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01.
arXiv (quant-ph) 2026-06-15

Path superposition activating perfect quantum teleportation ability for separable states

arXiv:2505.11398v2 Announce Type: replace Abstract: Quantum teleportation is a quintessential quantum communication protocol that enables the transmission of an arbitrary quantum state between two distant parties without physically transmitting the state with the help of shared entanglement and limited classical communication. We show that it is possible to relax the entanglement requirement in quantum teleportation if we have access to a certain strain of superposition of quantum processes. Two types of superposition of quantum processes are generally considered in the literature: superposition of paths identified with quantum maps and superposition of indefinite causal orders of the maps. We find that when superposition of paths is incorporated in the protocol, quantum teleportation with unit fidelity becomes possible with nonzero probability of 1/4 even when the two parties share certain classes of separable states, including pure product states. In contrast, the assistance of superposition of indefinite causal order of quantum maps in teleportation protocol does not enable any quantum advantage for shared pure product states. Furthermore, we show that separable Werner states can also yield quantum advantage in quantum teleportation assisted by the superposition of paths. Finally, we establish that the presence of quantum coherence in the control qubit is both necessary and sufficient to achieve quantum advantage in quantum teleportation assisted with superposition of paths. The results potentially uncover yet another role of quantum superposition, in general, in teleportation versus entanglement.

02.
arXiv (CS.AI) 2026-06-15

VISTA: View-Consistent Self-Verified Training for GUI Grounding

arXiv:2606.14579v1 Announce Type: new Abstract: When applying Group Relative Policy Optimization (GRPO) for GUI Grounding, rollouts are sampled from a single screenshot view; groups often become either all failures on difficult instances or all successes on easy ones, yielding no useful relative advantage. We propose VISTA (View-Consistent Self-Verified Training), a GRPO-based training framework that constructs each comparison group from multiple target-preserving views of the same GUI instance.Each view is generated by a crop that keeps the target element visible and remaps its box exactly, so model rollouts are compared across semantically equivalent but geometrically different inputs. To stabilize short coordinate generation without turning reinforcement learning into unconditional imitation, VISTA further adds a self-verified cross-view anchor: an oracle answer optimized with an advantage-weighted loss, excluded from the group baseline and activated only when the model has produced a maximum-reward rollout. Across five GUI-grounding benchmarks and multiple Qwen backbones, VISTA consistently improves grounding accuracy.On ScreenSpot-Pro, it raises Qwen3-VL 4B/8B/30B-A3B from 55.5/52.7/53.7 to 63.4/65.8/67.0. Robustness analyses further show higher worst-view accuracy and lower prediction flip rates.

03.
arXiv (math.PR) 2026-06-15

Sharp Favard length of random Cantor sets

arXiv:2512.17753v2 Announce Type: replace-cross Abstract: We show that for a large class of planar $1$-dimensional random fractals $S$, the Favard length $\operatorname{Fav}(S(r))$ of the neighborhood $S(r)$ is comparable to $\log^{-1}(1/r)$, matching a universal lower bound; up to now, this was only known in expectation for a few concrete models. In particular, we show that there exist $1$-Ahlfors regular sets with the fastest possible Favard length decay. For a wide class of planar one-dimensional "grid random fractals", including fractal percolation and its Ahlfors-regular variants, we further show that $\operatorname{Fav}(S(r))/\log(1/r)$ converges almost surely, and we identify the limit explicitly. Furthermore, we prove that for some $1$-dimensional Ahlfors-regular random fractals $S$, the Favard length of $S(r)$ decays instead like $\log\log(1/r)/\log(1/r)$, showing that the $1/\log(1/r)$ decay is not universal among random fractals, as might be expected from previous results.

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

Automated jailbreak attack targeting multiple defense strategies

arXiv:2606.16751v1 Announce Type: cross Abstract: Large language models (LLMs) have demonstrated remarkable capabilities across a wide range of tasks. However, their safety remains a critical concern due to their susceptibility to adversarial prompt-based attacks. In this paper, we present UNIATTACK, an adversarial testing framework designed from a defense-oriented perspective to systematically construct effective black-box attack prompts. Unlike prior approaches that rely on static templates or iterative model-specific tuning, UNIATTACK extracts minimal but high-impact attack features from diverse existing attacks, optimizes them via a specialized attacker LLM, and composes them into flexible templates through automated refinement process. This feature-centric construction enables one-shot attacks that generalize across multiple models and safety categories, providing a practical tool for assessing LLM robustness. Our evaluation results shows that compared to the baselines, UNIATTACK achieves an average attack success rate (ASR) improvement of 64.63\%-248.82\% on models deployed with multi-layered defense mechanisms and it only takes 0.03\%-4.96\% cost of the baselines. UNIATTACK artifact is available at https://anonymous.4open.science/r/UniAttack-Artifact-30F1.

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

PaLMR: Towards Faithful Visual Reasoning via Multimodal Process Alignment

Reinforcement learning has recently improved the reasoning ability of Large Language Models and Multimodal LLMs, yet prevailing reward designs emphasise final-answer correctness and consequently tolerate process hallucinations–cases where models reach the right answer while misperceiving visual evidence. We address this process-level misalignment with PaLMR, a framework that aligns not only outcomes but also the reasoning process itself. PaLMR comprises two complementary components: a perception-aligned data layer that constructs process-aware reasoning data with structured pseudo-ground-truths and verifiable visual facts, and a process-aligned optimisation layer that constructs a hierarchical reward fusion scheme with a process-aware scoring function to encourage visually faithful chains-of-thought and improve training stability. Experiments on Qwen2.5-VL-7B show that our approach substantially reduces reasoning hallucinations and improves visual reasoning fidelity, achieving state-of-the-art results on HallusionBench while maintaining strong performance on MMMU, MathVista, and MathVerse. These findings indicate that PaLMR offers a principled and practical route to process-aligned multimodal reasoning, advancing the reliability and interpretability of MLLMs.

06.
medRxiv (Medicine) 2026-06-15

Sociodemographic Disparities in Tafamidis Initiation and Clinical Outcomes in ATTR-CM Across the United States

BACKGROUND Transthyretin amyloid cardiomyopathy (ATTR-CM) is a progressive, life-threatening disease. Sociodemographic factors may influence time to treatment initiation and resulting clinical outcomes, yet these relationships are poorly characterized. OBJECTIVE Assess the effects of sex and race on tafamidis initiation and subsequent outcomes and their interaction with factors such as ATTR-CM type and social deprivation measures. METHODS A retrospective cohort analysis was conducted using the US Komodo Healthcare Map (01/2016-06/2024) among patients with amyloidosis, identified by ICD-10-CM diagnosis codes. Cumulative incidence of treatment initiation and survival probabilities for cardiovascular-related hospitalization (CVH) or death were estimated by Kaplan-Meier, stratified by sex and race. Cox proportional hazards models were fitted for both endpoints to estimate hazard ratios, adjusting for demographics and clinical characteristics. RESULTS Of 11,311 patients identified, White and Black patients (n=9,223) were included in subsequent analyses. Within 12 months of diagnosis, White women had the lowest cumulative incidence of tafamidis initiation (11.4%), followed by Black women (22.0%), Black men (26.7%), and White men (31.0%). Event-free survival at 12 months was lowest in Black women (42.9%), followed by Black men (46.8%), White women (48.6%), and White men (54.4%). Median (95% CI) time to CVH or death was shortest for Black women (8.0 months [6.8-10.0]) followed by Black men (9.9 months [8.8-12.0]), White women (11.0 months [9.6-13.0]), and White men (15.0 months [14.0-16.0]). CONCLUSIONS In this large, real-world cohort of US patients with ATTR-CM, sex and race contributed to disparities in tafamidis initiation and survival, underscoring compounded disparities in both access and outcomes.

07.
arXiv (CS.AI) 2026-06-16

RollArt: Disaggregated Multi-Task Agentic RL Training at Scale

arXiv:2512.22560v2 Announce Type: replace-cross Abstract: Agentic Reinforcement Learning (RL) trains LLMs through multi-turn interactions with environments, producing workloads that mix compute-bound prefill, bandwidth-bound decoding, CPU-heavy environment execution, and bursty reward evaluation. Existing systems either colocate all stages on a single GPU cluster or decouple them only at a coarse granularity, overlooking hardware heterogeneity and incurring substantial synchronization overhead across stages. We present ROLLART, a system for multi-task agentic RL on disaggregated infrastructure. ROLLART maps each pipeline stage to best-fit hardware, routing prefill-heavy tasks to compute-optimized GPUs, decode-heavy tasks to bandwidth-optimized GPUs, and environments to CPU clusters. It decouples rollout at the trajectory level, allowing generation, environment interaction, and reward scoring to proceed independently, so that slow or failed environments never block the others. ROLLART offloads stateless reward computation to serverless infrastructure and overlaps rollout with training via staleness-bounded asynchronous weight synchronization. Our results demonstrate that ROLLART effectively improves training throughput and achieves 1.31–2.05 \(\times\) training time reduction compared to various RL systems. We also evaluated ROLLART by training a hundreds-of-billions-parameter MoE model for Qoder product on an Alibaba cluster with above 3,000 GPUs, demonstrating its stability and scalability.

08.
bioRxiv (Bioinfo) 2026-06-18

fuzzyfold: a high-performance framework for stochastic RNA folding kinetics

Authors:

The analysis of nucleic acid secondary structures is overwhelmingly dominated by methods that analyze the thermodynamic equilibrium distribution and which ignore all dynamic aspects of nucleic acid folding. Yet, there are numerous popular examples of nucleic acid folding that rely on kinetic models, such as RNA riboswitches or DNA strand displacement systems. Here, I am presenting fuzzyfold, a Rust-based software package for nucleic acid secondary structure analysis with an explicit focus on stochastic modeling. The framework introduces three-way and four-way shift moves with a biophysically motivated rate-model parameterization, and it is developed with an emphasis on both model flexibility and performance, e.g. allowing for the generation of single co-transcriptional trajectories for thousand-nucleotide long RNA molecules in just a few minutes. The main strength of the fuzzyfold package, however, is its focus on user and developer interfaces for long-term development. It provides easily installable command-line interfaces, e.g. for aggregating data from multiple parallel trajectories efficiently into an ensemble-level dynamic analysis. For developers, the code-base supports straight-forward substitution of thermodynamic and kinetic free-energy models, and a flexible library interface with Python bindings, enabling integration of individual components into custom computational workflows.

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

CogCanvas: A Benchmark for Evaluating Multi-Subject Reference-Based Image Generation

Multi-subject reference-based image generation requires jointly preserving multiple human identities, binding per-person objects and fashion items, and respecting a specified background scene, a regime where current diffusion models remain brittle. Existing benchmarks evaluate only one axis at a time and none jointly captures multi-identity composition with human-object interaction, background grounding, and spatial plausibility. We introduce CogCanvas, a benchmark of 1,952 curated reference images spanning 100 celebrity identities, 115 distinctive objects and fashion items, and 29 real-world background scenes including landmarks, from which we construct 1,361 compositional prompts covering 2-5 person group sizes. The curation pipeline combines DINOv2-based deduplication, two-stage aesthetic filtering, and automated derivation of structured interaction and position graphs that serve as ground-truth supervision. CogCanvas supports three tasks, reference-based multi-human-object generation (primary), text-to-image compositional generation, and reference retrieval, under a unified six-axis evaluation protocol. We introduce two metrics tailored to the multi-reference setting: BG-Sim, which scores background fidelity on SAM 3-masked regions via DINOv3 feature similarity, and Attr-VQA, which uses a multimodal LLM to verify per-subject attribute binding and inter-person interactions against the structured graphs. Benchmarking five SOTA methods reveals that every model degrades substantially as group size grows from 2 to 5, with near-complete failure on object/fashion binding beyond three subjects.

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

EyeMVP: OCT-Informed Fundus Representation Learning via Paired CFP–OCT Pretraining

Color fundus photography (CFP) is the mainstay for large-scale retinal screening, yet its diagnostic capacity is constrained by the lack of depth-resolved structural information. Optical coherence tomography (OCT) provides cross-sectional retinal anatomy, but is less accessible in population-level screening. Here, we present EyeMVP, a cross-modal retinal foundation model that uses paired CFP–OCT pretraining to learn OCT-informed CFP representations. EyeMVP is pretrained on 674,893 strict same-eye same-day paired CFP–OCT image triples from 112,642 patients across eight hospitals in China. The model uses cross-modal masked reconstruction to enrich CFP representations with OCT-associated supervision, while requiring only CFP images at inference. To accommodate the non-aligned imaging geometry between en-face CFP and cross-sectional OCT, EyeMVP combines source-constrained cross-attention with CFP-derived structural masks. Across 16 downstream tasks, including classification, segmentation, few-shot adaptation, and cross-modal retrieval, EyeMVP outperforms representative retinal foundation models and shows consistent gains on tasks involving macular and optic nerve structure. For CFP-challenging macular diseases, EyeMVP achieves an AUROC of 0.948 for macular edema (vs.~0.852 for EyeCLIP) and 0.825 for myopic macular schisis. In an exploratory reader study, EyeMVP exceeds junior and intermediate ophthalmologist groups but does not reach senior ophthalmologist performance on macular edema, while showing numerically higher balanced accuracy than all reader groups on myopic macular schisis. These results suggest that pixel-level cross-modal reconstruction can enrich CFP representations with OCT-associated supervision, providing a practical route toward stronger CFP-based retinal analysis in screening settings.

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

CIWI-CKT: Chaos-Informed Wave Interference Feature Fusion and Cross-City Knowledge Transfer for Traffic Flow Forecasting

arXiv:2606.15642v1 Announce Type: cross Abstract: Accurate traffic flow prediction remains challenging in cross-city, data-scarce scenarios where limited historical data hinders model generalisation. The chaotic nature of traffic dynamics, complex spatio-temporal dependencies, and heterogeneous urban networks complicate few-shot learning across cities. Existing deep learning approaches either treat traffic as purely deterministic or lack mechanisms to model wave-like interference patterns essential for cross-regime traffic dynamics. To address these limitations, this paper proposes CIWI-CKT, a novel Chaos-Informed Wave Interference Feature Fusion framework with Cross-City Knowledge Transfer. Our framework introduces three core innovations: chaos-informed wave generation that extracts measurable chaos invariants and models traffic as adaptive wave components; meta-interference processing that captures wave interactions between support and query regimes while producing a predictability score for confidence estimation; and chaos-aware meta-learning that enables efficient cross-city knowledge transfer while preserving chaotic characteristics. We establish theoretical guarantees including chaos-to-wave stability, wave-induced dimension reduction, and meta-learning generalisation bounds. Extensive experiments on four real-world traffic datasets demonstrate that CIWI-CKT significantly outperforms state-of-the-art spatio-temporal graph learning, transfer learning, prompt-based, and few-shot methods, improving prediction accuracy while substantially reducing required training data.

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

Ensembles of Large Language Models for Identifying EQ-5D Studies in PubMed Based on Their Abstracts

The rapid increase in scientific publications leads to the fact that manual study screening in systematic literature reviews (SLRs) is increasingly resource consuming, inefficient, and inconsistent. Classifying studies that clearly report health-related quality-of-life results, such as EQ-5D data, requires a high level of clinical interpretation and poses challenges for human reviewers. This study investigates the use of Google's Gemini and Gemma large language models (LLMs) in automating EQ-5D detection in the PubMed biomedical database based only on published abstracts. A multi-phase framework is proposed that integrates few-shot prompting, weight ensembling aggregation, and a soft stacking meta-classifier. Nine LLMs are evaluated on a dataset of PubMed studies manually labeled by two experts regarding EQ-5D reporting. The weighted ensemble of gemini-2.5-pro, gemma-3-12b, and gemma-3-27b obtained a 0.74 weighted F1-score and 0.74 accuracy, exceeding individually attained results. The ensembling of top-performing models improved the balance between precision and recall compared to individual models, while the soft stacking approach provided greater reliability and interpretability. Feature analysis shows that the probability results from the models are important in guiding the final predictions. The findings suggest that an ensemble-based LLM setup is a reliable and scalable approach for automating screening in biomedical research.

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

Your Privacy My Cloak: Backdoor Attacks on Differentially Private Federated Learning

arXiv:2606.17035v1 Announce Type: new Abstract: Prior research suggests that differential privacy (DP) inherently enhances the robustness of federated learning (FL) against backdoor attacks. In this paper, we challenge this assumption. Through an empirical analysis of two baseline attack strategies, we uncover a fundamental tension in DP-FL: while bypassing DP allows state-of-the-art defenses to detect and filter malicious updates, complying with DP inadvertently masks their distinguishing statistical characteristics. Consequently, existing defenses become ineffective as DP reduces the raw backdoor signal. Building on this masking effect, we propose RING, a novel attack that explicitly exploits DP to conceal malicious contributions while maximizing attack impact. By collaboratively crafting adversarial perturbations, compromised clients reconstruct a strong backdoor signal during aggregation without triggering anomaly detection. RING operates as a perturbation layer that is agnostic to the underlying backdoor technique, making it broadly applicable and composable with existing attacks – a property that significantly amplifies the threat it poses to DP-FL. Extensive evaluations across four image and text datasets under non-iid distributions show that RING achieves an average attack success rate of 90.3% against six state-of-the-art defenses under a moderate privacy budget, an improvement of up to 26.08x over baseline strategies. Finally, we evaluate potential countermeasures and find that mitigating this threat incurs significant utility trade-offs, exposing a fundamental security gap in the deployment of differentially private FL.

14.
arXiv (CS.CV) 2026-06-12

Modality Forcing for Scalable Spatial Generation

Text-to-image (T2I) models contain rich spatial priors. Synthesizing photorealistic, cluttered scenes requires an understanding of geometry, including perspective and relative scale. Prior works adapt T2I models to leverage this prior for depth prediction, but they require dense depth data and involve complex recipes. We propose Modality Forcing, a simple, scalable post-training recipe for joint image-depth generation using a single DiT trained on sparse depth data. Modality Forcing enables conditional and joint generation of image and depth in any permutation by assigning separate noise levels per modality. Per-modality decoders let us train on sparse, real-world depth and achieve strong, generalizable depth prediction. We further show that Modality Forcing inherits the scalability of T2I pre-training: by training a set of T2I models from scratch (370M to 3.3B parameters), we find that larger models trained on more image data produce more accurate depth. Our strongest model is competitive with state-of-the-art monocular depth estimators and reduces AbsRel by 57% relative to existing joint image-depth generative models. These results provide strong evidence that image generation is a scalable pre-training objective for spatial perception. https://modality-forcing.github.io/

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

A Systematic Evaluation of Black-Box Uncertainty Estimation Methods for Large Language Models

arXiv:2606.19868v1 Announce Type: new Abstract: Although large language models (LLMs) have shown strong capabilities across a wide range of tasks, their outputs often remain unreliable and may contain hallucinations, making uncertainty estimation (UE) essential for building trustworthy LLMs. In practice, many mainstream LLMs are only accessible through restricted APIs, where internal signals such as logits and hidden states are unavailable, making black-box UE especially important. However, existing work on black-box UE for LLMs remains fragmented in methodology and lacks a unified empirical comparison. To address this gap, we present a systematic review of black-box UE methods and organize them into five categories: verbalization-based, sampling-based, explanation-based, multi-agent, and hybrid methods. We further build a unified evaluation framework and benchmark 24 representative methods across 4 models and 4 dataset settings. Our results show that no single method consistently dominates across all settings. Nevertheless, methods that reason over and compare candidates in the answer space are generally effective, and hybrid methods that combine multiple uncertainty signals perform well under most conditions. By releasing the benchmark data and a unified evaluation framework, we aim to facilitate reproducible comparisons and support future research, while our empirical findings provide practical guidance for developing future black-box UE methods for LLMs.

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

From Reasoning Traces to Reusable Modules: Understanding Compositional Generalization in Language Model Reasoning

arXiv:2606.18089v1 Announce Type: new Abstract: Post-training pipelines that combine supervised fine-tuning (SFT) with reinforcement learning (RL) have emerged as the key recipe for transforming large language models (LLMs) into robust reasoners. We argue that this combined success is driven by compositional generalization, which we formalize through a hierarchical latent selection model. In this framework, reasoning traces are generated by a cascade of discrete latent selection variables corresponding to reusable atomic modules, including both skills (local operations) and routing mechanisms (how intermediate information is selected, reused, and composed). Within this model, we theoretically show that SFT and RL play asymmetric, complementary roles: SFT supplies the raw module materials in compositional traces, and RL decomposes those traces to identify the latent atomic modules and enable compositional generalization. We design controlled experiments to validate this theory. Our results demonstrate that RL can extract atomic modules from compound traces supplied by SFT and recombine them to solve new configurations. Moreover, we find that training on compound traces yields stronger generalization than training on isolated atomic modules. Finally, we investigate the relationship between SFT and RL data and identify an effective protocol in which SFT ensures coverage of all atomic modules through compositional traces, while RL focuses on novel compositions outside the SFT support to drive exploration.

17.
arXiv (CS.CV) 2026-06-11

A Comprehensive Ecosystem for Open-Domain Customized Video Generation

Recent progress in video generation has shown impressive visual synthesis capabilities. However, open-domain customized video generation remains limited by the lack of large-scale, annotated datasets capturing diverse identity-specific attributes. To address this, we introduce PexelsCustom-1M, the first publicly available million-scale dataset for identity-preserving video generation, containing one million curated triplets across 8,000+ categories. Leveraging this, we propose CustoMDiT, a parameter-efficient framework that adapts a pretrained multimodal Diffusion Transformer into a customized video generator with only 8% additional learnable parameters. Our method surpasses prior state-of-the-art. However, benchmarks such as DreamBooth cover only 100 classes, which is insufficient for real-world applications. To overcome this, we construct OpenCustom, a new benchmark with 1,000+ categories, created via cross-dataset knowledge fusion from ImageNet and MS-COCO. Extensive experiments confirm the advantages of both our dataset and model. We will open-source the entire ecosystem–including dataset, pipeline, benchmark, and implementations–to support further research.

18.
arXiv (quant-ph) 2026-06-15

Dose-efficient Quantum Phase Estimation in Lossy Optical Interferometry

arXiv:2606.14254v1 Announce Type: new Abstract: Optical interferometry is a cornerstone technique for precise phase measurements across various fields. In many applications, for example, biological imaging, it often necessitates stringent limits on light intensity to prevent adverse effects on light-sensitive samples, a condition known as dose-limited regimes. Maximizing the precision per dose is therefore crucial. In quantum metrology, quantum correlations enable high precision in phase estimation while adhering to dose constraints. Nevertheless, photon loss, including absorption by a sample, substantially diminishes the benefits of quantum enhancement in interferometry. In this work, we experimentally investigate a dose-efficient approach to quantum phase estimation using sequential strategies in the presence of loss. Performance of sequential strategies with and without control is evaluated through quantum Fisher information (QFI) per dose. Experimental results show that both sequential strategies exceed the classical limit and outperform the parallel strategy using unbalanced N00N states. Notably, the control-enhanced sequential strategy attains superior QFI per dose, approaching the quantum limit. These results highlight the promise of sequential strategy for imaging and sensing in resource-constrained scenarios, marking a significant step toward practical and efficient quantum metrology in lossy environments.

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

VideoSketcher: Sequential Sketch Generation Using Video Model Priors

Sketching is inherently sequential: strokes are drawn progressively to explore and refine ideas. Yet most generative approaches treat sketches as static images, ignoring the temporal process underlying creative exploration. Modeling this sequential structure remains challenging: prior methods either rely on large-scale human-drawn datasets with limited diversity, or use large language models (LLMs) to produce drawing instructions, often at the cost of visual fidelity. We present VideoSketcher, a method for generating high-quality sketching processes by adapting pretrained text-to-video diffusion models to the sparse, continuous nature of sketch formation. Our key insight is that LLMs and video diffusion models offer complementary strengths: LLMs act as semantic planners that decompose concepts into step-by-step instructions, while video diffusion models serve as powerful "renderers" that translate them into temporally coherent sketch sequences. We introduce a two-stage fine-tuning strategy that decouples temporal structure from visual appearance: stroke ordering is learned from synthetic shape compositions, while style is distilled from as few as seven hand-drawn examples. Despite minimal supervision, our method can generate diverse, high-quality sequential sketches that faithfully follow specified drawing orders. Our framework naturally extends to brush style control and autoregressive generation, supporting artistic applications.

20.
bioRxiv (Bioinfo) 2026-06-11

STITCH links cellular morphology and gene expression in spatial transcriptomics

In situ spatial (ISS) sequencing can uncover co-variation between cellular morphology and gene expression in vivo. However, a principled and interpretable mathematical representation of morphology has not yet been applied in this context. In particular, current deep learning-based representations of cell images confound a cell's shape with its size. We present an interpretable representation of cellular boundary contours, based on tangent principal component analysis (TPCA) in a Kendall shape manifold, that captures size-independent contour shape features. This approach successfully recovers shape-perturbing genes in an RNAi screen than a previous metric geometry-based approach. We build on TPCA to develop STITCH (Shape-TranscriptomIc Correlation and Harmonization), an approach to reveal covariation between cell morphology with gene expression in ISS datasets. In a Xenium dataset, STITCH outperforms a deep learning-based approach in both recovering the layered organization of keratinocytes and a spatial gradient in nuclear eccentricity. Across samples in a melanoma CosMx dataset, STITCH reproducibly associates elongated and triangular fibroblasts with proximity to malignant cells and myofibroblast-like transcriptional program. Finally, STITCH independently recovers a known link between mesenchymal-like malignant cell states and increased cell area in two melanoma cohorts. STITCH can thus yield interpretable morphology-transcriptome relationships across cell types, patients, and spatial transcriptomics platforms.

21.
medRxiv (Medicine) 2026-06-22

Early-life nutritional environment is associated with late-life cognition in the Health and Retirement Study, a pellagra epidemic natural experiment

Early-life exposures are important to several late-life health outcomes. We sought to study the effect of an in utero nutritional environment and its interaction with Alzheimer's disease (AD) genetic risk on late-life cognitive function. We used a natural experiment created by the pellagra epidemic, a nutritional disease caused by a vitamin B3 deficiency, to evaluate the association between in utero pellagra epidemic exposure and late-life cognitive function in the Health and Retirement Study (N = 18,285). We also evaluated whether the in utero exposure could modify the AD polygenic score's (PGS) effect on cognition. In utero pellagra epidemic exposure was significantly associated with cognition ({beta} = -0.025). However, these effects were not isolated to the prenatal period as exposure during childhood periods also had an effect. The interaction between the in utero exposure and the AD PGS was significant, where the genetic effect on cognition was amplified with increasing (progressively worse) in utero exposure levels. These associations imply that the early-life nutritional environment affects late-life cognitive function and that these effects can modify genetic risk.

22.
arXiv (CS.LG) 2026-06-12

Metriplectic Conditional Flow Matching for Dissipative Dynamics

arXiv:2509.19526v2 Announce Type: replace Abstract: Metriplectic conditional flow matching (MCFM) learns dissipative dynamics without violating first principles. Neural surrogates often inject energy and destabilize long-horizon rollouts; MCFM instead builds the conservative-dissipative split into both the vector field and a structure preserving sampler. MCFM trains via conditional flow matching on short transitions, avoiding long rollout adjoints. In inference, a Strang-prox scheme alternates a symplectic update with a proximal metric step, ensuring discrete energy decay; an optional projection enforces strict decay when a trusted energy is available. We provide continuous and discrete time guarantees linking this parameterization and sampler to conservation, monotonic dissipation, and stable rollouts. On a controlled mechanical benchmark, MCFM yields phase portraits closer to ground truth and markedly fewer energy-increase and positive energy rate events than an equally expressive unconstrained neural flow, while matching terminal distributional fit.

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

Family-Aware Residual Architecture for Predicting Quantum Circuit Simulation Performance

arXiv:2606.11620v1 Announce Type: cross Abstract: Approximate tensor-network simulators enable classical simulation of quantum circuits beyond the reach of exact methods, but selecting optimal approximation parameters – such as bond dimension thresholds – remains a costly trial-and-error process. We present a family-aware neural architecture that predicts both the minimum approximation threshold required to achieve target fidelity and the expected wall-clock runtime for quantum circuit simulation, given only the circuit's OpenQASM description and execution context. Our key insight is that quantum circuits from different algorithmic families (e.g., QFT, Grover, VQE) exhibit fundamentally distinct simulation cost profiles due to their differing entanglement structures. We employ family-conditioned residual corrections – additive, family-specific adjustments atop a shared backbone, drawing on established conditional computation techniques – enabling the model to capture both universal circuit properties and algorithmic nuances. The architecture incorporates a pretrained family classifier (97.5% accuracy) and domain-informed algorithm fingerprint features derived from gate-composition heuristics. Evaluated on circuits spanning 7–130 qubits across 10 algorithm families, our system achieves 79.5% exact threshold accuracy (91.2% within one rung) and $R^2 = 0.82$ runtime correlation, with inference completing in approximately 50 ms – replacing trial-and-error simulation runs that may take minutes to hours. Ablation studies confirm that family-aware modeling provides the single largest performance improvement (+3.2 percentage points), validating the hypothesis that algorithm family is a first-class feature for simulation cost prediction.

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

A Stationarity-and-Coupling Criterion for Training-Free Time-Lagged Spectral Embeddings of Multivariate Time Series

arXiv:2606.13823v1 Announce Type: new Abstract: We study training-free fixed-length descriptors for multivariate time series and ask not merely whether such a descriptor performs well, but when it can be expected to work at all. Our object of study is $D(\tau)$, built from a time-lagged correlation matrix truncated at the Marchenko-Pastur edge so that only signal-bearing eigenvalues survive and classified by cosine similarity to class centroids with zero learned parameters. The central contribution is not the descriptor but a falsifiable applicability criterion for it. Working from a stationary Gaussian VAR(1) model, we argue that $D(\tau)$ separates two classes when the signals are approximately stationary and the class information lives in their cross-channel temporal coupling rather than in marginal per-channel power. We derive, semi-formally, three consequences: a distinguishability condition, why the static ($\tau=0$) covariance collapses to chance, and why a stationary but power-discriminated paradigm defeats the descriptor. The criterion is operational: a two-part pre-flight test – an augmented Dickey-Fuller stationarity check and a power-baseline saturation check – predicts applicability before any training. We validate both halves on a mixed assortment. On four paradigms that satisfy the criterion (Sleep-EDF, BCI-IV-2a, MIT-BIH, ESC-50) the descriptor is competitive with strong baselines at a fraction of their cost, reaching $88.5\pm4.5\%$ under 20-subject leave-one-subject-out on Sleep-EDF on a single CPU thread. On three that violate it – non-stationary ERPs, and financial-volatility and wearable-stress regimes that are power-discriminated – it fails exactly as the pre-flight predicts, and these negatives are the more informative half. We are explicit that $D(\tau)$ is not the most accurate representation; its value is a compact, training-free embedding whose domain of validity is known in advance.

25.
arXiv (CS.CL) 2026-06-12

Beyond Uniform Tokens: Adaptive Compression for Time Series Language Models

Large language models (LLMs) have enabled time series (TS) analysis by jointly modeling numerical observations and textual context through a shared token interface. However, TS tokens and prompt tokens exhibit fundamentally different information structures, making uniform token processing inefficient. In this paper, we study token efficiency in TS language modeling from an asymmetric-token perspective. We show that TS tokens have highly uneven spectral contributions, where many tokens share redundant frequency patterns while a small subset preserves critical temporal evidence. We also observe that prompt-token influence attenuates with model depth, suggesting that full prompt retention across all layers is unnecessary. Based on these findings, we develop an adaptive token budgeting framework that compresses TS tokens via frequency-domain structure and progressively reduces prompt tokens across layers. Experiments across forecasting, classification, imputation, and anomaly detection demonstrate up to 7.68$\times$ inference acceleration and performance gains in 78\% of evaluated settings, showing the effectiveness of asymmetric token compression for scalable TS foundation models.