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01.
arXiv (CS.LG) 2026-06-19

A Unified Perspective on the Dynamics of Deep Transformers

arXiv:2501.18322v2 Announce Type: replace Abstract: Transformers, which are state-of-the-art in most machine learning tasks, represent the data as sequences of vectors called tokens. This representation is then exploited by the attention function, which learns dependencies between tokens and is key to the success of Transformers. However, the iterative application of attention across layers induces complex dynamics that remain to be fully understood. To analyze these dynamics, we identify each input sequence with a probability measure and model its evolution as a Vlasov equation called Transformer PDE, whose velocity field is non-linear in the probability measure. Our first set of contributions focuses on compactly supported initial data. We show the Transformer PDE is well-posed and is the mean-field limit of an interacting particle system, thus generalizing and extending previous analysis to several variants of self-attention: multi-head attention, L2 attention, Sinkhorn attention, Sigmoid attention, and masked attention–leveraging a conditional Wasserstein framework. In a second set of contributions, we are the first to study non-compactly supported initial conditions, by focusing on Gaussian initial data. Again for different types of attention, we show that the Transformer PDE preserves the space of Gaussian measures, which allows us to analyze the Gaussian case theoretically and numerically to identify typical behaviors. This Gaussian analysis captures the evolution of data anisotropy through a deep Transformer. In particular, we highlight a clustering phenomenon that parallels previous results in the non-normalized discrete case.

02.
bioRxiv (Bioinfo) 2026-06-24

Generative Modeling of Mouse Embryogenesis for Fate and Disease Prediction

Embryonic development is orchestrated by complex gene regulatory networks, and learning regulatory dynamics from developmental data could allow us to understand, predict, and ultimately engineer cell fates. Here we introduce Navigo (https://github.com/aristoteleo/Navigo-release), a biologically grounded generative modeling framework that learns a developmental vector field by integrating flow matching at the population level with RNA kinetics modeling at the molecular level. Navigo accurately maps developmental trajectories across lineages on a mouse embryogenesis scRNA-seq atlas spanning 43 time points and comprising 12.4 million cells. Applied to cardiac development, Navigo enables disease modeling by mechanistically resolving regulatory networks that distinguish congenital heart disease subtypes. Navigo also predicts perturbation effects in a zero-shot manner, as validated on independent in vivo data from six knockout genotypes without perturbation-specific training, uncovering lineage-specific gene-compensation mechanisms. Moreover, Navigo guides rational cell-fate engineering, exemplified by fibroblast reprogramming analyses, including identifying pro-fibrotic barriers to cardiac fates and evaluating hundreds of pairwise transcription factor combinations for neuronal fate, each consisting of one bHLH factor and one POU factor. Overall, Navigo provides a generalizable AI platform for perturbation-effect prediction, disease modeling, and rational cell-fate engineering, advancing toward AI-based virtual embryos for developmental biology and regenerative medicine.

03.
medRxiv (Medicine) 2026-06-15

An epidemiological scenario for Mass Events During the World Cup

This brief work discusses potential superspreading events that may occur during the World Cup in Mexico. The study is particularly focused on the city of Guadalajara due to a large recent outbreak in January and February and insufficient vaccine coverage prior to 2026. Keywords: Superspreading; measles outbreak; branching process; individual reproduction number; World Cup

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

Ricci-Filtration: Boosting Retrieval-Augmented Generation Reranker to Query-Answer Tasks by Discrete Ricci Flow

arXiv:2606.15482v1 Announce Type: cross Abstract: Ricci flow is a curvature-guided diffusion process that deforms space by shrinking regions of high positive curvature and expanding those with negative curvature. Similarly, discrete Ricci flow on weighted graphs modifies edge weights by shrinking edges with positive Ricci curvature and stretching those with negative Ricci curvature, effectively increasing the separation between clusters. Inspired by these two cornerstone works, we propose a geometry-based RAG reranker enhancement procedure called Ricci-Filtration. By modeling the input query and initial retrieved chunks as a network, where the input query and chunks serve as nodes and embedding-based pairwise relations define an initial graph, Ricci-Filtration leverages discrete curvature and Ricci flow to evaluate the structural importance of each chunk with respect to the user query. The system first filters the initial chunks based on their geometric curvature relative to the query; then, a reranker processes the remaining chunks to enhance generative performance. We theoretically prove that normalized discrete Ricci flow can detect community structures by identifying distinct asymptotic behaviors in edge weights. This supports the removal of ``noisy'' document chunks characterized by large weights and negative Ricci curvature relative to the query node. Extensive experiments confirm that Ricci-Filtration outperforms several baseline reranking methods in accuracy, precision, recall, and F1 scores. Furthermore, ablation studies demonstrate that the Ricci-Filtration generally outperforms the baseline under various settings, highlighting the framework's robustness across different architectures.

05.
arXiv (quant-ph) 2026-06-19

The use of Peres lattices in periodically driven systems

arXiv:2606.20009v1 Announce Type: new Abstract: We demonstrate the strength of the method of Peres lattices in periodically driven quantum systems. The method, which has previously been used mostly in stationary systems, enables us to efficiently detect resonances in the driven system, to monitor the onset of chaos, and to recognize critical properties of the Floquet modes. It also allows quick comparisons of the spectra of Floquet modes for various driving Hamiltonians and transparent tests of the iterative approximation techniques based on effective stationary Hamiltonians.

06.
bioRxiv (Bioinfo) 2026-06-19

OmniPath Metabo: chemical structures, interactions and mechanisms to study the metabolome

Mechanistic and functional analysis of omics data largely relies on the incorporation of prior knowledge; however, connecting metabolomics data and knowledge is a major methodological challenge. This is largely driven by the diverse prior knowledge being fragmented across many databases requiring the merging of different database records across chemical structures, identifiers, and varying levels of structural specificity. Hence, this limits mechanistic interpretation and functional characterisation of the metabolome. Here, we present OmniPath Metabo, a comprehensive, harmonized, metabolome-centric database covering metabolites, lipids, food-derived compounds, and small molecule drugs, along with their associated receptors, transporters, enzymes, reactions, allosteric regulators, and disease associations. OmniPath Metabo harmonizes attributes using controlled vocabularies and ontologies, structures and built-in cheminformatics to map identifiers and track ambiguity. OmniPath Metabo is built directly from 40+ original resources and is freely accessible via an interactive web app and API at metabo.omnipathdb.org. OmniPath Metabo enables dynamic, context-specific construction of subnetworks to serve dedicated purposes, such as cell-cell communication or integrated multi-omics metabolite-driven regulation, connecting reactions, allosteric regulation, metabolite-receptor and metabolite-transporter interactions. Combining it with the over 170 other resources in OmniPath, it can be used for integrated networks of signaling, gene regulation, and metabolism. We showcase the application of OmniPath Metabo by analysing publicly available metabolomics data of lung cancer cell lines and metabolic footprints to mutational patterns. In summary, OmniPath Metabo transforms fragmented resources into a harmonised prior knowledge framework for a mechanistic and functional analysis of the metabolome.

07.
medRxiv (Medicine) 2026-06-18

From Paper Letters to an Integrated Digital Workflow: Improving Efficiency, Reliability, and Engagement in Health Guidance

Background: Post-checkup health guidance in Japan has traditionally relied on paper-based communication and manual administrative processes. These workflows are time-consuming, prone to transcription errors, and can delay timely engagement with health guidance recipients. Objective: To assess whether replacing a paper-based workflow with an integrated digital system using Microsoft Access, robotic process automation (RPA), and web-based responses could improve administrative efficiency, operational reliability, and engagement among health guidance recipients. Methods: This single-site quality improvement initiative redesigned the existing letter-based workflow. Access served as a central interface for managing recipients and generating guidance letters. RPA (EzRobot) automated repetitive clerical and billing-related tasks. A web form accessed via a QR code enabled recipients to respond digitally. Outcomes included manual administrative handling time per case, occurrence of transcription-related errors, health guidance completion rate, and guidance duration distribution. Results: Following implementation, staff active handling time per case decreased from approximately 10 minutes to less than 1 minute (approximately 30 seconds), while automated RPA execution typically required about 4-5 minutes per case without staff input. No transcription-related errors were detected during the post-implementation observation period. Health guidance completion rates improved from 28.3% to 39.2% (chi-square test, P=200 days decreased from 30.5% to 20.9% and cases with >=240 days decreased from 13.6% to 8.9% (R4 n=59, R5 n=158). Conclusion: An integrated Access-RPA-Web workflow was associated with improvements in administrative efficiency and operational reliability in post-checkup health guidance while retaining human verification and exception handling. This pragmatic, non-AI-dependent approach may offer a useful model for process-level improvement in preventive care settings.

08.
arXiv (CS.CV) 2026-06-11

Findings of the MAGMaR 2026 Shared Task

This overview paper presents the results of the shared task for the second workshop on Multimodal Augmented Generation via Multimodal Retrieval (MAGMaR). In this shared task participants submitted systems focused on either (i) video retrieval or (ii) grounded generation of articles given retrieved videos. Teams could submit to either task. For the retrieval task, we had 2 participating teams that submitted a total of 17 systems – all of which beat a baseline derived from the winner of last year's shared task. On the generation side, we had 4 teams submit 16 systems. All teams had at least one generated report that was labeled the best by a human annotator.

09.
PLOS Computational Biology 2026-06-18

scMagnifier: Resolving fine-grained cell subtypes via GRN-informed perturbations and consensus clustering

作者:

by Zhenhui He, Dong Kangning Resolving fine-grained cell subtypes in single-cell RNA sequencing (scRNA-seq) data remains challenging, as their subtle transcriptional differences are often obscured by technical noise and data sparsity. Here, we present scMagnifier, a consensus clustering framework that leverages gene regulatory network (GRN)-informed in silico perturbations to amplify subtle transcriptional differences and uncover latent cell subpopulations. scMagnifier perturbs candidate transcription factors (TFs), propagates perturbation effects through cluster-specific GRNs to simulate post-perturbation expression profiles, and integrates clustering results across multiple perturbations into stable subtype assignments. Additionally, scMagnifier introduces regulatory perturbation consensus UMAP (rpcUMAP), a perturbation-aware visualization that provides clearer separation between cell subtypes and guides the selection of the optimal number of clusters. In both single-batch and multi-batch benchmarks, scMagnifier consistently improves the resolution and accuracy of fine-grained cell type identification. Notably, when integrated with spatial clustering methods such as STAGATE, scMagnifier is compatible with spatial transcriptomics workflows and effectively reveals tumor cell subtypes and their spatial organization in ovarian cancer.

10.
medRxiv (Medicine) 2026-06-15

Efficacy of Painhunting Therapy for Event-Related Depression: A Randomized Controlled Trial with Crossover Replication

Background. Depression affects an estimated 332 million people worldwide and is a leading cause of disability, with up to 80% of major depressive episodes preceded by an identifiable adverse life event [17,18]. First-line treatments target symptoms rather than the precipitating event and are resource-intensive: standard CBT averages roughly 12 sessions, and antidepressant discontinuation carries relapse rates near 35% at six months [8]. These limitations create a clear rationale for brief, structured interventions that address the cognitive and somatic sequelae of adverse life events directly. Painhunting therapy is one such intervention, in which each session targets a discrete adverse event through a structured incident-processing procedure. Methods. We conducted a two-arm, parallel-group, single-site randomised controlled trial comparing Painhunting therapy (Arm A, immediate; n=42) with a waitlist control (Arm B, delayed; n=42) in adults with PHQ-9 >= 9 and active psychological distress related to an adverse life event. After the primary endpoint at T2 (approximately two weeks post-randomisation), Arm B crossed over to active treatment, with T3 as the post-crossover endpoint at approximately four weeks. The primary outcome was PHQ-9 at T2 (between-arm contrast); secondary outcomes were ICG, GAD-7, WHO-DAS 2.0 (12-item), and the Global Impression of Change (GIC). Pre-specified analyses included intention-to-treat, per-protocol, and single-exclusion sensitivity populations. Results. Eighty-four participants were randomised (198 applications, 134 completed screening questionnaire, 119 passed psychometric screening). At T2, mean PHQ-9 was 2.32 (SD 2.59) in Arm A and 16.56 (SD 6.76) in Arm B, yielding an ITT between-arm Cohen d = 2.78 (95% CI 2.19-3.76, p < 0.001). Within-arm paired reductions during each arm's active-treatment window reproduced this magnitude (Arm A T0 to T2 change 14.71, Morris d = 2.80; Arm B T2 to T3 change 14.19, Morris d = 2.77, eligible n=26). Treatment gains were durable at the T4 follow-up (week 8). Aligning each arm to its own end-of-treatment timepoint, the off-treatment drift to week 8 was almost identical between arms: Arm A rose 0.78 points from T2 to T4 (2.19 to 2.97, n=37) and Arm B rose 1.59 points from T3 to T4 (4.74 to 6.33, n=27), the latter falling to 0.77 points once a single documented relapse case (R59) is excluded (4.81 to 5.58, n=26). This small off-treatment rebound then stabilised rather than continuing: Arm A was essentially unchanged from T3 to T4 (change +0.05), with concordant maintenance on ICG, GAD-7, and WHO-DAS. At T4, 68% of Arm A and 41% of Arm B remained in remission (PHQ-9 < 5). Secondary measures (ICG, GAD-7, WHO-DAS) moved in the same direction and to comparable magnitude at every timepoint. The waitlist window in Arm B showed essentially no change on any measure (PHQ-9 change 0.22, p = 0.81). Sensitivity analyses excluding six sub-threshold T2 cases, the single treated-in-error case (R82), the R59 relapse case, and one late T2 submitter left all conclusions unchanged. Conclusions. Painhunting therapy produced large and statistically robust reductions in depression, complicated grief, anxiety, and functional disability over a brief course of three to four sessions, with effect sizes substantially exceeding benchmarks reported for established first-line psychotherapies including CBT and EMDR. Critically, these gains persisted at the week-8 follow-up: depression scores in the immediate-treatment arm were essentially unchanged from four weeks to eight weeks post-randomisation, indicating that the benefit reflects durable change rather than a transient post-session dip. Treatment-window concordance between arms, durability of gains at one month off-treatment, and the flat waitlist trajectory together strengthen the evidence for genuine efficacy rather than spontaneous remission. Baseline covariates including therapeutic alliance, treatment expectancy, self-efficacy, age, and sex showed near-zero associations with outcome, reducing the plausibility of allegiance bias or expectancy effects as primary drivers. The differential retention between arms (88% vs 64% at T3) is attributable to the waitlist design and is discussed as a limitation. These findings support proceeding to a confirmatory active-comparator trial against manualized CBT. Trial registration: ClinicalTrials.gov NCT07490691, prospectively registered.

11.
PLOS Medicine 2026-05-11

Connected or chained by social media? Child and adolescent mental health in a digital era

作者:

by Silja Kosola Social media has evolved from connection to compulsion, disproportionately harming children and adolescents. Addictive designs together with developmental vulnerability fuel mental health risks and highlight the urgent need for stricter age limits and stronger protections. In this Perspective, Silja Kosola outlines how social media disproportionately harms child and adolescent mental health, and argues that while recent policy changes aimed at protecting youth from social media are welcome, stricter age limits and greater accountability of social media companies are needed.

12.
arXiv (CS.CL) 2026-06-24

Societal Alignment Frameworks Can Improve LLM Alignment

Recent progress in large language models (LLMs) has focused on producing responses that meet human expectations and align with shared values - a process coined alignment. However, aligning LLMs remains challenging due to the inherent disconnect between the complexity of human values and the narrow nature of the technological approaches designed to address them. Current alignment methods often lead to misspecified objectives, reflecting the broader issue of incomplete contracts, the impracticality of specifying a contract between a model developer, and the model that accounts for every scenario in LLM alignment. In this paper, we argue that improving LLM alignment requires incorporating insights from societal alignment frameworks, including social, economic, and contractual alignment, and discuss potential solutions drawn from these domains. Given the role of uncertainty within societal alignment frameworks, we then investigate how it manifests in LLM alignment. We end our discussion by offering an alternative view on LLM alignment, framing the underspecified nature of its objectives as an opportunity rather than perfect their specification. Beyond technical improvements in LLM alignment, we discuss the need for participatory alignment interface designs.

13.
arXiv (CS.LG) 2026-06-19

Judging to Improve: A De-biased VLM-as-3D-Judge Protocol for Single-Image 3D Generation

arXiv:2606.20364v1 Announce Type: new Abstract: A companion study established a de-biased, cross-model VLM-as-3D-judge that reliably ranks single-image-to-3D mesh quality where cheap geometry and CLIP proxies fall short. This paper asks: can that judge's preferences specialize a strong open generator, TRELLIS, on one asset class (furniture), cheaply and without human labels? Taking the judge from ranking to optimization is where the work lives. Pushing a VLM judge into the training and evaluation loop exposes failure modes ranking never triggered, so our contribution is an optimization-grade hardening of the judge: a training judge (Qwen2.5-VL-7B) held distinct from an evaluation judge (InternVL3-8B) to break circularity; position-bias correction; and fixes for three failure modes (image overload, geometry-hiding splat renders, and reference-free judging that rewards clean-but-wrong outputs), with calibration evidence (clear-gap win-rate 0.83-1.0; base-vs-base ~0.5). Using this protocol as an independent evaluator, and working only from public models and data with lightweight parameter-efficient adaptation, we find our methods match the strong base rather than exceed it. Independent base samples carry essentially no learnable preference (0.94 order-flip rate), so signal must be engineered by quality-contrastive construction. Across six adaptation methods, two input regimes, and a severity sweep, the most targeted - conditioner repair under severe degradation - reaches parity (0.50) with the base, while no method clears the >=65% win-rate target. The result is mechanistic: clean inputs saturate the judge, flow-DIT fine-tuning washes out through the sampler, and conditioning repair is the locus that moves geometry. Win-rates are directional at n=8 objects. Matching a strong public-data base with cheap adaptation is itself informative: exceeding it needs more than lightweight PEFT on public data, and the judge protocol is reusable.

14.
arXiv (math.PR) 2026-06-24

Autoregressive Processes on Riemannian Manifolds

arXiv:2606.24771v1 Announce Type: cross Abstract: This paper introduces a Riemannian autoregressive (R-AR) model of order one, generalising classical discrete-time stochastic processes to manifold-valued data. The model is based on two parameters, a parameter $\mu$ representing the intrinsic central tendency as the Fréchet mean and an autoregressive parameter $\phi$ controlling the stationarity and ergodic properties. Due to the inherent dependence structure of the R-AR process, the estimation procedure for these parameters necessitates new asymptotic results for dependent processes on manifolds. Thus, we establish a strong law of large numbers for the sample Fréchet mean set of ergodic Markov chains in proper metric spaces. By proving this general consistency result, we move beyond the limitations of classical i.i.d. theory to provide the mathematical foundation required for the strong consistency of our proposed estimators. The framework is validated through numerical simulations in the hyperbolic plane and an application to aerosol size distributions on the Fisher-Rao manifold, demonstrating how the proposed model can characterise mean-reverting dynamics in nonlinear geometries.

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

Reasoning in Computer Vision: Taxonomy, Models, Tasks, and Methodologies

Visual reasoning matters for many computer vision tasks that go beyond surface-level object detection and classification. Despite progress in relational, symbolic, temporal, causal, and commonsense reasoning, existing surveys typically cover only one part of the problem, such as visual question answering, scene-graph generation, neuro-symbolic AI, or multimodal chain-of-thought, and rarely analyze reasoning types, methodologies, and evaluation protocols together. This survey addresses that gap. Following a structured literature review, we group visual reasoning into five major types (relational, symbolic, temporal, causal, and commonsense) and examine how each is implemented across methods that range from graph-based models, memory networks, attention mechanisms, and neuro-symbolic systems to reasoning with vision-language models (VLMs) and multimodal large language models (MLLMs), including visual chain-of-thought, visual programming, and tool-augmented and test-time reasoning. We then review evaluation protocols for functional correctness, structural consistency, and causal validity, and we analyze their limits in generalizability, reproducibility, faithfulness, and explanatory power. We also identify open challenges: scaling to complex scenes, integrating symbolic and neural paradigms more deeply, the shortage of comprehensive benchmarks, language-prior shortcuts and hallucination in foundation models, and reasoning under weak supervision. Finally, we set out a research agenda for vision systems and argue that connecting perception and reasoning is necessary for transparent, trustworthy, and cross-domain models, especially in high-stakes settings such as autonomous driving and medical diagnostics.

17.
Nature Medicine 2026-06-12

General-purpose large language models outperform specialized clinical AI tools on medical benchmarks

Specialized clinical artificial intelligence (AI) tools are entering medical practice despite scarce independent evaluation. We quantitatively evaluate two clinical AI tools, OpenEvidence and UpToDate Expert AI, built on large language models (LLMs) against three frontier LLMs: GPT-5.2, Gemini 3.1 Pro and Claude Opus 4.6. Our evaluation has three stages: (1) 500 MedQA questions testing medical knowledge, (2) 500 HealthBench items measuring alignment with clinicians and (3) the real clinical queries (RCQ) benchmark, built from 100 de-identified queries from physicians to a general-purpose language model in a live clinical environment. For the RCQ benchmark, 12 US clinicians performed randomized, blinded review of model outputs, producing 1,800 model–question annotations. Frontier LLMs outperformed clinical AI tools in all three evaluations. Clinical AI tools performed comparably to auto-enabled Google Search AI Overview on the RCQ. These findings highlight the need for independent, real-world evaluation of AI tools before they enter clinical settings. In an independent evaluation, frontier large language models outperformed specialized clinical artificial intelligence tools on medical knowledge, clinician alignment and real-world clinical queries.

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

Insulin4RL: Real-Time Insulin Management in the Intensive Care Unit for Offline Reinforcement Learning

arXiv:2606.19481v1 Announce Type: new Abstract: Offline reinforcement learning (ORL) offers the potential to improve the quality of clinical decision-making using historical electronic health record (EHR) data. Current training and evaluative practices in this field rely heavily on EHR datasets that have been temporally discretised into fixed, regular time intervals. Discretisation creates fictional representations of complex clinical scenarios and compromises the generalisability of retrospective model evaluations. In this paper, we introduce Insulin4RL, a healthcare ORL dataset featuring naturally irregular inputs and actions from real clinical trajectories. Derived from MIMIC-IV, Insulin4RL comprises over 375,000 labelled decisions across 12,209 patients requiring insulin infusion titration in the Intensive Care Unit. The dataset can thus be used for research into ORL model performance under realistic clinical sampling assumptions. We provide a description of the dataset's structure and characteristics, baseline performance metrics using model-free offline reinforcement learning, and a standardised evaluation protocol using fitted Q-evaluation. We conclude with suggested areas for future research that could be addressed using this resource.

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

The Perceived Fragility of Explanations in Audio Models: Manipulation of Attribution with Unchanged Predictions

arXiv:2606.14466v1 Announce Type: cross Abstract: This paper investigates the fragility of post-hoc explanation methods in audio deepfake detection. While previous work on explanation manipulation focused on images using standard $L_p$ metrics, we introduce a psychoacoustic framework that optimizes inaudible perturbations to decouple model attributions from final classifications. We evaluate this vulnerability across state-of-the-art architectures under strict prediction-preserving constraints. By evaluating the manipulation cost through domain-specific perceptual audio quality metrics alongside explanation alignment criteria, our framework demonstrates that an adversary can systematically distort automated explanation heatmaps while preserving the predicted deepfake label. Full code available at: https://github.com/cncPomper/Audio-XAI

20.
arXiv (CS.CV) 2026-06-16

Learning Topology-Aware Implicit Field for Unified Pulmonary Tree Modeling with Incomplete Topological Supervision

Pulmonary trees extracted from CT images frequently exhibit topological incompleteness, such as missing or disconnected branches, which substantially degrades downstream anatomical analysis and limits the applicability of existing pulmonary tree modeling pipelines. Current approaches typically rely on dense volumetric processing, explicit graph reasoning, or generic point cloud completion priors, leading to limited efficiency, weak structural awareness, and reduced robustness under realistic structural corruption. We propose TopoField, a topology-aware implicit modeling framework that treats topology repair as a first-class modeling problem and enables unified multi-task inference for pulmonary tree analysis. TopoField represents pulmonary anatomy using sparse surface and skeleton point clouds and learns a continuous implicit field that supports topology repair without relying on complete or explicit disconnection annotations, by training on synthetically introduced structural disruptions over already incomplete trees. Building upon the repaired implicit representation, anatomical labeling and lung segment reconstruction are jointly inferred through task-specific implicit functions within a single forward pass. Extensive experiments on the Lung3D+ dataset demonstrate that TopoField consistently improves topological completeness and achieves accurate anatomical labeling and lung segment reconstruction under challenging incomplete scenarios. We further validate TopoField on real incomplete outputs from an external segmentation model, demonstrating its applicability to realistic segmentation pipelines. Owing to its implicit formulation, TopoField attains high computational efficiency, completing all tasks in just over one second per case, highlighting its practicality for large-scale and time-sensitive clinical applications.

21.
medRxiv (Medicine) 2026-06-18

Urinary Creatine Riboside Complements PSA to Improve Disease Detection in the Diagnostic Gray Zone of Prostate Cancer

Circulating prostate-specific antigen (PSA) discriminates poorly in the diagnostic gray zone (3.0-9.99 ng/mL), where ~75% of biopsies yield no clinically significant prostate cancer (PCa). We evaluated whether urinary creatine riboside (CR), a tumor-derived metabolite excreted through the prostatic urethra, complements PSA for gray-zone detection and independently predicts prostate-cancer-specific mortality (PCSM). In the NCI-Maryland PCa Case-Control Study (951 cases, 962 controls; 47.6% African American men; median follow-up 11.5 years), urinary CR was quantified by UPLC-MS/MS. Within the PSA gray zone (n = 668), urinary CR was complementary to PSA, with markedly higher single-marker discrimination than PSA (AUC 0.93, 95% CI 0.88-0.98 vs 0.77, 0.66-0.89) and additive when combined ({Delta}AUC +0.17, p < 0.001; 91.4% sensitivity at 80% specificity). After adjustment for 11 clinical and sociodemographic covariates, urinary CR independently predicted PCSM complementary to PSA (Fine-Gray SHR 1.72, 1.35-2.19 for CR; 1.35, 1.08-1.68 for PSA; Harrell's C 0.85 for CR + PSA vs 0.77 for PSA alone), with strongest signal in African American men (SHR 2.43, 1.57-3.75 for CR). We conclude that urinary CR is a candidate non-invasive biomarker complementary to PSA - improving gray-zone triage and predicting PCSM; prospective validation in biopsy-referred cohorts is warranted.

22.
arXiv (math.PR) 2026-06-18

A random recursive tree model with doubling events

arXiv:2501.18466v3 Announce Type: replace Abstract: We introduce a new model of random tree that grows like a random recursive tree, except at some exceptional "doubling events" when the tree is replaced by two copies of itself attached to a new root. We prove asymptotic results for the size of this tree at large times, its degree distribution, and its height profile. We also prove a lower bound for its height. Because of the doubling events that affect the tree globally, the proofs are all much more intricate than in the case of the random recursive tree in which the growing operation is always local.

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

Learning Survival Models with Right-Censored Reporting Delays

arXiv:2510.04421v3 Announce Type: replace-cross Abstract: Survival analysis provides statistical methods to model the time until an event occurs. Reporting delays arise when event times are not observed at their occurrence but are only revealed upon reporting. This issue is particularly critical for timely risk evaluation when the observation window is short due to administrative censoring. In this study, we incorporate right-censored reporting delays by jointly modeling parametric hazards for the event and reporting processes. We then construct a consistent estimator for the model parameters and develop a Monte Carlo expectation-maximization algorithm to compute it. To address the challenges posed by administrative censoring, we leverage these findings and propose a transfer-learning procedure. Experimental results demonstrate that our method improves the accuracy of timely risk evaluation under administrative censoring.

24.
medRxiv (Medicine) 2026-06-12

Design, Implementation, and Evaluation of a Shadowing Program for Medical Students in the Basic Sciences Phase

Introduction Shadowing, as an educational method based on active observation, can foster a realistic understanding of professional roles and enhance the communication skills of medical students. This study aimed to design, implement, and evaluate a shadowing program for basic sciences medical students. Methods This development study was conducted based on the ADDIE model in five phases. The study population consisted of 799 medical students in semesters 2 to 5. The stages included Analysis (determining needs through literature review and expert panels), Design (specifying learning environments and evaluation methods), Development (preparing guides and educational tools), Implementation (within the Medical Ethics course), and Evaluation (using questionnaires and reflection forms). Findings This study aimed to design and evaluate an educational shadowing program based on the ADDIE model. In the Analysis phase, the profiles of 799 students and learning objectives were determined. In the Design phase, a structured program for four types of shadowing was designed. In the Development phase, all guides and educational tools were prepared. In the Implementation phase, the program was carried out with complete coverage and adherence to ethical considerations. Finally, the program evaluation showed that "Motivation to become a good physician" (3.75-3.95) and "Enhancing empathy" (3.50-3.94) received the highest scores, while "Increasing understanding of the basic science-clinical connection" (2.53-2.89) and "Willingness to attend on holidays" (1.87-2.31) received the lowest scores. Conclusion The findings indicate that implementing the shadowing program is an effective method for strengthening the professional attitudes and academic motivation of medical students. However, the program did not significantly improve students perception of the basic science-clinical connection, indicating a need for curricular refinement. The continuation and extension of this program to other levels and fields of medical sciences are recommended.

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

Post-Hoc Merging is Not Enough: Many-Shot Model Merging with Loss-Gap Balancing

arXiv:2606.16501v1 Announce Type: new Abstract: Model merging has become a practical post-training strategy for building a single multi-task large language model (LLM) by combining multiple task-specialized models. However, most existing approaches rely on post-hoc merging, in which task-specific models are merged only once after training. This one-shot aggregation often suffers from task interference, leading to information erasure across individual tasks. In this work, we show that replacing post-hoc merging with an iterative many-shot merging protocol is effective in improving multi-task performance. Building on this insight, we propose METIS, Mitigating Erasure from Task Interference for Stable many-shot merging. METIS is a loss-aware many-shot merging method that addresses information erasure in post-hoc merging through task-wise loss-gap weighting and consensus-based masking. Notably, METIS exhibits significant performance improvement on the worst-performing task, effectively mitigating information erasure. (Project page: https://imkyungjin.github.io/METIS/)