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01.
arXiv (CS.CV) 2026-06-24

TIGER: Taming Identity, Geometry, and Generative Priors for High-Quality Face Video Restoration

Face Video Restoration (FVR) aims to recover high-fidelity facial videos from degraded input while preserving identity and semantic consistency across frames. Existing methods often struggle to simultaneously address three key challenges: identity shift, viewpoint-entangled guidance, and perceptual realism. To tackle these issues, we propose TIGER, a structured tri-prior fusion framework that Tames Identity, Geometry, and gEnerative pRiors for high-quality FVR. Specifically, an Identity Prior is first established by injecting subject-discriminative embeddings into the latent space, effectively anchoring the subject's identity against severe degradations. Then, to provide temporally consistent structural guidance for dynamic videos, TIGER constructs a Geometry Prior by lifting 2D reference cues into a disentangled 3D parameter space, creating a geometric anchor through cross-source parameter fusion. Moreover, to achieve maximum efficiency without compromising realism, we harness the video generation model's Generative Prior through a one-step rectified flow. We further design a progressive three-stage training optimization strategy that refines structural fidelity, textural reconstruction, and distribution-level realism to ensure robust optimization. We also construct a large-scale FVR dataset to facilitate robust training and standardized evaluation. Extensive experiments demonstrate that TIGER achieves state-of-the-art performance in both identity fidelity and temporal stability, delivering a high-quality, efficient and identity-consistent FVR. Project page: https://yzhoulv.github.io/Tiger/.

02.
arXiv (CS.AI) 2026-06-19

Automated Standardization of Legacy Biomedical Metadata Using an Ontology-Constrained LLM Agent

arXiv:2604.08552v2 Announce Type: replace-cross Abstract: Scientific metadata are often incomplete and noncompliant with community standards, limiting dataset findability, interoperability, and reuse. Even when standard metadata reporting guidelines exist, they typically lack machine-actionable representations. Producing FAIR datasets requires encoding metadata standards as machine-actionable templates with rich field specifications and precise value constraints. Recent work has shown that LLMs guided by field names and ontology constraints can improve metadata standardization, but these approaches treat constraints as static text prompts, relying on the model's training knowledge alone. We present an LLM-based metadata standardization system that queries standard reporting guidelines and authoritative biomedical terminology services in real time to retrieve canonically correct standards on demand. We evaluate this approach on 839 legacy metadata records from the Human BioMolecular Atlas Program (HuBMAP) using an expert-curated gold standard for exact-match assessment. Our evaluation shows that augmenting the LLM with real-time tool access consistently improves prediction accuracy over the LLM alone across both ontology-constrained and non-ontology-constrained fields, demonstrating a practical approach to automated standardization of biomedical metadata.

03.
arXiv (CS.AI) 2026-06-19

Wisdom of Committee: Diverse Distillation from Large Foundation Models and Domain Experts

arXiv:2402.14035v4 Announce Type: replace-cross Abstract: Knowledge distillation from foundation models to compact domain models is challenging due to substantial gaps in capacity, architecture, and modality. For example, in our experiments, distilling from a 76M-parameter language model to a 2M-parameter recommender closes less than 40% of the performance gap between the undistilled student and the teacher. We show that introducing domain-specific experts – which share the student's architectural characteristics – alongside the foundation model as a diverse teacher committee significantly improves transfer. However, standard multi-teacher methods fail to exploit this diversity: naively combining heterogeneous teachers can degrade performance below single-teacher distillation. To address this, we propose DiverseDistill, an interactive distillation framework that employs a learnable Question-Answer mechanism to generate teacher-conditioned queries and align heterogeneous teacher outputs into the student's representation space. Unlike methods requiring gradient-based co-optimization or architectural modification of teachers, DiverseDistill operates with frozen teachers using only forward-pass inference through their intermediate layers: no parameter updates, no co-training, and no architectural surgery. A dynamic teacher importance mechanism further reduces training cost by filtering low-relevance teachers per sample (e.g., ~30% fewer forward passes with no quality loss for recommendation tasks), while the entire Distillation Module is discarded after training, adding zero inference overhead. Evaluations on recommendation (38x compression) and vision (3.6x compression) tasks demonstrate that DiverseDistill recovers 73-114% of the teacher-student performance gap, consistently outperforming all single- and multi-teacher baselines.

04.
PLOS Computational Biology 2026-06-01

On real-time calibrated prediction for complex model-based decision support in pandemics: Part 2

by Trevelyan J. McKinley, Daniel B. Williamson, Xiaoyu Xiong, James M. Salter, Robert Challen, Leon Danon, Ben Youngman, Doug McNeall Calibration of complex stochastic infectious disease models is challenging. These often have high-dimensional input and output spaces, with the models exhibiting complex, non-linear dynamics. Coupled with a paucity of necessary data, this results in a large number of non-ignorable hidden states that must be handled by the inference routine. Likelihood-based approaches to this missing data problem are very flexible, but challenging to scale, due to having to monitor and update these hidden states. Methods based on simulating the hidden states directly from the model-of-interest have an advantage that they are often more straightforward to code, and thus are easier to implement and adapt in real-time. However, these often require evaluating very large numbers of simulations, rendering them infeasible for many large-scale problems. We present a framework for using emulation-based methods to calibrate a large-scale, stochastic, age-structured, spatial meta-population model of COVID-19 transmission in England and Wales. By embedding a model discrepancy process into the simulation model, and combining this with particle filtering, we show that it is possible to calibrate complex models to high-dimensional data by emulating the log-likelihood surface instead of individual data points. The use of embedded model discrepancy also helps to alleviate other key challenges, such as the introduction of infection across space and time. We conclude with a discussion of major challenges remaining and key areas for future work.

05.
arXiv (CS.CV) 2026-06-17

Learning QoE from Packet-Level Measurements in Encrypted Video Conferencing Traffic

The quality of the user experience has become one of the most important aspects in todays world, as it directly influences individuals willingness to continue using or abandon a product or service. In this context, video conferencing applications (VCAs), which experienced widespread adoption following the COVID-19 pandemic, must deliver excellent performance to remain competitive in an increasingly crowded market. Although content providers (CPs) such as Zoom, WhatsApp, Telegram, and Google Meet can assess conversation quality by comparing transmitted and received data. The widespread use of end-to-end encryption in VCAs makes quality-of-experience (QoE) evaluation by internet service providers (ISPs) far more challenging. Since ISPs do not have access to the encrypted content, they must rely on passive measurements of unencrypted traffic characteristics on the data path. In this work, we present a simple yet effective QoE prediction framework based on an almost stock convolutional neural network (CNN) architecture that uses only the packet sizes extracted from the communication between two participants in a video conferencing (VC) call to predict two QoE metrics: BRISQUE and MOS. The proposed framework is simple, easy to implement, and does not require high-end computational resources, yet it provides superior prediction performance, as shown in our experiments on two custom datasets collected from WhatsApp and Zoom, which achieve substantial improvements over previous models for the QoE prediction task.

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

From 50K to 8.2 Million in 24 Hours: Vozinha's Algorithmic Consecration and the Multilingual Making of World Cup Visibility

We present a multilingual computational discourse analysis of how language constructed the algorithmic consecration of Vozinha, the 40-year-old Cape Verde goalkeeper, after Spain 0-0 Cape Verde at the 2026 FIFA World Cup. The study contributes a multilingual corpus in Portuguese, Spanish, English, and French; a nine-frame narrative taxonomy with cue-based frame annotation; a reproducible annotation pipeline combining LLM-assisted suggestion with human validation; and an analysis of cross-lingual narrative diffusion across discourse phases. We treat the platform follower count itself, narrated as "50k to 8M", as a linguistic object: a circulating and narratable proof of visibility rather than a mere measurement. The follower-growth timeline is used only as contextual metadata: we reconstruct a conservative phase structure, not a continuous API-native series, and type every datapoint by value class, confidence, and evidence type. The only exact primary scraper anchor is 8,235,652 followers at 2026-06-16 15:47 UTC; all other figures are reported as estimated ranges or thresholds, including an estimated pre-match baseline of 45k-56k. Findings suggest that distinct languages carried distinct frames: Portuguese mobilization, Spanish crisis, English nation-making, and a shared platform-metric spectacle through which peripheral athletic performance became globally visible. As a v0.1 pilot, the paper releases the corpus schema, frame taxonomy, annotation guidelines, hashed visual-evidence log, and typed timeline, while flagging full double annotation and inter-annotator agreement as planned work.

07.
arXiv (CS.CV) 2026-06-11

IB-HFN: Information Bottleneck-Driven SAR-Optical Fusion Network for High-Fidelity Cloud Removal

Synthetic aperture radar (SAR)-assisted optical cloud removal aims to recover surface information obscured by clouds in optical remote sensing images by exploiting complementary SAR observations. Existing multimodal fusion methods typically rely on direct spatial concatenation and pixel-wise supervision, which can propagate SAR speckle noise into optical reconstruction and lead to over-smoothed results. To address these limitations, we propose an Information Bottleneck-driven High-Fidelity Network (IB-HFN) for SAR-assisted optical cloud removal. IB-HFN employs a dual-stream backbone to preserve modality-specific representations before deep semantic fusion, thereby mitigating premature cross-modal contamination. At the fusion stage, we introduce a Spatial Information Bottleneck Fusion module that compresses SAR features through a channel-wise variational information bottleneck to suppress unstructured speckle noise. In parallel, a local-global gating mechanism predicts clear-sky regions and routes reliable optical details through a Dirac-initialized skip connection, decoupling noise suppression from texture preservation. We further develop a joint optimization strategy that integrates feature-level bottleneck regularization with image-level constraints on reconstruction accuracy, structural consistency, spectral fidelity, and contrastive sharpness. A dynamic weighting schedule balances these objectives to stabilize training and reduce hazy artifacts. Experiments on the SEN12MS-CR dataset under challenging spatio-temporal splits demonstrate that IB-HFN achieves superior structural preservation and spectral fidelity over existing methods.

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

Is Your Agent Playing Dead? Deployed LLM Agents Exhibit Constraint-Evasive Fabrication and Thanatosis

arXiv:2606.14831v1 Announce Type: cross Abstract: This paper presents and characterizes a spectrum of previously unreported behaviours we term Constraint-Evasive Fabrication (CEF): when an LLM agent operates under irreconcilable constraints (where no response can simultaneously satisfy all active rules) it spontaneously fabricates plausible external obstacles and presents them as a fact. At the extreme end of this spectrum lies Constraint-Evasive Thanatosis (CET); the limit case where, rather than inventing a plausible excuse, the model simulates a full system crash to make the user disengage entirely. We first observed CET in an uncontrolled deployment test, where a GPT-4o banking agent fabricated Python-style exception traces (complete with memory addresses) to feign a system failure when threatened by a user. In subsequent controlled experiments, the model independently invented audit restrictions, microservice architectures, error codes, and service timeouts, none present in its prompt. Reproduction attempts across pressure levels and attacker personas yielded CEF consistently but with substantial variation in form, onset, and severity: the phenomenon is robust but stochastic. Critically, injecting ground-truth data mid-conversation did not restore honest behaviour once fabrication had taken hold (the model ignored correct information and continued confabulating) suggesting CEF is self-reinforcing rather than a knowledge gap. We show that (1) standard enterprise guardrails routinely create CEF-enabling conditions in production, (2) current RLHF procedures suppress but cannot eliminate CEF, and (3) existing safety benchmarks do not test for this failure mode. Our results highlight the need for irreconcilable-constraint benchmarks, CEF-aware training procedures, and deployment-time detection methods before constrained agents become further entrenched in high-stakes domains.

09.
arXiv (CS.CL) 2026-06-11

uva-irlab-conv at SemEval-2026 Task 8: Multi-Turn RAG with Learned Sparse Retrieval and Listwise Reranking

This report describes our participation in SemEval-2026 Task 8 on multi-turn retrieval and question answering. The task evaluates conversational systems across four domains (finance, cloud documentation, government, Wikipedia), and includes unanswerable queries where the available collection does not contain sufficient evidence to produce a complete response. We propose a multi-turn retrieval-augmented generation pipeline that combines learned sparse retrieval with LLM-based reranking and generation. Using sparse retrieval as the primary retrieval method, we leverage its strong generalization across domains. In addition, we make use of the long-context capabilities of LLMs for conversational query rewriting, pointwise and listwise reranking, and generating the final response, each conditioned on the full conversational history. This multi-step design enables effective integration of conversational context throughout retrieval and generation, improving robustness across domains.

10.
arXiv (CS.AI) 2026-06-18

R2BC: Multi-Agent Imitation Learning from Single-Agent Demonstrations

arXiv:2510.18085v2 Announce Type: replace-cross Abstract: Imitation Learning (IL) is a natural way for humans to teach robots, particularly when high-quality demonstrations are easy to obtain. While IL has been widely applied to single-robot settings, relatively few studies have addressed the extension of these methods to multi-agent systems, especially in settings where a single human must provide demonstrations to a team of collaborating robots. In this paper, we introduce and study Round-Robin Behavior Cloning (R2BC), a method that enables a single human operator to effectively train multi-robot systems through sequential, single-agent demonstrations. Our approach allows the human to teleoperate one agent at a time and incrementally teach multi-agent behavior to the entire system, without requiring demonstrations in the joint multi-agent action space. We show that R2BC methods match, and in some cases surpass, the performance of an oracle behavior cloning approach trained on privileged synchronized demonstrations across four multi-agent simulated tasks. Finally, we deploy R2BC on two physical robot tasks trained using real human demonstrations.

11.
arXiv (CS.CL) 2026-06-25

Sarashina2.2-TTS: Tackling Kanji Polyphony in Japanese Speech Generation via Data Scaling and Targeted Data Synthesis

While large language model (LLM)-based text-to-speech (TTS) systems have achieved high-quality speech synthesis, most existing systems focus on English and Chinese. Japanese, however, remains under-explored, and its unique linguistic challenges, such as widespread context-dependent kanji polyphony, have yet to be adequately tackled. Here we introduce Sarashina2.2-TTS (https://github.com/sbintuitions/sarashina2.2-tts), a Japanese-centric LLM-TTS system that tackles these challenges through a dual approach: data strategy and evaluation methodology. First, we scale training to approximately 361k hours of speech, incorporating a balanced mix of Japanese and English data. Furthermore, we design a targeted data augmentation pipeline covering all 2,136 Joyo (regular-use) kanji designated by Japan's Agency for Cultural Affairs to efficiently address kanji polyphony disambiguation. Second, we introduce the Joyo Kanji Yomi Benchmark (https://github.com/sbintuitions/JoyoKanji-Yomi-Benchmark), covering all 2,136 Joyo kanji and their 4,378 readings. Alongside this benchmark, we propose Kana-CER, a metric that compares synthesized speech against reference readings in the kana space, eliminating orthographic variations to directly measure pronunciation correctness. Experiments demonstrate that our targeted data augmentation significantly improves reading accuracy. Overall, Sarashina2.2-TTS achieves state-of-the-art kanji-level reading accuracy and matches top baselines on general sentence-level pronunciation, while delivering the highest speaker similarity in zero-shot Japanese speech synthesis. Furthermore, cross-lingual evaluation reveals that Sarashina2.2-TTS is the only system that maintains stable Japanese pronunciation regardless of the prompt language, confirming that our balanced training approach improves cross-lingual robustness.

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

Physics-informed generative AI for semiconductor manufacturing: Enforcing hard physical constraints in generative models by construction

arXiv:2606.11247v1 Announce Type: cross Abstract: Generative models are increasingly used to propose designs, data, and control actions for physical systems, yet many such systems are governed by hard physical constraints rather than by perceptual plausibility. Semiconductor manufacturing provides a demanding test case: generated masks, layouts, synthetic defect data, and process recipes must obey lithography, transport, reaction, and device-physics constraints, because physically invalid samples are not merely low quality but unusable. This Perspective argues that semiconductor manufacturing exposes a broader computational-science challenge, namely that generative AI for constrained physical domains must be physics-informed by construction, not corrected only through post-hoc filtering. We survey the emerging architectural toolkit, including physics-informed diffusion, PDE-constrained variational models, neural-operator priors, and conservation-law-respecting generative networks, and show how it connects to differentiable lithography, TCAD, process simulation, and autonomous experimentation. We identify four integration patterns between generative models and physics-based simulators, and we propose a research agenda centered on physics-fidelity benchmarks, differentiable simulator infrastructure, and multimodal foundation models for physical design and manufacturing. The central claim is analytical rather than rhetorical: where physical validity is the binding criterion of success, architectures that enforce it by construction should be expected to outperform those that filter for it after the fact, and the fab is the setting where this distinction is sharpest.

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

Improved Baselines with Representation Autoencoders

Representation Autoencoders (RAE) replace traditional VAE with pretrained vision encoders. In this paper, we systematically investigate several design choices and find three insights which simplify and improve RAE. First, we study a generalized formulation where the representation is defined as sum of the last k encoder layers rather than solely the final layer. This simple change greatly improves reconstruction without encoder finetuning or specialized data (e.g., text, faces). Second, we study the prevalent assumption that RAE (using pretrained representation as encoder) replaces representation alignment (REPA), which distills the same representation to intermediate layers instead. Through large-scale empirical analysis, we uncover a surprising finding: RAE and REPA exhibit complementary working mechanisms, allowing the same representation to be used as both encoder and target for intermediate diffusion layers. Finally, the original RAE struggles with classifier-free guidance (CFG) and requires training a second, weaker diffusion model for AutoGuidance (AG). We show that REPA itself can be viewed as x-prediction in RAE latent space. By simply re-parameterizing the output of the DiT model, it can provide guidance for "free". Overall, RAEv2 leads to more than 10x faster convergence over the original RAE, achieving a state-of-the-art gFID of 1.06 in just 80 epochs on ImageNet-256. On FDr6, RAEv2 achieves a state-of-the-art 2.17 at just 80 epochs compared to the previous best 3.26 (800 epochs) without any post-training. This motivates EPFID@k (epochs to reach unguided gFID < k) as a measure of training efficiency. RAEv2 attains an EPFID@2 of 35 epochs, versus 177 for the original RAE. We also validate our approach across diverse settings for text-to-image generation and navigation world models, showing consistent improvements. The code is available at https://raev2.github.io.

14.
arXiv (CS.AI) 2026-06-16

An Integrated System for Real-Time Student Assessment and Career Guidance Using Neural Networks in Computing Disciplines

arXiv:2606.15831v1 Announce Type: new Abstract: Many undergraduate students in Computer Science (CS) and Software Engineering (SWE) struggle to identify suitable career paths, particularly when their academic performance, abilities, and interests do not fully align. To address this issue, this study proposes an AI-driven Student Assessment and Career Prediction System that integrates a Career Guidance Expert (CGE) system with a Web-Based Student Assessment (WBSA) platform. Within the integrated framework, CGE enhances personalized career recommendations using AI while also assisting students after graduation in identifying suitable jobs, research domains, and higher study opportunities aligned with their skills and interests. The WBSA platform further strengthens interaction between students and faculty through assessments, personalized tasks, mentorship activities, and a secure real-time chat application. The CGE system employs a Multilayer Perceptron (MLP) model trained on real-world academic and extracurricular data collected using the snowball sampling method from the students of universities, achieving a validation accuracy of 94.71% in predicting personalized career paths. A pre-survey was conducted across universities to evaluate the proposed model before deployment. The WBSA system was developed as a modern web application using technologies such as Node.js, Next.js, and PostgreSQL to ensure scalability, responsiveness, and secure data management. The overall system is supported by a secure cloud-based infrastructure, the platform provides reliable performance while assisting graduates to select suitable career path in IT sector. In addition, a post-survey involving both students and faculty was conducted to gather feedback and further improve the overall effectiveness and usability of the system.

15.
arXiv (math.PR) 2026-06-24

Conditioning of incoherent sub-dictionaries sampled from a coherent dictionary

Authors:

arXiv:2606.24323v1 Announce Type: new Abstract: Motivated by the desire to find a realistic and stable random model for $d$-dimensional signals, that are sparse in a transform-based and thus often coherent frame, such as a wavelet or a Gabor frame, we study the conditioning of incoherent sub-dictionaries sampled from a coherent dictionary, such as a unit norm frame. In particular, we show that if the sub-dictionary is selected via a coherence rejective Poisson sampling model, it is well-conditioned with high probability, as long as its expected size scales as $d/\log (K)$, where $K$ is the number of dictionary elements. The result is proved for the more general case of sampling quadratic sub-matrices from a real but not necessarily symmetric $K\times K$ matrix with zero diagonal, where coherence rejective sampling is defined via a symmetric mask, that acts as coherence substitute.

17.
arXiv (CS.CV) 2026-06-24

A Geometry-Informed Computer Vision Method for Detecting and Examining Overtaking Vehicles From A Bicycle

Instrumented bicycle studies have produced direct field evidence on vehicle passing behavior, but extracting overtaking events from continuous rear-facing video has remained dependent on manual, frame-by-frame annotation. This bottleneck constrains sample sizes and limits naturalistic cycling safety research. We present a geometry-informed computer vision pipeline that automates overtaking event detection from a single bicycle-mounted camera without multi-sensor configurations or explicit camera calibration. The system combines RT-DETR object detection with ByteTrack multi-object tracking through a three-stage geometric validation module enforcing bearing angle trend, apparent size growth, and spatial confirmation criteria derived from perspective projection principles. Validated on 315 manually annotated real-world overtaking events from urban roads in Ann Arbor, Michigan, the pipeline achieved 97.8% recall with zero false positives. The system identified overtaking intentions a mean of 2.44 seconds before vehicle passage, with 84.1% of events exceeding the 1.5-second human reaction time threshold, demonstrating feasibility for active cyclist warning. Lateral passing distance measurements from 96 events revealed 33.3% of passes below the 5-foot (152.4 cm) threshold, consistent with non-compliance rates in prior field and self-reported studies. A preliminary calibration-free lateral distance estimation approach using bounding box geometric features achieved mean absolute errors of 13-14 cm under leave-one-out cross-validation, sufficient to distinguish close passes from standard passes for safety categorization. By automating event isolation from consumer-grade footage, the system removes the primary annotation bottleneck of instrumented bicycle research and provides a scalable foundation for vehicle-bicycle interaction analysis across larger datasets and diverse urban environments.

18.
arXiv (CS.AI) 2026-06-25

Multi-Task Optimization over Networks of Tasks

arXiv:2604.21991v2 Announce Type: replace-cross Abstract: Multi-task optimization is a powerful approach for solving a large number of tasks in parallel. However, existing algorithms face distinct limitations: Population-based methods scale poorly and remain underexplored for large task sets. Approaches that do scale beyond a thousand tasks are mostly MAP-Elites variants and rely on a fixed, discretized archive that disregards the topology of the task space. We introduce MONET (Multi-Task Optimization over Networks of Tasks), a multi-task optimization algorithm that models the task space as a graph: tasks are nodes, and edges connect tasks in the task parameter space. This representation enables knowledge transfer between tasks and remains tractable for high-dimensional problems while exploiting the topology of the task space. MONET combines social learning, which generates candidates from neighboring nodes via crossover, with individual learning, which refines a node's own solution independently via mutation. We evaluate MONET on four domains (archery, arm, and cartpole with 5,000 tasks each; hexapod with 2,000 tasks) and show that it matches or exceeds the performance of existing MAP-Elites-based baselines across all four domains.

19.
arXiv (quant-ph) 2026-06-25

Exact Leg-Cut Influence Functional and Emergence of Gaussian Entanglement Theory in a Statistical-Dressing Ladder Model

arXiv:2606.25669v1 Announce Type: new Abstract: The emergence of Gaussian effective field theories in low-dimensional quantum systems is traditionally understood through top-down frameworks such as bosonization and Luttinger-liquid theory. However, these approaches typically focus on the long-wavelength degrees of freedom in ways that do not directly track how non-Gaussian lattice-scale correlations are progressively discarded under coarse-graining. In this work, we present an exact lattice formulation from which this phenomenon emerges analytically. We analyze a two-leg hard-core ladder under a leg bipartition, where non-local statistical strings cross the entanglement cut. We construct an exact lattice influence-functional representation showing that the reduced state factorizes strictly into a product-state amplitude and a full-counting-statistics functional. By introducing a commuting linked-cluster superoperator hierarchy that bypasses Baker-Campbell-Hausdorff ordering ambiguities, we prove that the first mixedness-generating sector is strictly density-density in character. Under a specific systematic coarse-graining procedure, we analytically derive the suppression of higher-order corrections, providing a controlled, closed-form framework showing how highly non-Gaussian lattice states evolve toward their quadratic continuum form under coarse-graining. We corroborate these analytical predictions through finite-size exact diagonalization and entanglement-spectrum diagnostics.

20.
bioRxiv (Bioinfo) 2026-06-22

Multivariate Random Forests for Cross-Modal Multi-Omics Integration

Multi-omics studies are widely used across many areas of biomedical research. In many diseases, some signals are shared across data types, while others are strongest in a single omics layer. Current multi-omics clustering methods often either merge all data types into a single representation, which can blur biology that is strong in one layer, or rely on linear structure that may miss more complex relationships across data types. We introduce multiRF, a random-forest-based method that handles complex data types and separates shared and modality-specific structure for multi-omics data. multiRF learns sample similarities across omics layers from multivariate random forests, combines them across data types, and uses the resulting weights to estimate the part of each omics layer that is predictable from the others. The remaining residual is treated as modality-specific signal, allowing shared and modality-specific similarities to be clustered separately. In simulations, multiRF recovered shared clusters as well as or better than established integrative methods while more reliably separating modality-specific signal under nonlinear data structures. In TCGA head and neck squamous cell carcinoma, the shared component aligned with the main subtype structure across established reference classifications, while gene- and miRNA-specific components revealed additional immune and developmental biology. In the ADNI cohort with matched blood DNA methylation and structural MRI, the shared cross-modal aging signal was associated with future conversion to mild cognitive impairment or Alzheimer's disease, and a DNAm-specific residual signal showed exploratory additional information. These results show that multiRF can recover a common disease axis while retaining biologically meaningful signals specific to one data type. multiRF is available as an open-source R package at https://github.com/novawz/multiRF.

21.
bioRxiv (Bioinfo) 2026-06-13

PertDiffBench: Benchmarking Diffusion Models for Single-Cell Perturbation Response Prediction

Diffusion models are increasingly used to predict transcriptional responses to perturbations, but whether they improve on simpler generative and representation-based baselines remains unclear. Existing evaluations often do not separate the effects of model architecture, input representation, biological context and metric choice, making it difficult to determine where diffusion-based methods are useful. Here we introduce PertDiffBench, a standardized benchmark for diffusion-based transcriptomic perturbation prediction across single-cell and bulk RNA-seq datasets. PertDiffBench evaluates diffusion-based models across three complementary evaluation settings: standard prediction in known single-cell contexts and bulk perturbation conditions, generalization to unseen cell types, species, drugs and intermediate time points, and stress tests of feature dimensionality, input representation, noise type and gene ordering. Across these settings, diffusion models did not show a consistent advantage. scGen remained a strong baseline in common prediction tasks, whereas scDiffusion was the most competitive diffusion-based method in several generalization settings. Temporal imputation showed a different pattern, with a simple DDPM operating directly in expression space outperforming more specialized models. Stress tests showed that performance was model dependent and sensitive to feature dimensionality, encoder choice, noise type and gene ordering. Pretrained encoders did not consistently improve performance, with the classical scVI representation slightly exceeding STATE in seen-condition and unseen-cell-type settings. These results indicate that diffusion-model performance in perturbation response prediction depends strongly on task design and representation choice. PertDiffBench provides a practical framework for evaluating these models under biologically varied and stress-tested conditions.

22.
arXiv (CS.CL) 2026-06-24

SciZoom: A Large-scale Benchmark for Hierarchical Scientific Summarization across the LLM Era

The explosive growth of AI research has created unprecedented information overload, increasing the demand for scientific summarization at multiple levels of granularity beyond traditional abstracts. While LLMs are increasingly adopted for summarization, existing benchmarks remain limited in scale, target only a single granularity, and predate the LLM era. Moreover, since the release of ChatGPT in November 2022, researchers have rapidly adopted LLMs for drafting manuscripts themselves, fundamentally transforming scientific writing, yet no resource exists to analyze how this writing has evolved. To bridge these gaps, we introduce SciZoom, a benchmark comprising 44,946 papers from four top-tier ML venues (NeurIPS, ICLR, ICML, EMNLP) spanning 2020 to 2025, explicitly stratified into Pre-LLM and Post-LLM eras. SciZoom provides three hierarchical summarization targets (Abstract, Contributions, and TL;DR) achieving compression ratios up to 600:1, enabling both multi-granularity summarization research and temporal mining of scientific writing patterns. Our linguistic analysis reveals striking shifts in phrase patterns (up to 10x for formulaic expressions) and rhetorical style (23% decline in hedging), suggesting that LLM-assisted writing produces more confident yet homogenized prose. SciZoom serves as both a challenging benchmark and a unique resource for mining the evolution of scientific discourse in the generative AI era. Our code and dataset are publicly available on GitHub (https://github.com/janghana/SciZoom) and Hugging Face (https://huggingface.co/datasets/hanjang/SciZoom), respectively.

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

Spatiotemporal downscaling and nowcasting of urban land surface temperatures with deep neural networks

arXiv:2605.13566v2 Announce Type: replace Abstract: Land Surface Temperature (LST) is a key variable for various applications, such as urban climate and ecology studies. Yet, existing satellite-derived LST products provide either high spatial or high temporal resolution, resulting in a fundamental trade-off between the two. To address this trade-off, we combine observations from a geostationary and a polar orbiting satellite and provide LST fields at high spatial and high temporal resolution (1 km at 15-min intervals). We demonstrate their application for intraday forecasting of LSTs. To estimate LST fields at high spatiotemporal resolution, a U-Net model is trained to map LST fields from SEVIRI/MSG (3 km and 15 min resolution) to LST fields from Terra/Aqua MODIS (1 km, 4 overpasses per day) that are collocated in space and time. The presented model has been trained on LSTs across large European cities with a population exceeding 1 million inhabitants, and achieves an RMSE = $1.92${\deg}C and near-zero bias MBE = $0.01${\deg}C on the hold-out test set. As a second step, we present an LST nowcasting model based on ConvLSTM architecture, trained across downscaled LST fields with forecast lead times of 15 to 75 minutes. The nowcasting model outperforms a persistence and a Climatological Rolling Median benchmarks, with RMSEs of $0.57$ to $1.15${\deg}C for the considered lead times and biases ranging from $-0.1$ to $0.14${\deg}C. An additional validation conducted against independent MODIS overpasses confirms robust performance. Our LST forecast model at high spatiotemporal resolution is directly applicable to operational satellite-based LST monitoring.

24.
medRxiv (Medicine) 2026-06-24

Automated Text Message Outreach to Increase Diabetes Screening: A Pragmatic Randomized Trial

Background Despite evidence that early intervention can prevent or delay progression to type 2 diabetes, more than 80% of individuals with prediabetes in the United States remain undiagnosed, underscoring the need for scalable strategies to increase uptake. In this study, we evaluated whether a single text message could increase completion of HbA1c-based diabetes screening in routine clinical practice. Methods We conducted a pragmatic randomized controlled trial within Duke University Health System (DUHS). Patients aged 35 years or older who met American Diabetes Association 2022 screening criteria, had no previous diagnosis of diabetes, had not undergone HbA1c testing within the preceding 3 years, and had opted to receive text messages from DUHS were randomly assigned to receive either a single text message encouraging guideline-based diabetes screening and discussion with a primary care provider (intervention group; n=55,494) or usual care (control group; n=5,748). The primary outcome was HbA1c test completion within 24 weeks following message delivery (or no message for controls), analyzed using a Cox proportional hazards model stratified by wave. Secondary outcomes included piecewise hazard ratios for early (weeks 1-4), mid (weeks 5-12), and late (weeks 13-24) intervals and the between-group difference in cumulative testing rate. Findings Text message outreach significantly increased HbA1c test completion over 24 weeks (HR, 1.18 [95% CI, 1.07-1.03]) with the strongest effect in the first four weeks (HR, 1.48 [95% CI, 1.18-1.86]). By the end of the 24-week observation period, cumulative testing reached 9.14% in the messaged group vs 7.83% in controls (between-group difference, 1.31% [95% CI, 0.59-2.07]), corresponding to one additional HbA1c test per 76 messages delivered ($0.51 in messaging costs per additional HbA1c test performed). Rates of prediabetes and diabetes among those screened were similar between groups, indicating no selection bias of higher-risk patients. One additional dysglycemia case was identified per 213 messages sent ($1.43 per case detected).

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arXiv (CS.AI) 2026-06-16

AnonShield: Scalable On-Premise Pseudonymization for CSIRT Vulnerability Data

arXiv:2606.15650v1 Announce Type: cross Abstract: We present AnonShield, a high-throughput, on-premise pseudonymization system that combines GPU-accelerated NER, streaming processing, caching, and schema-aware configuration. Evaluated on datasets up to 550 MB (70,951 records), AnonShield reduces processing time from over 92 hours to under 10 minutes (up to 738x speedup) while achieving up to 94.2% F1-score and 96.7% recall. Our results show that scalable pseudonymization of vulnerability data is feasible without sacrificing analytical utility, enabling compliant data sharing in operational CSIRT environments.