD), we first identified a 320-protein panel from 2,923 baseline proteins that improved prediction of incident CAD beyond clinical risk scores. Using reverse graph embedding, we reduced the proteomic data to two dimensions and mapped each incident case onto the resulting two-dimensional latent proteomic space. These proteomic dimensions show significant associations with cardiometabolic and kidney-related clinical markers. The patterns were replicated in the EPIC-Norfolk study. Phenome-wide Cox regression analyses further linked these proteomic dimensions to 10-year incidence rates for various diseases, including type 2 diabetes, obesity, and chronic kidney disease (CKD). Furthermore, adding the proteomic dimensions to clinical variable-based Cox regression model improved prediction of 10-year incidence of CKD and other diseases, demonstrating the value of proteomic dimensions beyond conventional clinical risk factors. Moreover, individuals with prevalent CAD (diagnosed before proteomic sampling) exhibited high, metabolically adverse dimension values, indicating that these axes capture cumulative metabolic burden. Pathway enrichment analyses implicated altered extracellular matrix organization and immune programs among the proteins contributing to the proteomic dimensions. CONCLUSIONS: Our findings demonstrate that plasma proteomic signatures can dissect the heterogeneity of individuals who develop CAD in continuous phenotypic gradients, improve prediction of CAD and comorbidities, and map underlying biological mechanisms.

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

Querying Counterfactuals on Tissue Graphs with Supervised Disentanglement

arXiv:2606.08493v2 Announce Type: replace-cross Abstract: Tissue graph counterfactuals ask how a cell's expression would change under altered spatial neighbor contexts. Such queries are central to predicting cell behavior in tissues, but lack a unified definition, with existing methods targeting specific intervention types or treating cells as i.i.d. In this work, we first formalize tissue graph counterfactuals as a class of spatial interventions that either rewire connections between cells (edge perturbation) or modify the expression of their neighbors (node perturbation). We then introduce Cellina (https://cellina.readthedocs.io) - a framework that uses supervised disentanglement to decompose a cell's intrinsic state from its spatial context, using the latter as a conditioning input for counterfactual predictions. Across benchmarks spanning over 2.5 million spatially-resolved cells in colorectal cancer and mouse brain, Cellina outperforms spatially-informed and non-spatial competitors in in-silico graph perturbations, disentanglement, and scalability. Additionally, we show that Cellina reveals biologically distinct cancer subdomains in an unsupervised manner and enables targeted neighbor perturbation simulations.

25.
arXiv (CS.CL) 2026-06-19

Diffusion Language Models: An Experimental Analysis

Large Language Models (LLMs) have revolutionized language modeling through autoregressive generation, enabling strong performance across a wide range of tasks. Recently, Diffusion Language Models (DLMs) have emerged as an alternative paradigm that generates text through iterative denoising rather than next-token prediction, allowing parallel refinement of entire sequences. While numerous diffusion-based architectures have been proposed, differences in evaluation protocols, datasets, inference budgets, and generation hyperparameters make it difficult to compare their capabilities and understand the trade-offs they offer. In this work, we present a systematic experimental analysis of modern DLMs. Specifically, we evaluate eight state-of-the-art DLMs across eight benchmarks spanning reasoning, coding, translation, knowledge, and structured problem solving, while explicitly considering both generation quality and computational efficiency. Beyond downstream evaluation, we analyze the impact of key inference-time factors, including denoising steps, context length, block size, and parallel unmasking strategies, and complement large-scale experiments with controlled comparisons of smaller models trained under identical conditions. Our analysis highlights the strengths and limitations of diffusion-based language modeling across different tasks, architectures, and inference budgets. We show that the behavior of DLMs is strongly influenced by generation-time design choices, leading to distinct trade-offs between performance and computational efficiency. Overall, our study provides practical insights into the capabilities and deployment characteristics of contemporary DLMs.