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01.
Nature Medicine 2026-06-12

The Hong Kong Genome Project is a flagship initiative for precision medicine in Chinese populations

Authors: Unknown Author

The Hong Kong Genome Project established a genome sequencing database that provides improved diagnoses for patients and more efficient, population-tailored carrier status screening. Actionable pharmacogenomic variants were identified in almost all participants, informing drug prescriptions. This work establishes a genomic resource and a transferable model for equitable precision medicine in underrepresented populations worldwide.

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

Machine-learned particle flow as a foundation model for collider physics

Authors:
Farouk Mokhtar↗Joosep Pata↗Michael Kagan↗Javier Duarte↗

arXiv:2606.14373v1 Announce Type: cross Abstract: The workflow from particle collision to physics analysis passes through a series of reconstruction steps that are traditionally modular and disconnected, with no shared representation linking low-level detector data to high-level analysis tasks. We show that casting event reconstruction as a machine learning problem naturally produces such a shared representation. We repurpose a machine learning model trained for particle-flow reconstruction (MLPF) to perform three distinct analysis tasks: jet flavor identification, jet energy regression, and missing momentum regression. By appending the per-particle latent representations learned during reconstruction as additional input features, we substantially improve over baselines that use kinematic features alone. We further demonstrate that a single linear layer trained using only the latent representations achieves competitive performance against state-of-the-art baseline architectures, and outperforms the baseline for missing momentum regression with approximately 35 times fewer parameters. These results demonstrate that the latent representations learned during reconstruction encode essential physics information needed for downstream analysis, establishing MLPF as a foundation model and offering a concrete step toward an end-to-end pipeline from detector data to physics analysis.

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

ShapeBench: A Scalable Benchmark and Diagnostic Suite for Standardized Evaluation in Aerodynamic Shape Optimization

Authors:
Shaghayegh Fazliani↗Krissh Chawla↗Jack Guo↗Yiren Shen↗Matthias Ihme↗Madeleine Udell↗

arXiv:2605.20763v2 Announce Type: replace Abstract: Rapid progress in aerodynamic shape optimization (ASO) has outpaced currently-available standardized evaluation frameworks. Fair comparison requires a unified benchmark spanning diverse shape classes, objective formulations, and matched-budget state-of-the-art baselines. We introduce ShapeBench, an open-source ASO benchmark with a unified API spanning 103 tasks across eight shape categories and multiple optimization regimes. Each ShapeBench task includes a validated surrogate for fast search; when feasible, a high-fidelity Computational Fluid Dynamics (CFD) pipeline for final verification is available, enabling systematic fidelity-gap analysis. ShapeBench provides a reproducible protocol with well-configured baselines to compare fairly using a consistent budget metric, allowing for comparison among both classical and LLM-driven methods, including general-purpose optimizers and a new domain-specialized evolutionary LLM baseline, ShapeEvolve. Results on ShapeBench demonstrate substantial variance in optimizer rankings across shape categories and problem formulations, with mean pairwise Spearman $\rho = 0.013$, so single-task conclusions do not reliably generalize across problem classes. The benchmark is also far from saturation; classical methods are rarely applicable across all shape categories and tasks, further highlighting the need for more general-purpose approaches.

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

DYNA : Dynamic Episodic Memory Networks for Augmenting Large Language Models with Temporal Knowledge Graphs in Continuous Learning

Authors:
Ali Sarabadani↗Mahtab Tajvidiyan↗

Large Language Models (LLMs) struggle to incorporate new knowledge without forgetting or costly retraining. We propose DYNA, a lightweight framework that augments a frozen LLM with a temporal knowledge graph where events are nodes and temporal relations are directed, timestamped edges. The graph serves as an external, updatable memory. At query time, DYNA retrieves relevant nodes via random walks and centrality measures, then augments the LLM's response. Evaluated on three temporal recall tasks, DYNA reduces catastrophic forgetting by ~7% compared to fine-tuning and improves temporal ordering by ~5% over standard RAG. Higher graph clustering coefficients correlate with better retrieval, showing that graph structure matters. Contributions: (1) episodic memory as temporal KG, (2) retraining-free LLM augmentation, (3) graph properties as predictors of retrieval performance.

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05.
bioRxiv (Bioinfo) 2026-06-16

Phylogenetic tree inference using generative models

Authors:
Dotan↗Schers↗Wygoda↗Pupko↗Belinkov↗

Accurate inference of phylogenetic trees is fundamental to evolutionary biology, yet existing methods rely on complex pipelines involving multiple sequence alignment, explicit evolutionary models, and computationally intensive tree search procedures. Here, we present BetaInfer, a generative framework that reformulates phylogenetic tree inference as a sequence transduction problem. BetaInfer leverages hybrid transformer-based architectures to directly map sets of unaligned sequences to phylogenetic trees represented in Newick format. Trained on large-scale simulated evolutionary data with known ground truth, BetaInfer learns to capture complex evolutionary signals directly from sequence data. Ensemble-based generation of multiple candidate trees further improves robustness, reducing reconstruction error by over 30% relative to single predictions. Across extensive evaluations on both simulated and empirical datasets, BetaInfer achieves competitive performance relative to state-of-the-art phylogenetic pipelines, matching, and in some cases exceeding, the accuracy of established likelihood-based and distance-based methods under a wide range of conditions. Interpretability analyses reveal that BetaInfer leverages internal pairwise-distance computations to synthesize evolutionary relationships into an integrated, global representation that supports direct tree generation. Together, these results demonstrate that generative models can serve as a viable and scalable alternative to standard phylogenetic pipelines.

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

Meta-classification of one-class classification models using ranking correlation and nearest neighbor

Authors:
Toshitaka Hayashi↗Hamido Fujita↗Dalibor Cimr↗Richard Cimler↗Jitka K\"uhnov\'a↗

arXiv:2606.17858v1 Announce Type: new Abstract: Machine Learning (ML) techniques have been applied to various problems. However, applying ML to ML models is an unexplored direction. For this purpose, this paper considers a meta-classification of one-class classification (OCC) models, because all ML models could be approximated as OCC models. The proposal represents OCC models as normality rankings and classifies them using nearest-neighbor and ranking-correlation metrics. The experiment classifies OCC models, where classes correspond to training datasets, algorithms, and hyperparameters. The proposal achieves high accuracy when class labels are datasets. Moreover, it can classify algorithms when the training datasets contain the same class. In addition, the discussion highlights that the classification of OCC models is essentially the classification of datasets that treats multiple samples as a single input. The experiment demonstrates the classification of datasets using sleeping records. The proposed method can provide a unified solution for classifying OCC models, datasets, and rankings. Source code is uploaded to the public repository https://github.com/ToshiHayashi/ClassOCC.

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

CzechDocs: A Multiway Parallel Dataset of Formatted Documents for Minority Languages in Czechia

Authors:
Josef Jon↗Ond\v{r}ej Bojar↗

We present CzechDocs, a multiway parallel dataset of formatted documents (HTML, DOCX, and PDF) covering Czech and minority languages used in Czechia-primarily Ukrainian and English, with smaller portions of Vietnamese, Russian and other languages. The dataset is designed to support the evaluation of machine translation systems that aim to preserve document formatting during translation. We provide a comparison of the most common approaches to format-preserving machine translation on a validation subset of the dataset. This validation split, together with the evaluation toolkit, is publicly released for further research. A held-out test split will be reserved for a future shared task focused on document-level translation with formatting preservation.

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08.
arXiv (CS.LG) 2026-06-15

Where Black-box Drug-Target Interaction Prediction Models Look: Cross-Method Explainability

Authors:
Ali Vefghi↗Zahed Rahmati↗Mohammad Akbari↗

arXiv:2606.14245v1 Announce Type: new Abstract: Drug-target interaction (DTI) and affinity (DTA) predictors increasingly achieve strong benchmark scores, yet their internal use of sequence, fingerprint, and graph features often remains opaque. We present an interpretability audit of BridgeDPI architecture on three different datasets including Gao, Human, and C.elegans. This study combines gradient-based attributions – integrated gradients, saliency, layer-wise relevance propagation, SmoothGrad, and SmoothGrad-IG – with feature-wise occlusion ablation and strict intersection consensus across methods to reduce single-explainer bias. We summarize sensitivity and signed effects at raw inputs, at the bridge similarity scaffold, and through the graph convolution, including edge-level sensitivities and targeted edge removals. The results show that explainability is most informative when treated as model criticism: it reveals modality dominance, padding and special-token artifacts, dataset-dependent cooperative versus suppressive effects across layers, and chemistry-consistent fragment and composition motifs where methods agree. These analyses do not substitute for structural or experimental ground truth, yet they can provide testable hypotheses for downstream validation in computational drug discovery pipelines. More broadly, applying modern XAI to contemporary DTI/DTA models is still an early pass over the rich structure implicit in trained weights and data – yet even this first layer of scrutiny already helps researchers relate predictions to drug- and target-side representations and to prioritize external validation.

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09.
arXiv (CS.AI) 2026-06-12

MP3: Multi-Period Pattern Pre-training forSpatio-Temporal Forecasting

Authors:
Lilan Peng↗Yandi Liu↗Qingren Yao↗Chongshou Li↗Tianrui Li↗

arXiv:2606.13119v1 Announce Type: cross Abstract: Spatio-Temporal forecasting is crucial in diverse fields, such as transportation, climate, and energy. Urban spatio-temporal data exhibits temporal mirage: similar short-window inputs have divergent future trends, and vice versa. Existing spatio-temporal graph neural networks (STGNNs) cannot effectively identify such mirages. We argue that the core reason lies in the short-window inputs that have incomplete period observation, heterogeneous global spatial correlation, and cross-period superposition causality. To bridge this gap, we develop a novel Multi- Period Pattern Pre-training (MP3), a plug-and-play pre-training plugin for distinguishing temporal mirages. MP3 presents two core innovations: (1) The multi-period pattern learning is designed to learn multi-period patterns from long time series. Specifically, multi-period temporal modeling leverages edge convolution to identify different multi-period patterns. Multi-period spatial modeling uses a bottleneck project and a global memory bank to capture heterogeneous global spatial relations efficiently. Cross-period pattern interaction employs a causality-enhanced Transformer to capture dependencies across different period patterns. (2) This plugin can seamlessly integrate into existing STGNN backbones to strengthen their forecasting performance. The experiment on five STGNN baselines across five real-world datasets (including a large-scale dataset CA) verify the effectiveness, superior scalability and strong adaptability of MP3, which brings consistent and robust performance improvements across all evaluated baselines. On average, MP3 reduces the MAE 4.7% and the RMSE 5.0%. The code can be available at https://github.com/YAN-outlook/MP3.

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10.
PLOS Computational Biology 2026-06-11

Robust discovery of mutational signatures using power posteriors

Authors:
Catherine Xue↗

by Catherine Xue, Jeffrey W. Miller, Scott L. Carter, Jonathan H. Huggins Mutational processes, such as the molecular effects of carcinogenic agents or defective DNA repair mechanisms, produce different mutation types with characteristic frequency profiles, known as mutational signatures. Non-negative matrix factorization (NMF) has been successfully used to discover many mutational signatures, yielding novel insights into cancer etiology and informing targeted therapies. However, the NMF model is only a rough approximation to reality, and even small departures from this assumed model can have large negative effects on the accuracy and reliability of the results. We propose BayesPowerNMF, a Bayesian NMF method that provides nonparametric robustness to model misspecification, principled automated selection of the number of latent processes, and uncertainty quantification of model parameters. In extensive simulation studies, we find that our proposed approach recovers more true signatures with greater accuracy than current leading methods. On whole-genome sequencing data for six cancer types from the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, we find that our method is able to accurately recover more signatures than the current state-of-the-art.

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11.
medRxiv (Medicine) 2026-06-18

Multicluster measles outbreak with a substantial proportion of modified cases in Tokyo, Japan, January-May 2026

Authors:
Nishikawa↗Kurita↗Sugawara↗Matsuda↗Morikawa↗Imokawa↗Iwamura↗Suzuki↗Kodaira↗Kikuchi↗Takahashi↗Nishizuka↗…

Tokyo experienced a measles outbreak (260 cases) in early 2026 despite elimination status. Adults aged 20-39 years were most affected, and 38% of cases were modified measles, increasing with prior vaccination. Although incidence rose until April, the effective reproduction number; R(t) fell below 1, consistent with outbreak control. Multiple clusters were identified, but many cases lacked epidemiological links, suggesting that modified measles is less likely to be considered in differential diagnosis. Intensive contact tracing and surveillance contributed to limiting transmission.

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12.
arXiv (CS.CL) 2026-06-17

DICE: Diffusion Large Language Models Excel at Generating CUDA Kernels

Authors:
Haolei Bai↗Lingcheng Kong↗Xueyi Chen↗Jianmian Wang↗Zhiqiang Tao↗Huan Wang↗

Diffusion large language models (dLLMs) have emerged as a compelling alternative to autoregressive (AR) LLMs, owing to their capacity for parallel token generation. This paradigm is particularly well-suited for code generation, where holistic structural planning and non-sequential refinement are critical. Despite this potential, tailoring dLLMs for CUDA kernel generation remains challenging, obstructed not only by the high specialization but also by the severe lack of high-quality training data. To address these challenges, we construct CuKe, an augmented supervised fine-tuning dataset optimized for high-performance CUDA kernels. On top of it, we propose a bi-phase curated reinforcement learning (BiC-RL) framework consisting of a CUDA kernel infilling stage and an end-to-end CUDA kernel generation stage. Leveraging this training framework, we introduce DICE, a series of diffusion large language models designed for CUDA kernel generation, spanning three parameter scales, 1.7B, 4B, and 8B. Extensive experiments on KernelBench demonstrate that DICE significantly outperforms both autoregressive and diffusion LLMs of comparable scale, establishing a new state-of-the-art for CUDA kernel generation.

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13.
arXiv (CS.AI) 2026-06-17

Discrete Autoregressive Transformer for Generative Mechanism Synthesis

Authors:
Anar Nurizada↗Anurag Purwar↗

arXiv:2606.17409v1 Announce Type: cross Abstract: Planar path synthesis requires mechanisms whose coupler curves match a prescribed trajectory; the mapping from curve to linkage is inherently one-to-many across four-, six-, and eight-bar topologies. We address this design problem with simulation-grounded evaluation on a curated corpus of over one million mechanisms, reporting Chamfer distance and dynamic time warping after forward kinematics and geometric alignment. We formulate synthesis as conditional autoregressive sequence modeling: joint coordinates are uniformly quantized to tokens and generated by a decoder-only transformer with a variational-autoencoder (VAE) latent of the target curve and an explicit mechanism-type token. Training combines token cross-entropy with a Gaussian-smoothed bin auxiliary loss that respects ordinal structure among bins. At inference, a bounded latent-noise schedule decodes all mechanism types at each noise level; we retain the top five candidates by geometric error, yielding diverse accurate families without dataset lookup. On held-out tests, aggregate mean Chamfer distance is $0.0132$ and mean dynamic time warping is $0.153$; a latent $k$-nearest-neighbor baseline that conditions on training-set neighbor latents in VAE space achieves matched-topology mean Chamfer distance $0.0071$ and mean dynamic time warping $0.117$ using the same decoder.

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14.
arXiv (CS.AI) 2026-06-15

An Analysis of the Coordination Gap between Joint and Modular Learning for Job Shop Scheduling with Transportation Resources

Authors:
Moritz Link↗Jonathan Hoss↗Noah Klarmann↗

arXiv:2604.24117v2 Announce Type: replace Abstract: Efficient job-shop scheduling with transportation resources is critical for high-performance manufacturing. With the rise of "decentralized factories", multi-agent reinforcement learning has emerged as a promising approach for the combined scheduling of production and transportation tasks. Prior work has largely focused on developing novel cooperative architectures while overlooking the question of when joint training is necessary. Joint training denotes the simultaneous training of job and automatic guided vehicle scheduling agents, whereas modular training involves independently training each agent followed by post-hoc integration. In this study, we systematically investigate the conditions under which joint training is essential for optimal performance in the job-shop scheduling problem with transportation resources. Through a rigorous sensitivity analysis of resource scarcity and temporal dominance, we quantify the coordination gap – the performance difference between these two training modalities. In our evaluation, joint training outperforms the majority of dispatching rule combinations and modular training approaches. However, the coordination gap advantage diminishes in bottleneck environments, particularly under severe transport and processing constraints. These findings indicate that modular training represents a viable alternative in environments where a single scheduling task dominates. Overall, our work provides practical guidance for selecting between training modalities based on environmental conditions, enabling decision-makers to optimize reinforcement learning-based scheduling performance.

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15.
medRxiv (Medicine) 2026-06-22

Hyperlipidemia Pharmacotherapy in Skilled Nursing Facilities: A Real-World Evidence Study

Authors:
Ashraf↗Mathers↗K. E↗Wagner↗Saumur↗

Objectives: To estimate hyperlipidemia medication order prevalence and associated variables in U.S. skilled nursing facility (SNF) residents. Design: Retrospective, observational study. Setting and Participants: Electronic Health Record data from 447,080 SNF residents with a hyperlipidemia diagnosis identified in PointClickCare's Life Sciences clinical database (January-April 2025) were reviewed. Methods: The presence and absence of medication orders for hyperlipidemia treatments recommended by the American Heart Association were assessed. Descriptive analyses summarized demographic and clinical characteristics, and a modified Poisson regression model was used to estimate risk ratios for having a medication order, adjusting for demographic, clinical, and facility characteristics. Results: Overall, 83.3% of residents diagnosed with hyperlipidemia had at least one hyperlipidemia medication order. Statins were ordered by 96.2% of active order residents, while other medication classes i.e., omega-3 fatty acids, cholesterol absorption inhibitors, fibrates were less common (

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

Creativity Reconsidered: Generative AI and the Problem of Intentional Agency

Authors:
James S. Pearson↗Matthew J. Dennis↗Marc Cheong↗

arXiv:2601.15797v2 Announce Type: replace Abstract: Many theorists maintain that conscious intentional agency is a necessary condition of creativity. We argue that this requirement, which we call the Intentional Agency Condition (IAC), should be abandoned. We motivate this by highlighting the problems this criterion encounters in the face of recent advances in generative AI, which is ostensibly creative despite being incapable of intentional agency. We present two corpus analyses to illustrate the rapidly increasing tendency of people to predicate creativity to generative AI. In response to this predicament, theorists of creativity have proposed a range of conflicting solutions, which we critically evaluate. We find that none of these satisfyingly resolves the initial predicament, and we therefore propose a novel approach. Our claim is that ascriptions of creativity are dependent on what we call creative ability. This solution explains why intentional agency is important for judgements of creativity, without being a necessary condition. Our approach thereby accommodates AI creativity without dismissing the intuition that perceived intentions are of key importance for ascriptions of creativity.

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17.
arXiv (CS.CV) 2026-06-12

ECA: Efficient Continual Alignment for Open-Ended Image-to-Text Generation

Authors:
Jiangtao Kong↗Peijun Zhao↗Chun-Fu Chen↗Youngwook Do↗Shaohan Hu↗Tianyi Zhou↗Huajie Shao↗

Incremental Learning (IL) for Open-ended Image-to-Text Generation (OpenITG) enables models to continuously generate accurate, contextually relevant text for new images while preserving previously acquired knowledge. Unlike prior studies, this paper addresses a more practical scenario in which the predominant category of visual data shifts over time as environments evolve. In this context, we introduce a new notion of continual alignment, which incrementally adapts the alignment module within pre-trained VLMs to preserve high-quality cross-modal representations. Based on this idea, we propose Efficient Continual Alignment (ECA), a novel exemplar-free IL approach for OpenITG. The key challenge is enabling the model to acquire new, task-specific features while minimizing interference with the established alignment without accessing raw data from previous tasks. To address this, ECA employs three core mechanisms: a Mixture of Query (MoQ) module that adapts task-specific query tokens, a Fisher Dynamic Expansion (FeDEx) that dynamically expands model structure based on a Fisher Information Matrix (FIM)-based metric, and an embedding dictionary with Dictionary Replay (DR) to retain past knowledge. To evaluate ECA's performance, we construct four new IL OpenITG benchmarks that better reflect real-world scenarios. Experimental results demonstrate that ECA significantly mitigates catastrophic forgetting and improves IL performance compared to baseline methods. Code and benchmarks are available at https://github.com/Snowball0823/ECA.

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18.
arXiv (CS.LG) 2026-06-19

Fisher-Geometric Sharpness and the Implicit Bias of SGD toward Flat Minima

Authors:
Md Sakir Ahmed↗Kumaresh Sarmah↗Hemen Dutta↗

arXiv:2606.20469v1 Announce Type: new Abstract: A widely held intuition in deep learning is that stochastic gradient descent (SGD) implicitly favors flat minima and that flat minima generalize better, but standard Euclidean measures of flatness such as the trace or maximum eigenvalue of the loss Hessian are not invariant under reparametrizations that preserve the network function, which undermines the theoretical foundations of this narrative. In this study we resolve this issue by grounding flatness in the Riemannian geometry of the statistical manifold induced by the Fisher Information Matrix (FIM). We define Riemannian sharpness mathematically and prove that it is invariant under smooth, function-preserving reparametrizations, which directly addresses the critique of Dinh et al. in the paper ``Sharp minima can generalize for deep nets''.We note that this invariance is a property of the true FIM; the diagonal empirical estimator used in practice (and in all experiments below) inherits invariance only approximately, and exact invariance under arbitrary reparametrizations would require structured estimators such as K-FAC. We formalize the gradient noise of mini-batch SGD as having a covariance structure proportional to the FIM, derive the stationary distribution of the resulting stochastic differential equation, and then show that the probability mass is exponentially concentrated at Riemannian-flat minima. A PAC-Bayes generalization bound controlled explicitly by SR formally links this geometric bias to test performance. Our experiments on MNIST and CIFAR-10 confirm that SR reliably tracks generalization in ways that Euclidean sharpness does not, and that its scaling with $\eta/B$ matches the theoretical predictions. Together these results provide a rigorous, reparametrization-invariant account of why flat minima generalize.

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

The N-Body Problem: Parallel Execution from Single-Person Egocentric Video

Authors:
Zhifan Zhu↗Yifei Huang↗Yoichi Sato↗Dima Damen↗

Humans can intuitively parallelise complex activities, but can a model predict this from observing a single person? Given one egocentric video, we introduce the N-Body Problem: predicting how N individuals, can hypothetically perform the same set of tasks. The goal is to maximise speed-up, but naive assignment of video segments to individuals often violates real-world constraints, leading to physically impossible scenarios like two people using the same object or occupying the same space. To quantify this, we formalise the N-Body Problem and propose a suite of metrics to evaluate both performance (speed-up, task coverage) and feasibility (spatial collisions, object conflicts and causal constraints). As a proof of concept, we introduce a structured prompting strategy that guides a Vision-Language Model (VLM) to reason about the 3D environment, object usage, and temporal dependencies, producing a viable parallel execution. On 100 videos from EPIC-Kitchens and HD-EPIC, for $N = 2$, our structured prompt improves action coverage by 45% over a baseline prompt for Gemini 2.5 Pro, while simultaneously slashing collision rates, object and causal conflicts by 51%, 52% and 55% respectively.

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20.
arXiv (math.PR) 2026-06-12

Dimension-free Markov–Bernstein inequalities for product measures

Authors:
Egor Kosov↗

arXiv:2606.13575v1 Announce Type: cross Abstract: We study dimension-free Markov–Bernstein inequalities for polynomials with respect to product probability measures. In the Gaussian case, for $p\ge4$, we prove that \[ \|\nabla f\|_{L^p(\gamma^n)} \le C(p)d^{\frac12+\theta_p} \|f\|_{L^p(\gamma^n)} \] for every polynomial $f$ of degree at most $d$, where $\theta_p\le \frac{2}{3p}$ and $\theta_p=0$ whenever $p$ is an even integer. Thus, for even integer exponents, we establish the sharp dependence on the degree conjectured by Eskenazis–Ivanisvili. For general $p\ge4$, the estimate improves upon their dimension-free inequality. We also obtain dimension-free Markov–Bernstein inequalities with sharp dependence on the degree for even integer exponents beyond the Gaussian setting. We first prove such estimates for the uniform distribution on the unit cube and then extend them to products of absolutely continuous measures with unimodal densities. Finally, we treat products of one-dimensional Freud measures with densities proportional to $e^{-|t|^{2m}}$.

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21.
Nature (Science) 2026-06-10

A vast whale necropolis has been found

Authors:
Stephen J. Godfrey↗

In the Indian Ocean, a deep-sea area roughly 1,200 kilometres long and 7 kilometres deep was found to harbour an ecological landmark site of whale remains. In the Indian Ocean, a deep-sea area roughly 1,200 kilometres long and 7 kilometres deep was found to harbour an ecological landmark site of whale remains.

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22.
bioRxiv (Bioinfo) 2026-06-21

Machine learning evaluation of gene expression-based ALS subtypes across brain and blood tissues

Authors:
Gomez↗E. A↗Al Khleifat↗Troakes↗Al-Chalabi↗Iacoangeli↗

The clinical and molecular heterogeneity observed in amyotrophic lateral sclerosis (ALS) presents a challenge for diagnosis, prognosis, and treatment. RNA sequencing of post-mortem brain samples from ALS patients has identified several subtypes with distinct molecular signatures. We sought to evaluate these subtypes across diverse tissues and datasets and assess the feasibility of supervised machine learning models for sample classification. Unsupervised clustering and pathway analysis were performed to confirm the presence of ALS subtypes in motor cortex samples. Three machine learning strategies were then used to create models based on post-mortem motor cortex expression data of 112 people with ALS from the London Neurodegenerative Diseases Brain Bank. These models were subsequently improved through feature selection and evaluated in independent cohorts from motor cortex (n = 257, NYGC ALS Consortium) and blood (n = 96, Macquarie University Neurodegenerative Disease Biobank) samples. Multi-class linear discriminant analysis (LDA) models were then used for subtype classification. Clustering of ALS post-mortem motor cortex samples confirmed the presence of three subtypes: neuroinflammation (ALS-Neu), extracellular matrix organisation and muscle contraction (ALS-OxA), and synaptic and neuropeptide signalling (ALS-SNs). Among all machine learning strategies, random forests produced the most accurate and stable models for binary classification (~93% accuracy across the three subtypes). After feature selection, random forest models were able to classify samples from an independent post-mortem motor cortex cohort in their respective subtypes (AUC of ~0.98 across the three subtypes). When these models were evaluated in blood using LDA, we found consistent clustering patterns, with samples aligning in the same subtype regions of the post-mortem motor cortex samples, with ALS-SNs being the subtype in which samples were classified with the highest confidence (LDA class probability ~86%). Moreover, classification for this subtype improved when blood samples were collected closer to death. Our findings support the presence of three gene expression-based ALS subtypes in motor cortex samples and the utility of machine learning strategies for subtype classification. We also observed that the subtypes identified in the brain partially match those in the blood, with samples from the late stages of the disease more likely to be correctly predicted into the ALS-SNs cluster. This suggests a longitudinal effect in subtype identification that requires further investigation.

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23.
arXiv (CS.AI) 2026-06-18

DeepInflation: an AI agent for research and model discovery of inflation

Authors:
Ze-Yu Peng↗Hao-Shi Yuan↗Qi Lai↗Jun-Qian Jiang↗Gen Ye↗Jun Zhang↗Yun-Song Piao↗

arXiv:2601.14288v2 Announce Type: replace-cross Abstract: We present DeepInflation, an AI agent designed for research and model discovery in inflationary cosmology. Built upon a multi-agent architecture, DeepInflation integrates Large Language Models (LLMs) with a symbolic regression (SR) engine and a retrieval-augmented generation (RAG) knowledge base. This framework enables the agent to automatically explore and verify the vast landscape of inflationary potentials while grounding its outputs in established theoretical literature. We demonstrate that DeepInflation can successfully discover simple and viable single-field slow-roll inflationary potentials consistent with the latest observations (with the ACT DR6 results taken as an example) or any given $n_s$ and $r$, and provide accurate theoretical context for obscure inflationary scenarios. DeepInflation serves as a prototype for a new generation of autonomous scientific discovery engines in cosmology, which enables researchers and non-experts alike to explore the inflationary landscape using natural language. This agent is available at https://github.com/pengzy-cosmo/DeepInflation.

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

From Construction to Injection: Edit-Based Fingerprints for Large Language Models

Authors:
Yue Li↗Xin Yi↗Dongsheng Shi↗Yongyi Cui↗Gerard de Melo↗Linlin Wang↗

Reliable model fingerprints are essential for protecting large language models (LLMs) against unauthorized redistribution and commercial misuse. In black-box deployment, verification is hindered by defensive filtering of suspected fingerprint queries, as well as by downstream model modifications that may weaken embedded ownership evidence. These risks require fingerprints to be robust in both construction and injection. For construction, prior paradigms face an imperceptibility trade-off: natural-language fingerprints may be accidentally activated, whereas garbled fingerprints are statistically exposed and easier to filter. For injection, existing methods struggle to preserve persistent trigger–target behaviors under model modification. We propose an end-to-end injected fingerprinting framework to address these challenges. Code-mixing Fingerprints (CF) use lowest-perplexity code-mixing under a high-complexity constraint to mitigate this two-sided imperceptibility trade-off. Multi-Candidate Editing (MCEdit) constructs structurally redundant, margin-separated trigger–target mappings to enable graceful degradation under model modification. Extensive evaluations on imperceptibility, detectability, and harmlessness demonstrate robust ownership verification with negligible impact on utility.

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25.
arXiv (CS.LG) 2026-06-16

DiRecT: Safe Diffusion-Based Planning via Receding-Horizon Denoising

Authors:
Paolo Giaretta↗Zeyang Li↗Navid Azizan↗

arXiv:2606.15359v1 Announce Type: new Abstract: Diffusion models have emerged as powerful tools for planning and control by learning multimodal distributions over actions and trajectories. Yet reliable inference-time safety enforcement remains a key barrier to their deployment in safety-critical tasks. Existing approaches typically project each denoising iterate onto the feasible set, even though constraints are defined only on the final clean trajectory. Enforcing feasibility on noisy intermediate samples can therefore overconstrain the sampling dynamics, substantially degrading sample quality. To address this limitation, we introduce DiRecT (Diffusion-based planning via Receding-horizon denoising with Terminal constraints), a training-free algorithm for constrained sampling from diffusion models via stochastic optimal control (SOC). DiRecT enforces constraints only on the final clean sample, avoiding unnecessary restrictions on the intermediate denoising dynamics. Inspired by model predictive control, we derive a principled receding-horizon surrogate for the otherwise intractable constrained SOC formulation, yielding an efficient algorithm that cleanly separates stochastic denoising from constraint satisfaction, progressively steering samples toward feasible final trajectories without distorting the learned diffusion dynamics. Furthermore, DiRecT is highly flexible: it can leverage off-the-shelf or domain-specific optimizers, incorporate priors over environment dynamics, and optimize additional soft rewards. Extensive experiments on safe planning benchmarks demonstrate that DiRecT substantially improves deployment safety and task performance over existing diffusion-based planning baselines.

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