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01.
arXiv (quant-ph) 2026-06-16

The Distribution Postulate in Algorithmic Bohmian Mechanics

作者:
Jeffrey A. Barrett↗Eddy Keming Chen↗Josiah Lopez-Wild↗

arXiv:2606.16165v1 Announce Type: new Abstract: In order to make the right empirical predictions Bohmian mechanics requires a special statistical boundary condition – the distribution postulate – but it is unclear how best to understand this condition. We show how one might use the theory of algorithmic randomness to formulate the distribution postulate as an objective constraining law. The framework requires us to say something about admissible quantum-mechanical states and measurements. In return, algorithmic Bohmian mechanics (aBM) guarantees the standard Born statistics for a collection of canonical quantum experiments in the limit, not just with high probability. The algorithmic distribution postulate provides a sharp typicality condition, clarifies the status of quantum probabilities in the deterministic theory, and provides a concrete example of how notions provided by the theory of algorithmic randomness can aid in specifying the content of a physical law.

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02.
arXiv (CS.AI) 2026-06-12

MiniMax Sparse Attention

作者:
Xunhao Lai↗Weiqi Xu↗Yufeng Yang↗Qiaorui Chen↗Yang Xu↗Lunbin Zeng↗Xiaolong Li↗Haohai Sun↗Haichao Zhu↗Vito Zhang↗Pengyu Zhao↗

arXiv:2606.13392v1 Announce Type: new Abstract: Ultra-long-context capability is becoming indispensable for frontier LLMs: agentic workflows, repository-scale code reasoning, and persistent memory all require the model to jointly attend over hundreds of thousands to millions of tokens, yet the quadratic cost of softmax attention makes this untenable at deployment scale. We introduce MiniMax Sparse Attention (MSA), a blockwise sparse attention built upon Grouped Query Attention (GQA). A lightweight Index Branch scores key-value blocks and independently selects a Top-k subset for each GQA group, enabling group-specific sparse retrieval while maintaining efficient block-level execution; the Main Branch then performs exact block-sparse attention over only the selected blocks. Designed around a principle of simplicity and scalability, MSA is deliberately streamlined, making it straightforward to deploy efficiently across a broad range of GPUs. To translate sparsity into practical speedups, we co-design MSA with a GPU execution path that uses exp-free Top-k selection and KV-outer sparse attention to improve tensor-core utilization under block-granular access. On a 109B-parameter model with native multimodal training, MSA performs on par with GQA while reducing per-token attention compute by 28.4x at 1M context. Paired with our co-designed kernel, MSA achieves 14.2x prefill and 7.6x decoding wall-clock speedups on H800. Our inference kernel is available at: https://github.com/MiniMax-AI/MSA. A production-grade natively multimodal model powered by MSA has been publicly released at: https://huggingface.co/MiniMaxAI/MiniMax-M3.

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03.
arXiv (CS.AI) 2026-06-12

Mod-Guide: An LLM-based Content Moderation Feedback System to Address Insensitive Speech toward Indigenous Ethnic and Religious Minority Communities

作者:
Dipto Das↗Achhiya Sultana↗Ankit Singh Chauhan↗Saadia Binte Alam↗Mohammad Shidujaman↗Shion Guha↗Sunandan Chakraborty↗Syed Ishtiaque Ahmed↗

arXiv:2606.13397v1 Announce Type: cross Abstract: Language operates as a mechanism of both marginalization and resistance, especially for minority communities navigating insensitive and harmful speech online. As content moderation increasingly depends on large language models (LLMs), concerns arise about whether these systems can recognize culturally insensitive speech-language that disregards or marginalizes the cultural and religious perspectives of historically underrepresented communities, often through implicit erasure, misrepresentation, or normative framing, rather than overt hostility. Focusing on Bangladesh's Hindu and Chakma communities – the country's largest religious and Indigenous ethnic minorities, respectively – this paper investigates the epistemic limits of LLM-based moderation systems and explores methods for incorporating minority perspectives. We co-created a culturally grounded corpus of insensitive speech with community members and integrated their narratives into moderation pipelines using retrieval augmented generation (RAG). Our tool, Mod-Guide, improves LLM sensitivity to minority viewpoints by leveraging contextual cues derived from lived experience. Through mixed-method evaluations involving both minority and majority participants, we demonstrate that RAG-enhanced moderation responses are more contextually accurate and perceived differently across ethnic lines. This work advances research in human-computer interaction, AI ethics, and social computing by foregrounding restorative justice and hermeneutical inclusion in the design of content moderation systems.

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04.
arXiv (CS.AI) 2026-06-12

Emotional regulation improves deep learning-based image classification

作者:
Riccardo Emanuele Landi↗Jo\~ao M. F. Rodrigues↗Marta Chinnici↗

arXiv:2606.13081v1 Announce Type: cross Abstract: Emotion significantly influences cognition, enhancing memory and learning under certain conditions. Drawing on this principle, emotion-augmented deep learning investigates how affective states can improve neural network architectures and learning paradigms, achieving better generalization than non-emotional models. However, existing methods often rely solely on objective neurophysiological factors, neglecting the role of subjectivity in emotion. To bridge this gap, the present study introduces Emotional Regulation, a novel framework for modeling emotion in deep learning through artificial subjective experience. The method employs pre-training based on affective stimuli, balancing non-emotional and emotionally-influenced responses in downstream task optimization. Extensive experimentation was conducted in image classification, pre-training ResNet and ViT architectures on four emotional datasets, using CIFAR-10 and -100 as target benchmarks. Results reveal improvements over the aforementioned backbones, providing evidence of Emotional Regulation as a promising method for defining emotion-augmented deep learning through artificial subjective experience. Furthermore, the proposed approach overcomes the related work in image classification based on CIFAR, revealing Emotional Regulation as the new state-of-the-art in emotion-augmented deep learning for large-scale vision datasets. The study also enforces evidence of the impact of affective states in improving machine learning tasks' optimization, encouraging further investigation on emotion-inspired architectures.

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

The Illusion of Multi-Agent Advantage

作者:
Prathyusha Jwalapuram↗Hehai Lin↗Chuyuan Li↗Fangkai Jiao↗Sudong Wang↗Yifei Ming↗Zixuan Ke↗Chengwei Qin↗Giuseppe Carenini↗Shafiq Joty↗

Prevailing wisdom posits that Multi-Agent Systems (MAS) are superior to Single-Agent Systems (SAS), citing advantages like context protection, parallel processing and distributed decision-making. However, empirical support for this claim relies primarily on comparisons with SAS baselines using benchmarks that prioritize isolated reasoning tasks, which do not adequately assess these advantages. Focusing on automatically generated MAS that are designed for enhanced generalizability over manually-designed counterparts, we perform a rigorous, systematic evaluation against SAS, specifically Chain-of-Thought with Self-Consistency (CoT-SC). Across traditional reasoning datasets and tasks with interactive multi-step workflows (e.g., BrowseComp-Plus), we demonstrate that automatic MAS consistently underperform CoT-SC despite being up to 10x more expensive. To isolate these failures from limitations inherent to task structure, we introduce a diagnostic synthetic dataset tailored for MAS featuring explicit task decomposition, context separation and parallelization potential. We show that expert-architected MAS consistently outperforms automatically generated architectures in both raw performance and cost-efficiency on this dataset, demonstrating that existing evaluation frameworks mask critical architectural gaps and inefficiencies of complex MAS by failing to account for the marginal utility of increased computational cost. Critically, systematic deconstruction of the generated MAS architectures reveals that current automated design paradigms produce architectural bloat that prioritizes superficial complexity which does not translate into functional utility, exposing a fundamental misalignment with multi-agent principles.

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

UniReason-Med: A Shared Grounded Reasoning Interface for 2D-to-3D Transfer in Medical VQA

作者:
Mengzhuo Chen↗Yan Shu↗Chi Liu↗Hongming Piao↗Xidong Wang↗Derek Li↗Bryan Dai↗

We study whether grounded reasoning supervision from abundant 2D medical images can improve 3D medical VQA when both input types are aligned through a common reasoning interface. We introduce UniReason-Med, a single-checkpoint framework that processes either a 2D image or a slice-serialized 3D volume at inference time, generating interleaved textual reasoning and localized visual evidence through shared box syntax, region-token injection, and a common grounded reasoning policy. To train this interface, we construct UniMed-CoT, a 220K instruction-tuning dataset with interleaved textual reasoning and grounded visual evidence, including 170K 2D and 50K 3D samples. Through supervised fine-tuning followed by outcome-level reinforcement learning, UniReason-Med learns to generate grounded reasoning traces without IoU/Dice-based localization rewards during RL. Data-mixture and component ablations show that joint 2D+3D grounded supervision substantially improves 3D reasoning over 3D-only training, while grounding and region-token injection consistently benefit both 2D and 3D tasks. These results suggest that a shared grounded reasoning interface can transfer reasoning structure from 2D images to slice-serialized volumetric medical understanding. The code and data are publicly available at https://github.com/IQuestLab/unireason-med.

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

AI-Driven Test Case Generation from Natural Language Requirements: A Survey of Techniques and Research Gaps

作者:
Orimoloye Folorunsho↗Hassan Reza↗

arXiv:2606.06563v2 Announce Type: replace-cross Abstract: Software testing is critical for verifying that systems meet specified requirements, yet remains among the most time-consuming and expensive activities in development. Requirements-based test generation allows test cases to be derived early from requirements artifacts, but generating them directly from natural language is challenging due to inherent ambiguity and imprecision. Recent advances in AI, natural language processing (NLP), and large language models (LLMs) have made automating this pipeline increasingly feasible, while introducing new risks including hallucination, reduced traceability, and inconsistent evaluation. This survey addresses four research questions: what AI and NLP techniques have been proposed for generating test cases from natural language requirements; what tools and frameworks support these approaches; how generated test cases are evaluated; and what research gaps remain. Following Kitchenham and Charters' systematic review guidelines, we searched major scholarly databases spanning 2000-2025 and, after applying strict inclusion criteria, identified 21 primary studies. The literature is organized into three evolutionary eras, revealing that no existing approach simultaneously satisfies six key quality dimensions: automation, ambiguity handling, domain applicability, traceability, evaluation thoroughness, and hallucination control. The survey makes three main contributions: a three-era evolutionary synthesis of AI-based test generation; a six-criteria gap analysis showing no current approach fully addresses all quality dimensions; and four actionable research guidelines targeting hallucination, traceability, complexity sensitivity, and compliance.

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08.
Nature (Science) 2026-06-08

Fifty years since a simple equation described the chaos of biology

作者:
Michael P. H. Stumpf↗

An exploration of chaos theory in population dynamics showed that unpredictable systems can often be modelled using surprisingly simple mathematics. An exploration of chaos theory in population dynamics showed that unpredictable systems can often be modelled using surprisingly simple mathematics.

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09.
arXiv (math.PR) 2026-06-15

Mixing Times for the Facilitated Exclusion Process

作者:
James Ayre↗Paul Chleboun↗

arXiv:2402.18999v2 Announce Type: replace Abstract: The facilitated simple exclusion process (FEP) is a one-dimensional exclusion process with a dynamical constraint. We establish bounds on the mixing time of the FEP on the segment, with closed boundaries, and the circle. The FEP on these spaces exhibits transient states that, if the macroscopic density of particles is at least $1/2$, the process will eventually exit to reach an ergodic component. If the macroscopic density is less than $1/2$ the process will hit an absorbing state. We show that the symmetric FEP (SFEP) on the segment $\{1,\ldots,N\}$, with $k>N/2$ particles, has mixing time of order $N^{2}\log(N-k)$ and exhibits the pre-cutoff phenomenon. For the asymmetric FEP (AFEP) on the segment, we show that there exists initial conditions for which the hitting time of the ergodic component is exponentially slow in the number of holes $N-k$. In particular, when $N-k$ is large enough, the hitting time of the ergodic component determines the mixing time. For the SFEP on the circle of size $N$, and macroscopic particle density $\rho \in(1/2,1)$, we establish bounds on the mixing time of order $N^{2}\log N$ for the process restricted to its ergodic component. We also give an upper bound on the hitting time of the ergodic component of order $N^{2}\log N$ for a large class of initial conditions. The proofs rely on couplings with exclusion processes (both open and closed boundaries) via a novel lattice path (height function) construction of the FEP.

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

Contrastive Regularization for Accent-Robust ASR

作者:
Van-Phat Thai↗Aradhya Dhruv↗Duc-Thinh Pham↗Sameer Alam↗

arXiv:2605.03297v2 Announce Type: replace-cross Abstract: ASR systems based on self-supervised acoustic pretraining and CTC fine-tuning achieve strong performance on native speech but remain sensitive to accent variability. We investigate supervised contrastive learning (SupCon) as a lightweight, accent-invariant auxiliary objective for CTC fine-tuning. An utterance-level contrastive loss regularizes encoder representations without architectural modification or explicit accent supervision. Experiments on the L2-ARCTIC benchmark show consistent WER reductions across multiple pretrained encoders, with up to 25 – 29\% relative reduction under unseen-accent evaluation. Analysis using within-transcript cosine dispersion indicates that SupCon promotes more compact and stable representation geometry under accent variability. Overall, SupCon provides an effective and model-agnostic regularization strategy for improving accent robustness.

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12.
arXiv (CS.AI) 2026-06-16

Model Graph Inductive Learning for Knowledge Graph Completion

作者:
Mohommad Esmaei Khani↗Mahdieh Hasheminejad↗Ali Taherkhani↗Hossein Hajiabolhassan↗

arXiv:2606.16509v1 Announce Type: new Abstract: Link prediction in knowledge graphs fundamentally depends on the quality of learned embeddings for entities and relations. However, most existing methods derive these embeddings by aggregating only the local neighborhood of each entity, neglecting the global structure of the knowledge graph. This limited view prevents models from capturing higher-level structural patterns that are essential for accurate and generalizable link prediction. To address these limitations, we introduce Model Graph Inductive Learning (MGIL), a framework that constructs a model graph by clustering entities based on the similarity of their incoming and outgoing relational structures or their entity types. A GNN is then applied to this model graph to produce embeddings that capture the global view of the knowledge graph. These embeddings subsequently serve as high-quality initial features %embeddings for the original knowledge graph, replacing random initialization and leading to more stable and expressive representations. Extensive experiments on standard and recently proposed inductive benchmarks demonstrate that MGIL achieves state-of-the-art or highly competitive performance in inductive link prediction, highlighting its effectiveness across diverse graph settings.

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13.
arXiv (CS.LG) 2026-06-11

Minimal surfaces, Knots, and Neural Networks

作者:
Tancredi Schettini Gherardini↗Marco Usula↗

arXiv:2605.26234v2 Announce Type: replace-cross Abstract: A recent conjecture by Joel Fine posits a relationship between the coefficients of the HOMFLY polynomial of a knot $K$ in the 3-sphere $S^3$, and the signed count of minimal surfaces in hyperbolic 4-space $\mathrm{H}^4$ meeting the sphere at infinity at $K$, with prescribed genus and self-intersection number. In this paper, we develop a novel machine learning framework based on Physics-Informed Neural Networks (PINNs) to solve the minimal surface equation in hyperbolic space. We utilise this framework to test Fine's Conjecture by constructing near-minimal surfaces bounding various families of knots in $S^3$. Furthermore, we develop an algorithmic method to find self-intersections and compute their sign. For every knot analysed, the computationally discovered minimal surfaces and their self-intersection numbers perfectly align with the predictions of Fine's Conjecture, providing empirical evidence for it.

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

CEVAR: Centerline Embedding Extraction for Endovascular Aneurysm Repair

作者:
Roman Naeem↗Timo Niiniskorpi↗Charlotte Sandstr\"om↗Naman Desai↗Anders Jeppsson↗Ida H\"aggstr\"om↗Fredrik Kahl↗H{\aa}kan Roos↗Jennifer Alv\'en↗

Long-term mortality rates after endovascular aneurysm repair (EVAR) remain elevated due to post-EVAR rupture caused by loss of seal in stent graft sealing zones. Structured CT review using centerline measurements improves detection, but current workflows require manual centerline editing and expert operators. We propose a transformer framework for automated, protocol-driven sealing zone assessment that combines 3D centerline tracking with embedding-based geometric prediction. Two state-of-the-art image-to-graph models are evaluated for aorto-iliac centerline extraction from follow-up CT and for measurement of stent position, vessel diameters, and seal lengths according to EVAR4C protocol. Across the full test set and a challenging no-contrast subset, the proposed fully automatic method outperforms the commercial semi-automatic workflow.

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

Rethinking the Trust Region in LLM Reinforcement Learning

作者:
Penghui Qi↗Xiangxin Zhou↗Zichen Liu↗Tianyu Pang↗Chao Du↗Min Lin↗Wee Sun Lee↗

Reinforcement learning (RL) has become a cornerstone for fine-tuning Large Language Models (LLMs), with Proximal Policy Optimization (PPO) serving as the de facto standard algorithm. Despite its ubiquity, we argue that the core ratio clipping mechanism in PPO is structurally ill-suited for the large vocabularies inherent to LLMs. PPO constrains policy updates based on the probability ratio of sampled tokens, which serves as a noisy single-sample Monte Carlo estimate of the true policy divergence. This creates a sub-optimal learning dynamic: updates to low-probability tokens are aggressively over-penalized, while potentially catastrophic shifts in high-probability tokens are under-constrained, leading to training inefficiency and instability. To address this, we propose Divergence Proximal Policy Optimization (DPPO), which substitutes heuristic clipping with a more principled constraint based on a direct estimate of policy divergence (e.g., Total Variation or KL). To avoid huge memory footprint, we introduce the efficient Binary and Top-K approximations to capture the essential divergence with negligible overhead. Extensive empirical evaluations demonstrate that DPPO achieves superior training stability and efficiency compared to existing methods, offering a more robust foundation for RL-based LLM fine-tuning. Our code is available at https://github.com/sail-sg/Stable-RL.

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17.
arXiv (CS.CV) 2026-06-15

A Pragmatic VLA Foundation Model

作者:
Wei Wu↗Fan Lu↗Yunnan Wang↗Shuai Yang↗Shi Liu↗Fangjing Wang↗Qian Zhu↗He Sun↗Yong Wang↗Shuailei Ma↗Yiyu Ren↗Kejia Zhang↗…

Offering great potential in robotic manipulation, a capable Vision-Language-Action (VLA) foundation model is expected to faithfully generalize across tasks and platforms while ensuring cost efficiency (e.g., data and GPU hours required for adaptation). To this end, we develop LingBot-VLA with around 20,000 hours of real-world data from 9 popular dual-arm robot configurations. Through a systematic assessment on 3 robotic platforms, each completing 100 tasks with 130 post-training episodes per task, our model achieves clear superiority over competitors, showcasing its strong performance and broad generalizability. We have also built an efficient codebase, which delivers a throughput of 261 samples per second with an 8-GPU training setup, representing a 1.5~2.8$\times$ (depending on the relied VLM base model) speedup over existing VLA-oriented codebases. The above features ensure that our model is well-suited for real-world deployment. To advance the field of robot learning, we provide open access to the code, base model, and benchmark data, with a focus on enabling more challenging tasks and promoting sound evaluation standards.

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

Distilling Drifting Transformers with Representation Autoencoders

作者:
Jiawei Zhang↗Mengfei Xia↗Gen Li↗Yuantao Gu↗

arXiv:2606.15553v1 Announce Type: cross Abstract: Representation Autoencoders (RAEs) have improved diffusion and flow models by semantically richer latent space owing to the strongly label-wise clustered DINO features in the pretrained encoders. Yet in the distillation stage, the severe anisotropy and large curvatures caused by the rich semantic representations would hinder the convergence and performance, making the trajectory-based distillation unstable. In this work, we argue that the RAE latent space is compatible with distillation via the newly proposed Drifting Models. We first quantitatively study the curvatures and isotropy statistics across different autoencoders, and theoretically reveal that Drifting Model itself is highly likely to fail on extremely scattered spaces like reconstruction-based VAEs. These motivate us to apply the drifting paradigm directly to representation autoencoders. Our proposed method, Drift-RAE, distills pretrained flow models in RAE latent spaces using Drifting, together with insightful modifications that improve training stability by thereotically aligning drifting fields with other frameworks. Regarding the experimental evidences, we achieve 1.77 FID on ImageNet 256 dataset using only 10k distillation steps, surpassing state-of-the-art RAE distillation methods and appearing comparative with the original Drifting Model without requiring an auxiliary MAE feature extractor. The code will be made publicly available.

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19.
arXiv (CS.AI) 2026-06-16

RoboPIN: Grounded Embodied Reasoning via Pinned Chain-of-Thought

作者:
Yaoting Huang↗Yifu Yuan↗Linqi Han↗Chengwen Li↗Shuoheng Zhang↗Xianze Yao↗Hongyao Tang↗Yan Zheng↗Jianye Hao↗

arXiv:2606.15753v1 Announce Type: new Abstract: Embodied reasoning requires models to perceive task-relevant objects and spaces in physical environments and maintain consistent visual grounding throughout multi-step reasoning. However, current vision-language models rely on text-only or coordinate-augmented chain-of-thought, where entity references remain implicit and ambiguous. This may cause the reasoning process to decouple from visual evidence, entity references to drift across steps, and a causal disconnection between the reasoning trajectory and the final answer, with these problems further amplified in multi-view scenarios due to cross-view appearance changes. To address these issues, we propose Pinned Chain-of-Thought (\pincot{}), a structured reasoning paradigm that pins every reasoning step to visual evidence. \pincot{} introduces the concept of \reasoninganchor{}, which binds each task-relevant entity to a structured visual anchor with entity name, unique identity, view index, and spatial grounding, enabling consistent entity tracking across reasoning steps and views. We build a fully automated data generation pipeline to construct \dataset{}, a high-quality \pincot{}-formatted reasoning dataset. We then train \method{} through three-stage post-training that progressively injects embodied knowledge, structured reasoning ability, and process-supervised alignment, with rewards that directly constrain both anchor localization and identity consistency during reasoning. On 14 benchmarks covering embodied spatial reasoning, multi-view reasoning, and pointing, \method{} with only 4B parameters consistently outperforms 7B level open-source embodied models, achieving a 12\% average improvement over the strongest 7B baseline, Mimo-Embodied. Further analysis shows that \pincot{} improves grounding accuracy and cross-step identity consistency, validating the effectiveness of process supervision.

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20.
arXiv (CS.AI) 2026-06-11

Intelligent Automation for Embodied Benchmark Construction: Pipelines, Embodiments, Simulators, and Trends

作者:
Jinshan Lai↗Jianwei Hu↗Baoyang Jiang↗Fengchun Zhang↗Leyuan Wang↗Haotian Li↗Yida Wang↗Tingxuan Huang↗Xi Ren↗Qiang Ma↗

arXiv:2606.12207v1 Announce Type: cross Abstract: Embodied intelligence now spans navigation, household assistance, manipulation, autonomous driving, aerial agents, and multimodal large-model control. This expansion has made benchmark construction a central bottleneck for reliable evaluation. Unlike static datasets, embodied benchmarks combine task specifications, environments, robot data, demonstrations, annotations, metrics, evaluation scripts, and release policies into a single evaluation system. This survey reviews the literature through a five-stage construction pipeline: requirement and task construction, data acquisition, data cleaning and annotation, benchmark suite generation and metric definition, and evaluation execution with diagnostic feedback. For each stage, the survey analyzes the transition from manual curation to traditional automation, foundation-model assistance, and agentic closed-loop workflows. It also compares qualitative construction costs across human labor, data and asset acquisition, compute and simulation, validation and debugging, governance and maintenance, and rework risk. The main conclusion is that automation does not simply reduce benchmark cost. Instead, it often shifts cost toward validation, auditability, version control, and long-term governance. Progress in embodied evaluation will therefore depend not only on larger benchmark suites, but also on construction pipelines that are diagnosable, auditable, and responsibly refreshable.

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21.
bioRxiv (Bioinfo) 2026-06-10

SPARQ-MI leverages end-to-end spatial single-cell analysis of the tumor microenvironment

作者:
Kiwitz↗Turiello↗Effern↗Toma↗Landsberg↗Hoelzel↗Thurley↗

Detailed spatial analysis of the tumor micro-environment (TME) through multiplexed fluorescence imaging requires quantitative image-processing and data-analysis methods. While data-preprocessing down to segmentation of individual cells is captured by available methods, statistical analysis of single-cell features is compromised by the uneven noise distribution especially in complex tissues such as the TME, as well as by labor-intensive manual cell-type annotation and region segmentation. Here, we present SPARQ-MI (Spatial Phenotyping, Architecture Reconstruction and Quantification from Multiplexed Imaging) for streamlined spatial single-cell analysis, along with a tissue microarray PhenoCycler data-set with 37 fluorescent channels from melanoma patients under immunotherapy. We demonstrate that SPARQ-MI enables robust reconstruction of the cellular and spatial composition in this and other tissue types. Our analysis reveals associations of the cell-state and spatial location of CD8 T cells with response to immunotherapy. Overall, SPARQ-MI allows for quantitative analysis of complex fluorescence histology samples under minimal user input, and accounting for spatially uneven coverage of antibody signals, setting the stage for quantitative analysis of clinical samples.

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22.
arXiv (math.PR) 2026-06-11

On Skorokhod Problems for Reflected and Singular Stochastic Heat Equations

作者:
Martin Grothaus↗Nicolas Renner↗

arXiv:2606.11951v1 Announce Type: new Abstract: We prove a Skorokhod decomposition for the Markov processes $X^a$ and $X$ associated to the gradient Dirichlet forms with respect to the measures $\rho^a\mu^{\beta}$ and $\rho\mu^{\beta}$, respectively. Here, $\mu^{\beta}$ is the law of the standard Brownian bridge $\beta$, while $\rho^a$ and $\rho$ denote densities which are given by $\rho^a(z) := \mathbf{1}_{[0,\infty)}(\bar{z}_a)$ and $\rho(z) := \int_0^1 \mathbf{1}_{[0,\infty)}(\bar{z}_x) \, dx$, respectively, for all $z\in L^2(0,1)$ which have a (unique) continuous representative $\bar{z}$ which vanishes at zero and one. To this end, we derive infinite-dimensional integration by parts formulas (IbPFs) w.r.t. $\rho^a\mu^{\beta}$ and $\rho\mu^{\beta}$, which contain Hida distributions alongside the usual drift terms. We represent these Hida distributions by integration w.r.t. vector measures of bounded variation. The vector measures in question are constructed via an approximation argument, making use of a generalization of Prokhorov's theorem for vector measures. We further prove that, almost surely, the sample paths of $X^a$ and $X$ take values in the equivalence class of continuous functions vanishing at zero and one for all and $dt$-almost all times, respectively. The main motivation for studying $\rho^a\mu^{\beta}$ and $\rho\mu^{\beta}$ lies in the fact that the distributional terms in their IbPFs are simplifications of the distributional term in the IbPF w.r.t. the law of the reflected Brownian bridge on the unit interval $\mu^{|\beta|}$. Representing the latter by integration w.r.t. a vector measure of bounded variation is still an open problem.

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23.
arXiv (quant-ph) 2026-06-12

Proper and improper mixed states serve as different prior beliefs for quantum state retrodiction

作者:
Mingxuan Liu↗Valerio Scarani↗Ge Bai↗

arXiv:2502.10030v2 Announce Type: replace Abstract: A mixed quantum state can be taken as capturing an unspecified form of ignorance; or as describing the lack of knowledge about the true pure state of the system ("proper mixture"); or as arising from entanglement with another system that has been disregarded ("improper mixture"). These different views yield identical density matrices and therefore identical predictions for future measurements. But when used as prior beliefs for inferring the past state from later observations ("retrodiction"), they lead to different updated beliefs. This is a purely quantum feature of Bayesian agency. Based on this observation, we establish a framework for retrodicting on any quantum belief and we prove a necessary and sufficient condition for the equivalence of beliefs. We also illustrate how these differences have operational consequences in quantum state recovery.

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24.
bioRxiv (Bioinfo) 2026-06-14

Prediction of parsimonious and temporally sensitive sets of cell fate engineering transcription factors with IMCell

作者:
Su↗E. Y↗Ly↗Cahan↗

Transcription factor (TF) cocktails used in cell identity reprogramming protocols have largely been developed from experimental approaches. A handful of computational approaches have been reported, though have not been widely adopted by the scientific community. To standardize their use and assess their performance, we built CompForce, a platform that integrates these tools. Using CompForce, we found that existing computational methods offer modest improvements over differential expression on both synthetic and literature-curated data, and that their lackluster and inconsistent performance could be attributed to a reliance on local centrality metrics. To improve upon these methods, we developed IMCell, a prediction method that is inspired by the influence maximization problem. Unlike existing tools, IMCell returns optimized TF sets rather than ranked TF lists. We demonstrate that IMCell vastly out-performs existing tools, and further extend it to dynamic, stepwise contexts. The tools presented here are available in the R packages CompForce and IMCell.

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

Layer-Resolved Optimal Transport for Hallucination Detection in NMT and Abstractive Summarization

作者:
Mariia Onyshchuk↗Maksym-Vasyl Tarnavskyi↗Marta Sumyk↗

Optimal transport (OT) has been shown to detect hallucinations in neural machine translation (NMT) by measuring the geometric distance between cross-attention distributions and a reference distribution, without any supervision. We extend this analysis to all six decoder layers of the Fairseq DE-EN model ($N=3{,}414$), showing that Wass-to-Unif and Wass-to-Data are complementary detectors specialised across hallucination types, that detection is concentrated in layers L1–L4 with L5 anti-predictive for subtler types, and that hallucinated translations lack the exploratory attention phase present in correct translations from the first decoding step. We further evaluate whether the geometric signal transfers to abstractive summarization faithfulness detection: our unsupervised OT detector on AggreFact ($N=1{,}116$) achieves $57.2\%$/$57.6\%$ balanced accuracy on CNN/XSum – above chance but substantially below supervised MiniCheck-Flan-T5-L($69.9\%$/$74.3\%$). This gap is principled: unlike NMT hallucinations, unfaithful summaries can attend correctly to source tokens while misrepresenting their content, a failure mode invisible to concentration-based OT metrics by construction. Structural experiments on T5-base confirm consistent decoder organisation across depth, with Layer~3 showing peak concentration and Layer~12 being most critical for generation quality. Together, the results establish OT on cross-attention as a reliable detector when the failure mode is source disengagement, a principled interpretability tool regardless of task, and fundamentally limited when faithfulness failures occur downstream of attention.

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