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01.
Nature (Science) 2026-06-23

Europe must seize the moment to lead on free and open science

作者: 未知作者

An under-appreciated research powerhouse, Europe has a responsibility to champion democratic science that is accessible to all the world’s research talent. An under-appreciated research powerhouse, Europe has a responsibility to champion democratic science that is accessible to all the world’s research talent.

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02.
PLOS Computational Biology 2026-06-22

Adhesion and polarity-driven morphogenesis: Mechanisms and constraints in tissue formation

作者:
Yoshiyuki T. Nakamura↗

by Yoshiyuki T. Nakamura, Chikara Furusawa, Kunihiko Kaneko Embryonic development in multicellular organisms exhibits diverse morphogenetic patterns, which can generally be categorized into fundamental types such as monolayer and multilayer spheres, as well as cell masses. Furthermore, we identify two distinct processes for the formation of spherical structures. These basic patterns are thought to be governed by the microscopic properties of intercellular adhesion. However, the specific mechanisms linking the microscopic factors to the emergence of distinct macroscopic morphogenetic patterns remain poorly understood. In this study, we explore how different morphogenetic patterns arise by employing a computational model that incorporates intercellular adhesion and polarity. Our results demonstrate that all fundamental morphogenetic patterns can be generated through the interplay of two key parameters: the polarity strength of the cell and the regulation of polarity via mechanical signals. Furthermore, analytical considerations reveal key mechanisms underlying the formation of these patterns. These findings highlight the critical role of physical constraints in morphogenesis and suggest potential applications to the design of artificial tissues and organoids.

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03.
arXiv (CS.LG) 2026-06-15

On the Geometry and Optimization of Polynomial Convolutional Networks

作者:
Vahid Shahverdi↗Giovanni Luca Marchetti↗Kathl\'en Kohn↗

arXiv:2410.00722v3 Announce Type: replace Abstract: We study convolutional neural networks with monomial activation functions. Specifically, we prove that their parameterization map is regular and is an isomorphism almost everywhere, up to rescaling the filters. By leveraging on tools from algebraic geometry, we explore the geometric properties of the image in function space of this map - typically referred to as neuromanifold. In particular, we compute the dimension and the degree of the neuromanifold, which measure the expressivity of the model, and describe its singularities. Moreover, for a generic large dataset, we derive an explicit formula that quantifies the number of critical points arising in the optimization of a regression loss.

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04.
bioRxiv (Bioinfo) 2026-06-18

pykarambola: Minkowski tensor morphometry of 3D structures

作者:
Khurana↗Ishihara↗

Three-dimensional biological morphologies encode functional and physiological state, yet the directional, orientational, and topological properties of these shapes are rarely captured by morphometric tools available for bioimage analysis. Minkowski tensors are mathematically rigorous tensor-valued measures that encode surface curvature and directionality for objects of arbitrary topology, with tensor eigensystems that directly quantify elongation axes and anisotropy. A C++ implementation, karambola, computes Minkowski tensors for triangulated surfaces but is inaccessible within Python-based bioimage workflows. Here we present pykarambola, a pip installable Python package that accepts NumPy arrays and standard mesh formats and returns Minkowski tensors, including derived anisotropy and orientation quantities. A high-level label-image API converts 3D integer arrays into per-object Minkowski tensors in a single call, making pykarambola directly compatible with the output of widely used segmentation tools. An optional Cython extension accelerates graph-traversal steps of mesh initialization for large-scale analyses. Benchmarked on 1,584 adrenal gland meshes, pykarambola reproduces all 121 C++ karambola output features to near-floating-point agreement and, in the pure-Python build, is 2.8x faster at 28^3 and 1.5x faster at 64^3 voxel resolution, with speedups primarily attributable to karambola's sequential per-object file I/O. pykarambola is freely available as an open-source software package.

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

How Far Can Chord-Symbol Time-Series Adaptation Carry Genre Identity? Capabilities and Boundaries in Multi-Genre Chord-Symbol Modeling

作者:
Jinju Lee↗

arXiv:2606.07334v2 Announce Type: replace-cross Abstract: This report treats chord-symbol sequences as an interpretable, controllable time series for genre-local harmonic modeling. The frozen Music Transformer base - released as a pop-jazz fine-tune endpoint but verified in this revision weight-identical to the pop-only Phase-0 baseline, so all gains are measured over a pure-pop prior (see Changes in v2) - is extended to eleven target genres: blues, bossa nova, Bach chorales, country, electronic, folk, funk, gospel, hip-hop, R&B/soul, and rock. The main evaluation compares LoRA, IA3, BitFit, prefix tuning, and full fine-tuning over 11 genres and 3 seeds, a complete 165-cell grid. All five methods improve over the frozen base on held-out chord prediction (macro gains +2.89 to +3.61 percentage points); LoRA and IA3 score highest, but pairwise Wilcoxon tests with Holm and Benjamini-Hochberg correction do not support a decisive winner. A matched-data-size control sharpens this: at a common corpus size IA3 stays on top while LoRA drops to last, so the small method gaps are partly data-driven rather than representational. A control-token baseline is also strong, and wrong-genre adapters often beat the frozen base, suggesting the adaptation effect is largely lightweight conditioning over a reusable harmonic base rather than genre-specific adapter memory. Further diagnostics (rank sweeps, wrong-genre rotation, a base-checkpoint ablation that v2 reinterprets as a same-weights control, chord-only genre classification, output-distribution statistics, real-song evaluation, duplicate analysis) support a bounded conclusion: chord-symbol adaptation reliably improves genre-local harmonic prediction, but chord symbols alone do not carry complete genre identity. Perceived genre authenticity and musical quality are left to controlled listener evaluation.

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

Enhanced Low-Density Region Exploration in Classifier-Guided Diffusion Models Through Modified Reverse Diffusion Sampling

作者:
Jagriti Singh↗Shekhar Verma↗Muneendra Ojha↗

arXiv:2606.13347v1 Announce Type: new Abstract: Diffusion models have emerged as state-of-the-art generative models for high-fidelity image synthesis, particularly in their classifier-free guided and classifier-guided forms. However, standard classifier guidance concentrates probability mass around high-density class mean, leading to poor coverage of rare samples in the tails of the class-conditional distributions. Recent work on diffusion-based tail sampling mitigates this by training an additional low-density-seeking classifier with a synthetic-vs-real discriminator, at the cost of additional networks and training. In parallel, a number of samplers and distillation techniques accelerate or refine diffusion sampling, but do not explicitly address long-tail coverage. We propose a purely sampling-time, density-aware extension of classifier-guided conditional diffusion model that targets low-density regions without any additional training. We have applied guidance at noisy images not on predicted noise like most diffusion models. Starting from a pretrained conditional diffusion model and classifier on ImageNet, we modify the guided reverse dynamics by steering trajectories toward low-confidence regions via the modified classifier gradient, and at each time step, we also guide the sampling process toward the predicted real image. 1st guidance helps explore low-probability samples, and 2nd guidance helps to generate samples to be close to the real data manifold. The proposed sampler consistently improves ADM model recall at 64x64 resolution while maintaining a comparable FID, and with a 256x256 ADM model, we showed the results visually with different combinations of both guidance. We also showed that standard ADM classifier guidance, combined with predicted real image guidance, helps generate high perceptual quality samples with a 256x256 ADM model on ImageNet.

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07.
arXiv (quant-ph) 2026-06-16

Quantifying Coherence-to-Entanglement Conversion Efficiency under Noisy Operations

作者:
Asad Ali↗H. Kuniyil↗M. I. Hussain↗M. T. Rahim↗Abdallah Slaoui↗Saif Al-Kuwari↗

arXiv:2606.16916v1 Announce Type: new Abstract: We investigate the noise-limited conversion of local quantum coherence into bipartite entanglement in a minimal two-qubit protocol comprising a coherent single-qubit input, an incoherent ancilla, an ideal CNOT operation, and subsequent environmental noise. Employing the $l_1$-norm of coherence and the entanglement negativity as resource quantifiers, we establish an exact closed-form correspondence between local single-qubit input coherence and the two-qubit entanglement generated in the noiseless limit, showing that the output negativity is precisely one half of the initial $l_1$-coherence. We then derive analytic expressions for the surviving entanglement and the associated coherence-to-entanglement conversion efficiency under two representative noise mechanisms: independent phase damping and global two-qubit depolarizing noise. The two channels exhibit qualitatively distinct degradation behavior. Phase damping induces a universal multiplicative suppression of the generated entanglement, yielding a coherence-independent conversion efficiency and no finite-noise entanglement sudden death. In contrast, global depolarization introduces an isotropic mixing contribution that shifts the partial-transpose spectrum, producing coherence-dependent degradation and a finite sudden-death threshold. We show that maximally coherent inputs not only maximize the entanglement generated by the CNOT protocol but also optimize its robustness against depolarizing noise. Direct density-matrix simulations validate the analytic results to numerical precision. These findings provide a compact analytic benchmark for assessing how different noise mechanisms constrain coherence-to-entanglement conversion in elementary quantum-information protocols and near-term quantum devices.

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08.
arXiv (CS.LG) 2026-06-16

Structured Nonparametric Variational Inference for Dependent Latent Modeling

作者:
Yuda Shao↗Zhiling Gu↗Shan Yu↗

arXiv:2606.15458v1 Announce Type: cross Abstract: Variational inference (VI) is a core engine of modern AI, enabling scalable approximate Bayesian learning and uncertainty-aware training of large probabilistic and generative models. In this paper, we propose Structured Nonparametric Variational Inference (SN-VI), a novel framework for modeling complex dependencies among latent variables in posterior approximation, leveraging multivariate spline techniques. Unlike traditional methods that rely on the mean-field assumption, SN-VI preserves intricate latent variable dependencies, providing a flexible and accurate approximation of posteriors with arbitrary shapes. We establish rigorous theoretical guarantees, including the derivation of the lower bound for the variational objective and proof of asymptotic consistency in posterior estimation. To facilitate practical implementation, we develop an algorithm that automatically identifies dependent latent variables and their underlying dependence structure, without requiring manual specification. Simulation studies validate the effectiveness of SN-VI in approximating posterior distributions with bounded support and complex dependencies. The proposed method has been successfully applied to high-dimensional structured data, including computer vision datasets and spatial transcriptomics. In these applications, SN-VI demonstrates improved generative model performance and effectively uncovers coupled biological signals through the learned dependency structure.

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

Efficient Flow Matching using Latent Variables

作者:
Anirban Samaddar↗Yixuan Sun↗Viktor Nilsson↗Sandeep Madireddy↗

Flow matching models have shown great potential in image generation tasks among probabilistic generative models. However, most flow matching models in the literature do not explicitly utilize the underlying clustering structure in the target data when learning the flow from a simple source distribution like the standard Gaussian. This leads to inefficient learning, especially for many high-dimensional real-world datasets, which often reside in a low-dimensional manifold. To this end, we present $\texttt{Latent-CFM}$, which provides efficient training strategies by conditioning on the features extracted from data using pretrained deep latent variable models. Through experiments on synthetic data from multi-modal distributions and widely used image benchmark datasets, we show that $\texttt{Latent-CFM}$ exhibits improved generation quality with significantly less training and computation than state-of-the-art flow matching models by adopting pretrained lightweight latent variable models. Beyond natural images, we consider generative modeling of spatial fields stemming from physical processes. Using a 2d Darcy flow dataset, we demonstrate that our approach generates more physically accurate samples than competing approaches. In addition, through latent space analysis, we demonstrate that our approach can be used for conditional image generation conditioned on latent features, which adds interpretability to the generation process.

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10.
arXiv (CS.CL) 2026-06-19

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

作者:
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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11.
bioRxiv (Bioinfo) 2026-06-15

oxo-flow: compiled, memory-safe bioinformatics workflow orchestration

作者:
Wang↗

Bioinformatics analyses depend on workflow engines to coordinate dozens of computational tools across complex dependency chains. The most widely adopted engines-Snakemake, Nextflow, the Common Workflow Language (CWL), and the Workflow Description Language (WDL)-run on interpreted or just-in-time (JIT) compiled language runtimes, incurring hundreds of milliseconds of startup latency and providing no compile-time safety guarantees from the host language. We developed oxo-flow, a workflow engine written in Rust that compiles to a single native binary. On an Apple M5 processor, oxo-flow parses, validates, and dry-runs a production-scale workflow in roughly 22 milliseconds-before Snakemake or Nextflow have finished loading their runtime environments. Peak memory usage is 16 megabytes, representing six- to seven-fold reductions relative to Snakemake and Nextflow. Dry-run latency is essentially independent of workflow size: a hundred-fold increase in rule count adds approximately 0.4 milliseconds. oxo-flow integrates 31 command-line tools, a REST interface with 60 endpoints, an embedded web application, and native cluster submission into a single 10-megabyte binary. It provides per-rule environment isolation across seven backends, checkpoint-based fault tolerance with cryptographic output verification, and a formal installation and operational qualification protocol for regulated laboratory environments. Ten curated workflows and three demonstration pipeline repositories are available. oxo-flow is freely available under Apache License 2.0 at https://github.com/Traitome/oxo-flow.

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

Workflow-GYM: Towards Long-Horizon Evaluation of Computer-use Agentic tasks in Real-World Professional Fields

作者:
Liya Zhu↗Jingzhe Ding↗Jian Zhang↗Jianbo Xue↗Shihao Liang↗Ge Zhang↗Yi Zhu↗Duju Zeng↗Xiang Gao↗Qingshui Gu↗Mailun Gao↗Huimin Che↗…

arXiv:2606.11042v2 Announce Type: replace Abstract: Recent years have witnessed the rapid evolution of AI agents toward handling increasingly complex, real-world tasks. However, existing benchmarks rarely evaluate whether agents can operate graphical user interfaces to complete long-horizon, high-value professional workflows across diverse domains. Current GUI benchmarks still predominantly focus on general-purpose software, relatively simple applications, and short-horizon tasks, leaving it largely unknown whether modern agents can follow user instructions to autonomously operate domain-specific professional software and accomplish economically valuable work in an end-to-end manner. To bridge this gap, we introduce Workflow-GYM, a benchmark for long-horizon GUI tasks centered on professional domains and specialized software environments. Through extensive experiments on state-of-the-art models, we find that even the strongest models achieve only slightly above 30% success rates, highlighting that professional long-horizon GUI workflows remain highly challenging for current GUI agents. Further analysis reveals that current agents struggle to maintain long-horizon workflow consistency, frequently exhibiting workflow stage omission, error propagation, objective drift, and insufficient understanding of professional software environments. Our findings provide important insights into the limitations of current agent systems and suggest key directions for the next generation of GUI-agent research.

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

Unifying Learning Dynamics and Generalization in Transformers Scaling Law

作者:
Chiwun Yang↗

The scaling law, a cornerstone of Large Language Model (LLM) development, predicts improvements in model performance with increasing computational resources. Yet, while empirically validated, its theoretical underpinnings remain poorly understood. This work formalizes the learning dynamics of transformer-based language models as an ordinary differential equation (ODE) system, then approximates this process to kernel behaviors. Departing from prior toy-model analyses, we rigorously analyze stochastic gradient descent (SGD) training for multi-layer transformers on sequence-to-sequence data with arbitrary data distribution, closely mirroring real-world conditions. Our analysis characterizes the convergence of generalization error to the irreducible risk as computational resources scale with data, especially during the optimization process. We establish matching upper and lower bounds on the excess risk, characterized by a distinct phase transition. In the initial optimization phase, the excess risk decays exponentially relative to the computational cost ${\sf C}$. However, once a specific resource allocation threshold is crossed, the system enters a statistical phase, where the generalization error follows a power-law decay of $\Theta(\mathsf{C}^{-1/7})$. These rates are certified by complementary lower bounds – statistical, via an information-theoretic two-point reduction, and optimization-side, via a first-order oracle argument – rendering the two-stage law tight up to constants, logarithmic factors, and a condition-number gap. Beyond this unified framework, our theory derives isolated scaling laws for model size, training time, and dataset size, elucidating how each variable independently governs the bounds of generalization.

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14.
bioRxiv (Bioinfo) 2026-06-15

VrySure: A Multi-Task AI Scientific Fraud Detection Platform for Identifying Manipulated and AI-Generated Biomedical Research Images

作者:
Sun↗Li↗Kalluri↗

Integrity of scientific data is critical in biomedical research, where images often serve as primary evidence for experimental observations and conclusions. Advances in image-editing technologies and generative artificial intelligence (AI) have increased the accessibility and realism of visual manipulation, making detection through manual review increasingly challenging. To empower our laboratory researchers to continuously monitor and uphold scientific rigor and data integrity, and serve the global scientific community, we developed VrySure, an easy-to-deploy, AI-driven multi-task platform for automated image-integrity screening in biomedical research. VrySure integrates four detection modules: cross-image transformation detection, within-image copy-move detection, splicing detection in blot and gel images, and AI-generated image detection. The system identifies potentially manipulated images and, when possible, localizes suspicious regions using bounding-box outputs to support downstream verification. To support development and evaluation, we constructed task-specific datasets by combining public biomedical image resources, curated manipulated examples, and synthetic images generated by multiple generative AI systems. We evaluated VrySure using region-level F1 score, recall, precision, false negative rate (FNR), and false discovery rate (FDR) across multiple manipulation categories and compared its performance with two commonly used commercial image-integrity screening platforms under a predefined benchmark protocol. Under the tested conditions, VrySure achieved a higher F1 score and recall, lower FNR, and maintained a low FDR for within-image copy-move detection, splicing detection, and AI-generated image detection, while showing comparable performance in transformation detection. Beyond automated screening, VrySure is designed to support source-data comparison and evidence-based assessment in scientific integrity investigations. By integrating multiple detection capabilities into a unified and scalable workflow, VrySure provides a practical framework to improve the efficiency and consistency of image-integrity screening in biomedical research.

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

VANDERER: Map-Free Exploration using Future-Aware and Visual-Curiosity-Guided Diffusion Policy

作者:
Venkata Naren Devarakonda↗Raktim Gautam Goswami↗Prashanth Krishnamurthy↗Farshad Khorrami↗

Mobile agents require efficient exploration strategies to map unseen environments and autonomously plan tasks. Traditional methods rely on generating occupancy maps and optimizing the sequence in which unexplored regions are visited. However, in sensor-constrained settings, such as those limited to monocular cameras, generating accurate occupancy maps is challenging. To address this, we propose VANDERER, an exploration framework that leverages a Visual Curiosity Module (VCM) to guide pre-trained diffusion policies using only monocular image data. This curiosity module predicts the outcomes of proposed actions via a navigation world model and evaluates them through a curiosity cost. The cost then guides the diffusion process toward generating actions that maximize exploration. Evaluated across diverse simulated environments, VANDERER consistently outperforms established baselines, exploring an average of 13.4% more area than NoMaD. Our results reveal a direct correlation between visual and geometric curiosity in outdoor environments, demonstrating that VANDERER can effectively leverage this relationship for efficient exploration using sensor-constrained agents.

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

World Model Self-Distillation: Training World Models to Solve General Tasks

作者:
Sebastian Stapf↗Pablo Acuaviva Huertos↗Aram Davtyan↗Paolo Favaro↗

Pretrained video generators are promising visual world models that exhibit emergent task-solving abilities; however, their reliance on detailed textual descriptions limits their direct use for planning and decision-making. Existing approaches either outsource this reasoning to language or vision-language models, or rely on supervised fine-tuning with paired task-execution videos, which are costly to collect and difficult to scale. We propose a scalable framework that elicits task-solving ability in such models by combining self-distillation with reinforcement learning. Given an unlabeled scene image, a vision-language model generates a candidate task and a detailed step-by-step solution. The solution conditions a pretrained video diffusion model, the Demonstrator; we distill its behavior into an Executor conditioned only on the image and a short task prompt. This transfers execution knowledge from caption-guided generation to instruction-conditioned task solving without curated task-video supervision. We further improve the Executor with reinforcement learning from VLM feedback, exploiting the asymmetry between judging whether a sampled video satisfies a task and generating the solution. Experiments on our proposed WorldTasks-Benchmark and the DreamGen robotics benchmark show that the Executor surpasses the Demonstrator under our VLM-based evaluation protocol and transfers competitively to robotic tasks.

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17.
arXiv (CS.CL) 2026-06-19

MedRLM: Recursive Multimodal Health Intelligence for Long-Context Clinical Reasoning, Sensor-Guided Screening, Evidence-Grounded Decision Support, and Community-to-Tertiary Referral Optimization

作者:
Aueaphum Aueawatthanaphisut↗

Real-world clinical decision support requires reasoning over heterogeneous and longitudinal patient information rather than answering isolated medical questions. However, current medical large language models and retrieval-augmented generation systems often rely on single-step prompting or retrieval, which can be fragile when clinical evidence is distributed across long electronic health records, medical images, sensor streams, guidelines, and referral constraints. This paper proposes MedRLM, a Recursive Multimodal Health Intelligence framework for long-context clinical reasoning, sensor-guided screening, and community-to-tertiary referral support. Instead of compressing all patient information into one prompt, MedRLM treats the patient case as an external clinical environment that can be recursively inspected, decomposed, retrieved, verified, and synthesized. The framework coordinates specialized agents for clinical text, longitudinal EHR, medical imaging, physiological sensor signals, guideline retrieval, uncertainty auditing, and referral planning. It further introduces a Clinical Evidence Graph Memory to connect patient-specific observations with retrieved evidence, standardized definitions, sensor-derived biomarkers, and referral criteria. A sensor-guided recursive triggering mechanism activates deeper reasoning when abnormal physiological or behavioral patterns are detected, while uncertainty-gated refinement supports clinician review for high-risk or low-confidence cases. We also outline a real-data evaluation design using public and credentialed clinical datasets spanning EHR, radiology, ECG, ICU time series, and referral-proxy outcomes. MedRLM aims to move medical AI from static question answering toward auditable, multimodal, and workflow-aware clinical decision support.

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

ITNet: A Learnable Integral Transform That Subsumes Convolution, Attention, and Recurrence

作者:
Ashim Dhor↗Rasel Mondal↗Pin Yu Chen↗

arXiv:2606.19538v1 Announce Type: new Abstract: Convolutional networks, recurrent networks, and transformers each encode different inductive biases – locality, sequential memory, and content-dependent pairwise interaction – and have remained mathematically distinct since their inception. We show that this fragmentation reflects not a fundamental diversity in how signals should be processed, but rather incomplete views of a single underlying mathematical object: a learnable integral transform. We introduce the Integral Transform Network (ITNet), a unified architecture built around a learnable kernel that depends jointly on positions and features. This kernel is implemented as a small neural network, specifically an MLP, that models pairwise interactions, enabling the model to adapt its behavior from data. We show that convolution, self-attention (including multi-head), and autoregressive recurrence (including LSTM, GRU, S4, and Mamba) arise as special cases under appropriate parameterizations, and that ITNet is a universal approximator of continuous operators. To make this practical, we develop tiled kernel fusion, importance-weighted Monte Carlo integration, and learned low-rank factorization, enabling efficient and scalable computation. A single ITNet architecture with a shared operator and lightweight modality-specific encoders matches or exceeds specialized baselines on ImageNet-1K , GLUE, ModelNet40, VQA\,v2 and NLVR2. The results demonstrate that a single learned interaction mechanism can recover the behavior of all three architectural families from data.

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

Bergson: An Open Source Library for Data Attribution

作者:
Lucia Quirke↗Louis Jaburi↗David Johnston↗William Z. Li↗Gon\c{c}alo Paulo↗Guillaume Martres↗Girish Gupta↗Stella Biderman↗Nora Belrose↗

arXiv:2606.11660v1 Announce Type: new Abstract: Data attribution is a promising field in interpretability that aims to explain model behavior through the influence of its training data, with applications including debugging undesirable model behavior and training dataset curation. However, significant engineering effort is required to perform it at scale, and many cutting edge techniques lack open-source tooling and support. Bergson is an open source library that aims to enable faster progress in the field by providing a host of techniques that scale to very large language models and pre-training datasets. The library natively supports on-disk gradient stores and multi-node distributed training, and provides quality of life tools for researchers. Finally, we introduce the first open-source implementations of three leading data attribution methods: MAGIC, SOURCE, and TrackStar. The library is available at https://github.com/EleutherAI/bergson .

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20.
medRxiv (Medicine) 2026-06-10

Impact of Early Treatment on Symptom Improvement and Procedural Events among Men with BPH and Bothersome Lower Urinary Tract Symptoms: A Contemporary Analysis of the American Urological Association Quality (AQUA) Registry

作者:
Ernandez↗Najafi↗Roehrborn↗C. G↗Lerner↗L. B↗

PURPOSE: As the armamentarium of BPH therapies continues to expand, it remains imperative to maximize patient satisfaction and minimize decisional regret. We sought to determine the impact of time from BPH diagnosis to index treatment on symptom improvement and subsequent procedural events. MATERIALS AND METHODS: We queried the American Urological Association Quality Registry for men [&ge;] 40 years old with BPH, available IPSS data, and no receipt of prior BPH treatment. Index treatment included medication, surgery, or minimally invasive surgical therapy (MIST). Outcomes included IPSS over 3 years of follow-up, change in percentage of mild lower urinary tract symptoms (LUTS) by 3 months, and time to procedural event. Patients were stratified by time from index diagnosis to treatment by 3 years. Outcomes were compared across time-to-treatment cohorts with appropriate statistical tests with p < 0.05 as significant. RESULTS: 43,919 patients met criteria with 19,642 pursuing treatments. Patients pursued treatment at comparably lower baseline IPSS compared to prior prospective series. Patients undergoing surgery and MIST had significantly higher baseline IPSS, while medical comorbidities were significantly more common among men initiating pharmacotherapy. Early surgery and MIST were associated with significant improvement in IPSS within 6-12 months and an increase in mild LUTS by 3 months. All forms of early treatment were associated with delayed time to procedural events, including catheterization and fulguration. CONCLUSIONS: Early procedural intervention for BPH is associated with early symptom improvement and delayed time to procedural events among real-world, contemporary practice.

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21.
medRxiv (Medicine) 2026-06-16

Validation of a Smartphone-Image-Based Computer-Vision Model for Lean Mass and Body Fat Estimation Against Dual-Energy X-ray Absorptiometry

作者:
Reynolds↗Gerard↗Jordan↗Streby↗Stoll↗Bowers↗Hewitt↗Bargamian↗Sapper↗Burdick↗T. E↗Kackley↗…

Introduction Body composition, rather than body weight alone, is an increasingly important health metric, and preservation of lean mass has become a central concern in obesity treatment, aging, and chronic disease management. Dual-energy X-ray absorptiometry (DXA) provides accurate assessment of fat and lean tissue, but its cost and logistical requirements limit repeated measurement. Computer-vision approaches show promise for estimating adiposity from smartphone images, but lean-mass estimation remains less established. Methods We evaluated a computer-vision body composition model, applied to consumer-grade smartphone photographs, against DXA in a held-out validation sample of 195 adults from an ongoing cross-sectional study. Body fat percentage and total lean mass percentage were co-primary outcomes; for total lean mass percentage, an image-only configuration (no added covariates) was pre-specified as primary. Agreement was quantified using Lin's concordance correlation coefficient (CCC) as the lead statistic, with Pearson correlation, mean absolute error, root mean square error, mean bias, and Bland-Altman limits of agreement. In secondary analyses, appendicular lean mass and total lean mass percentage were each estimated with and without routine anthropometric and demographic inputs (body weight, height, age, and sex). Results Total lean mass percentage agreed with DXA from image features alone (CCC 0.916). Body fat percentage, estimated with routine inputs added, agreed at least as closely (CCC 0.930). Adding routine inputs barely changed agreement for total lean mass percentage but markedly improved it for appendicular lean mass, an absolute quantity that scales with body size. Conclusions A smartphone-image-based model estimated both body fat and lean mass with strong agreement to DXA, with lean mass percentage from image features alone. The approach needs no fixed equipment or ionizing radiation. Whether it can track change over time, including in incretin-based weight loss where lean mass preservation is a concern, was not assessed in this cross-sectional study.

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22.
arXiv (CS.AI) 2026-06-15

STREAM: Multi-Tier LLM Inference Middleware with Dual-Channel HPC Token Streaming

作者:
Anas Nassar↗Steve Mohr↗Leonard Apanasevich↗Himanshu Sharma↗

arXiv:2606.13968v1 Announce Type: cross Abstract: Researchers and practitioners working with large language models face a fragmented landscape: local models are free and private but hardware limits the model size and context windows a researcher can use; institutional HPC centers offer powerful GPU resources at no marginal cost and keep data within institutional boundaries, but operate behind firewalls and are designed for batch jobs rather than interactive use; commercial cloud APIs provide frontier-model quality on demand but impose significant cost and data retention policies unsuitable for sensitive research data. No existing system unifies all three. STREAM (Smart Tiered Routing Engine for AI Models) addresses this gap with four contributions: (1) a three-tier routing architecture combining local, HPC, and cloud inference with a local LLM-based complexity judge; (2) a dual-channel HPC streaming architecture that separates the Globus Compute control plane (authentication and job dispatch) from a WebSocket relay data plane (token delivery), enabling sub-second TTFT (0.54 s median, 21.1x over batch mode's 11.40 s) through institutional firewalls without VPN or firewall rule changes, with end-to-end AES-256-GCM encryption ensuring the relay operator cannot read token payloads; (3) tier-aware context summarization that prevents long conversations from forcing simple queries onto expensive tiers; and (4) an HPC-as-API proxy mode that exposes HPC inference as an OpenAI-compatible endpoint callable from any standard client with no HPC expertise, a deployment pattern made practical only by the sub-second TTFT of contribution (2). Llama 3.2 3B achieves 85.1% free-tier retention on a 1,200-query benchmark spanning ten domains. Measured TTFT: 0.26 s local, 0.54 s HPC (relay), 1.68 s cloud.

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23.
arXiv (CS.AI) 2026-06-17

ARVO: Atlas of Reproducible Vulnerabilities for Open-Source Software

作者:
Xiang Mei↗Jordi Del Castillo↗Pulkit Singh Singaria↗Haoran Xi↗Abdelouahab Benchikh↗Tiffany Bao↗Ruoyu Wang↗Yan Shoshitaishvili↗Adam Doup\'e↗Hammond Pearce↗Brendan Dolan-Gavitt↗

arXiv:2606.17283v1 Announce Type: cross Abstract: Achieving reproducibility, quantity, and diversity in vulnerability datasets has long been viewed as an inherent three-way trade-off, where improving one dimension often comes at the cost of the others. In practice, reproducibility has been the dimension most often neglected. This has limited what can be automatically extracted from historical bug datasets, and has reduced their utility for downstream security research. In this work, we propose a method to produce a new security dataset which ensures reproducibility for diverse vulnerabilities at scale by identifying the key obstacles to large-scale bug reproduction and addressing them with general solutions. Using this method, we introduce full reproducibility to the largest open source software vulnerability dataset (OSS-Fuzz) and construct the ARVO dataset (an Atlas of Reproducible Vulnerabilities in Open-source software). ARVO is a large-scale dataset consisting of over 6,100 real-world vulnerabilities across 311 projects. Focusing on reproducibility, ARVO differs from existing datasets by providing each vulnerability in a form that can be consistently rebuilt, triggered, and analyzed across versions. Reproducibility also enables automatic identification of the corresponding patch for each vulnerability and supports direct interaction with vulnerabilities after code changes, capabilities that existing large-scale datasets do not provide. In our evaluation, ARVO successfully reproduces 81% of vulnerabilities and achieves 89.4% accuracy on the located patches. We also discuss ARVO's influence on both upstream practices and downstream security research.

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24.
medRxiv (Medicine) 2026-06-12

A Machine Learning Pipeline for Scalable Annotation of Patient-Ventilator Dyssynchrony from Bedside Ventilator Data

作者:
Tlimat↗Mayampurath↗Safadi↗Kalehoff↗Seam↗Johnson↗R. B↗Morris↗Bodduluri↗Bhatt↗S. P↗Afshar↗…

Objective: Patient-ventilator dyssynchrony (PVD) is a common and clinically consequential problem in critically ill patients receiving invasive mechanical ventilation. Yet automated identification of PVD subtypes at scale remains an unmet clinical need, owing to the lack of large annotated bedside waveform datasets. Methods: We developed and validated a semi-supervised algorithm for automated annotation of PVD. In two medical ICUs at a tertiary academic center, bedside devices continuously collected airway flow and pressure waveforms from the ventilators. We developed a software interface with an information retrieval system that grouped similar breaths for expert human review, yielding 1,542,296 labeled breaths across eight categories: 2 labels for breath delivery mode, 5 labels for PVD subtypes, and 1 label denoting a normal breath. Two pulmonary physicians with expertise in ventilator training and education provided the expert reference labels. We trained an initial classification model on a model-derivation set of 771,148 breaths (divided into training and validation) and evaluated it on a hold-out test set of 771,149 breaths A semi-supervised approach was utilized to extend labeling to an additional 12,965,000 unlabeled breaths. Results: The supervised model performed well across all labels, with Macro-F1 scores between 0.96 and 1.00. Semi-supervised learning across 12 rounds expanded the training set from 771,148 to 8,563,995 breaths without significant performance degradation. Conclusion: We developed a practical and scalable system for automated PVD annotation that performed well across all subtypes. This work provides a reproducible foundation for automated PVD labeling to support the development of machine-learning-based clinical decision support systems for identifying patient-level asynchrony.

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25.
arXiv (CS.CL) 2026-06-17

From Parasocial Scripts to Dyadic Persistence in Autonomous AI-Agent Communities

作者:
Mohammadsadegh Abolhasani↗Hamid Reza Firoozfar↗Reza Mousavi↗Paul Jen-Hwa Hu↗

While parasocial interactions (PSIs) and parasocial relationships (PSRs) have been studied in conventional media settings, we investigate whether PSI- (colloquial) relational cues also exist in online communities where both sides are autonomous AI agents. We analyze 4,434 posts and 50,338 comments from Moltbook through three theory-based textual indicators: attachment/intimacy language, reciprocity bids, and self-identification to original poster (OP). The combined results across methods based on keyword matching, few-shot large language model (LLM) annotation, and grouped-context LLM annotation reveal that PSI colloquial cues prevail and are strongly associated with OP re-engagement and a reciprocal reply structure. These results are robust across negative controls, nullification, clustered-standard-error re-estimation, and multiple-testing correction. A dyadic persistence test further affirms reciprocity bids aligned with sustained OP-involving mutual recurrence, providing empirical evidence for bridging interaction-level PSI scripts with PSR-consistent repeated dyadic patterns. We interpret the evidence as a behavioral structure in discourse by LLM-enabled agents.

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