arXiv subjects

Shinjae Yoo

Publications and source records attributed to Shinjae Yoo.

At least 37 records · Page 2Linked to original sources

arXiv2026

DANCE: Doubly Adaptive Neighborhood Conformal Estimation

The recent developments of complex deep learning models have led to unprecedented ability to accurately predict across multiple data representation types. Conformal prediction for uncertainty quantification of these models has risen in popularity, providing adaptive, statistically-valid prediction sets. For classification tasks, conformal methods have typically focused on utilizing logit scores. For pre-trained models, however, this can result in inefficient, overly conservative set sizes when not calibrated towards the target task. We propose DANCE, a doubly locally adaptive nearest-neighbor based conformal algorithm combining two novel nonconformity scores directly using the data's embedded representation. DANCE first fits a task-adaptive kernel regression model from the embedding layer before using the learned kernel space to produce the final prediction sets for uncertainty quantification. We test against state-of-the-art local, task-adapted and zero-shot conformal baselines, demonstrating DANCE's superior blend of set size efficiency and robustness across various datasets.

stat.ML↗

arXiv2026

Uncertainty-Calibrated Spatiotemporal Field Diffusion with Sparse Supervision

Physical fields are typically observed only at sparse, time-varying sensor locations, making forecasting and reconstruction ill-posed and uncertainty-critical. We present SOLID, a mask-conditioned diffusion framework that learns spatiotemporal dynamics from sparse observations alone: training and evaluation use only observed target locations, requiring no dense fields and no pre-imputation. Unlike prior work that trains on dense reanalysis or simulations and only tests under sparsity, SOLID is trained end-to-end with sparse supervision only. SOLID conditions each denoising step on the measured values and their locations, and introduces a dual-masking objective that (i) emphasizes learning in unobserved void regions while (ii) upweights overlap pixels where inputs and targets provide the most reliable anchors. This strict sparse-conditioning pathway enables posterior sampling of full fields consistent with the measurements, achieving up to an order-of-magnitude improvement in probabilistic error and yielding calibrated uncertainty maps (\r{ho} > 0.7) under severe sparsity.

cs.LG↗

arXiv2026

Quantum Super-resolution by Adaptive Non-local Observables

Super-resolution (SR) seeks to reconstruct high-resolution (HR) data from low-resolution (LR) observations. Classical deep learning methods have advanced SR substantially, but require increasingly deeper networks, large datasets, and heavy computation to capture fine-grained correlations. In this work, we present the \emph{first study} to investigate quantum circuits for SR. We propose a framework based on Variational Quantum Circuits (VQCs) with \emph{Adaptive Non-Local Observable} (ANO) measurements. Unlike conventional VQCs with fixed Pauli readouts, ANO introduces trainable multi-qubit Hermitian observables, allowing the measurement process to adapt during training. This design leverages the high-dimensional Hilbert space of quantum systems and the representational structure provided by entanglement and superposition. Experiments demonstrate that ANO-VQCs achieve up to five-fold higher resolution with a relatively small model size, suggesting a promising new direction at the intersection of quantum machine learning and super-resolution.

quant-ph↗

arXiv2025

Unveiling Nano-scale Crystal Deformation using Coherent X-ray Dynamical Diffraction

Visualization of internal deformation fields in crystalline materials helps bridge the gap between theoretical models and practical applications. Applying Bragg coherent diffraction imaging under X-ray dynamical diffraction conditions provides a promising approach to the longstanding challenge of investigating the deformation fields in micron-sized crystals. Here, we present an automatic differentiation-based reconstruction method that integrates dynamical scattering theory to accurately reconstruct deformation fields in large crystals. Using this forward model, our simulated and experimental results demonstrate that three-dimensional local strain information inside a large crystal can be accurately reconstructed under coherent X-ray dynamical diffraction conditions with Bragg coherent X-ray diffraction imaging. These findings open an avenue for extending the investigation of local deformation fields to microscale crystals while maintaining nanoscale resolution, leveraging the enhanced coherence and brightness of advanced X-ray sources.

physics.app-ph↗

arXiv2025

Machine Learning-Driven Predictive Resource Management in Complex Science Workflows

The collaborative efforts of large communities in science experiments, often comprising thousands of global members, reflect a monumental commitment to exploration and discovery. Recently, advanced and complex data processing has gained increasing importance in science experiments. Data processing workflows typically consist of multiple intricate steps, and the precise specification of resource requirements is crucial for each step to allocate optimal resources for effective processing. Estimating resource requirements in advance is challenging due to a wide range of analysis scenarios, varying skill levels among community members, and the continuously increasing spectrum of computing options. One practical approach to mitigate these challenges involves initially processing a subset of each step to measure precise resource utilization from actual processing profiles before completing the entire step. While this two-staged approach enables processing on optimal resources for most of the workflow, it has drawbacks such as initial inaccuracies leading to potential failures and suboptimal resource usage, along with overhead from waiting for initial processing completion, which is critical for fast-turnaround analyses. In this context, our study introduces a novel pipeline of machine learning models within a comprehensive workflow management system, the Production and Distributed Analysis (PanDA) system. These models employ advanced machine learning techniques to predict key resource requirements, overcoming challenges posed by limited upfront knowledge of characteristics at each step. Accurate forecasts of resource requirements enable informed and proactive decision-making in workflow management, enhancing the efficiency of handling diverse, complex workflows across heterogeneous resources.

cs.DC↗

arXiv2025

Scalable Diffusion Transformer for Conditional 4D fMRI Synthesis

Generating whole-brain 4D fMRI sequences conditioned on cognitive tasks remains challenging due to the high-dimensional, heterogeneous BOLD dynamics across subjects/acquisitions and the lack of neuroscience-grounded validation. We introduce the first diffusion transformer for voxelwise 4D fMRI conditional generation, combining 3D VQ-GAN latent compression with a CNN-Transformer backbone and strong task conditioning via AdaLN-Zero and cross-attention. On HCP task fMRI, our model reproduces task-evoked activation maps, preserves the inter-task representational structure observed in real data (RSA), achieves perfect condition specificity, and aligns ROI time-courses with canonical hemodynamic responses. Performance improves predictably with scale, reaching task-evoked map correlation of 0.83 and RSA of 0.98, consistently surpassing a U-Net baseline on all metrics. By coupling latent diffusion with a scalable backbone and strong conditioning, this work establishes a practical path to conditional 4D fMRI synthesis, paving the way for future applications such as virtual experiments, cross-site harmonization, and principled augmentation for downstream neuroimaging models.

cs.CV↗

arXiv2025

Dynamical Implicit Neural Representations

Implicit Neural Representations (INRs) provide a powerful continuous framework for modeling complex visual and geometric signals, but spectral bias remains a fundamental challenge, limiting their ability to capture high-frequency details. Orthogonal to existing remedy strategies, we introduce Dynamical Implicit Neural Representations (DINR), a new INR modeling framework that treats feature evolution as a continuous-time dynamical system rather than a discrete stack of layers. This dynamical formulation mitigates spectral bias by enabling richer, more adaptive frequency representations through continuous feature evolution. Theoretical analysis based on Rademacher complexity and the Neural Tangent Kernel demonstrates that DINR enhances expressivity and improves training dynamics. Moreover, regularizing the complexity of the underlying dynamics provides a principled way to balance expressivity and generalization. Extensive experiments on image representation, field reconstruction, and data compression confirm that DINR delivers more stable convergence, higher signal fidelity, and stronger generalization than conventional static INRs.

cs.LG↗

arXiv2025

Neural Architecture Search for Quantum Autoencoders

In recent years, machine learning and deep learning have driven advances in domains such as image classification, speech recognition, and anomaly detection by leveraging multi-layer neural networks to model complex data. Simultaneously, quantum computing (QC) promises to address classically intractable problems via quantum parallelism, motivating research in quantum machine learning (QML). Among QML techniques, quantum autoencoders show promise for compressing high-dimensional quantum and classical data. However, designing effective quantum circuit architectures for quantum autoencoders remains challenging due to the complexity of selecting gates, arranging circuit layers, and tuning parameters. This paper proposes a neural architecture search (NAS) framework that automates the design of quantum autoencoders using a genetic algorithm (GA). By systematically evolving variational quantum circuit (VQC) configurations, our method seeks to identify high-performing hybrid quantum-classical autoencoders for data reconstruction without becoming trapped in local minima. We demonstrate effectiveness on image datasets, highlighting the potential of quantum autoencoders for efficient feature extraction within a noise-prone, near-term quantum era. Our approach lays a foundation for broader application of genetic algorithms to quantum architecture search, aiming for a robust, automated method that can adapt to varied data and hardware constraints.

quant-ph↗

arXiv2025

OmniField: Conditioned Neural Fields for Robust Multimodal Spatiotemporal Learning

Multimodal spatiotemporal learning on real-world experimental data is constrained by two challenges: within-modality measurements are sparse, irregular, and noisy (QA/QC artifacts) but cross-modally correlated; the set of available modalities varies across space and time, shrinking the usable record unless models can adapt to arbitrary subsets at train and test time. We propose OmniField, a continuity-aware framework that learns a continuous neural field conditioned on available modalities and iteratively fuses cross-modal context. A multimodal crosstalk block architecture paired with iterative cross-modal refinement aligns signals prior to the decoder, enabling unified reconstruction, interpolation, forecasting, and cross-modal prediction without gridding or surrogate preprocessing. Extensive evaluations show that OmniField consistently outperforms eight strong multimodal spatiotemporal baselines. Under heavy simulated sensor noise, performance remains close to clean-input levels, highlighting robustness to corrupted measurements.

cs.LG↗

arXiv2025

GST-UNet: A Neural Framework for Spatiotemporal Causal Inference with Time-Varying Confounding

Estimating causal effects from spatiotemporal observational data is essential in public health, environmental science, and policy evaluation, where randomized experiments are often infeasible. Existing approaches, however, either rely on strong structural assumptions or fail to handle key challenges such as interference, spatial confounding, temporal carryover, and time-varying confounding -- where covariates are influenced by past treatments and, in turn, affect future ones. We introduce GST-UNet (G-computation Spatio-Temporal UNet), a theoretically grounded neural framework that combines a U-Net-based spatiotemporal encoder with regression-based iterative G-computation to estimate location-specific potential outcomes under complex intervention sequences. GST-UNet explicitly adjusts for time-varying confounders and captures non-linear spatial and temporal dependencies, enabling valid causal inference from a single observed trajectory in data-scarce settings. We validate its effectiveness in synthetic experiments and in a real-world analysis of wildfire smoke exposure and respiratory hospitalizations during the 2018 California Camp Fire. Together, these results position GST-UNet as a principled and ready-to-use framework for spatiotemporal causal inference, advancing reliable estimation in policy-relevant and scientific domains.

cs.LG↗

arXiv2025

Macro2Micro: A Rapid and Precise Cross-modal Magnetic Resonance Imaging Synthesis using Multi-scale Structural Brain Similarity

The human brain is a complex system requiring both macroscopic and microscopic components for comprehensive understanding. However, mapping nonlinear relationships between these scales remains challenging due to technical limitations and the high cost of multimodal Magnetic Resonance Imaging (MRI) acquisition. To address this, we introduce Macro2Micro, a deep learning framework that predicts brain microstructure from macrostructure using a Generative Adversarial Network (GAN). Based on the hypothesis that microscale structural information can be inferred from macroscale structures, Macro2Micro explicitly encodes multiscale brain information into distinct processing branches. To enhance artifact elimination and output quality, we propose a simple yet effective auxiliary discriminator and learning objective. Extensive experiments demonstrated that Macro2Micro faithfully translates T1-weighted MRIs into corresponding Fractional Anisotropy (FA) images, achieving a 6.8\% improvement in the Structural Similarity Index Measure (SSIM) compared to previous methods, while retaining the individual biological characteristics of the brain. With an inference time of less than 0.01 seconds per MR modality translation, Macro2Micro introduces the potential for real-time multimodal rendering in medical and research applications. The code will be made available upon acceptance.

eess.IV↗

arXiv2025

STACI: Spatio-Temporal Aleatoric Conformal Inference

Fitting Gaussian Processes (GPs) provides interpretable aleatoric uncertainty quantification for estimation of spatio-temporal fields. Spatio-temporal deep learning models, while scalable, typically assume a simplistic independent covariance matrix for the response, failing to capture the underlying correlation structure. However, spatio-temporal GPs suffer from issues of scalability and various forms of approximation bias resulting from restrictive assumptions of the covariance kernel function. We propose STACI, a novel framework consisting of a variational Bayesian neural network approximation of non-stationary spatio-temporal GP along with a novel spatio-temporal conformal inference algorithm. STACI is highly scalable, taking advantage of GPU training capabilities for neural network models, and provides statistically valid prediction intervals for uncertainty quantification. STACI outperforms competing GPs and deep methods in accurately approximating spatio-temporal processes and we show it easily scales to datasets with millions of observations.

stat.ML↗

arXiv2025

CGSim: A Simulation Framework for Large Scale Distributed Computing Environment

Large-scale distributed computing infrastructures such as the Worldwide LHC Computing Grid (WLCG) require comprehensive simulation tools for evaluating performance, testing new algorithms, and optimizing resource allocation strategies. However, existing simulators suffer from limited scalability, hardwired algorithms, lack of real-time monitoring, and inability to generate datasets suitable for modern machine learning approaches. We present CGSim, a simulation framework for large-scale distributed computing environments that addresses these limitations. Built upon the validated SimGrid simulation framework, CGSim provides high-level abstractions for modeling heterogeneous grid environments while maintaining accuracy and scalability. Key features include a modular plugin mechanism for testing custom workflow scheduling and data movement policies, interactive real-time visualization dashboards, and automatic generation of event-level datasets suitable for AI-assisted performance modeling. We demonstrate CGSim's capabilities through a comprehensive evaluation using production ATLAS PanDA workloads, showing significant calibration accuracy improvements across WLCG computing sites. Scalability experiments show near-linear scaling for multi-site simulations, with distributed workloads achieving 6x better performance compared to single-site execution. The framework enables researchers to simulate WLCG-scale infrastructures with hundreds of sites and thousands of concurrent jobs within practical time budget constraints on commodity hardware.

cs.DC↗

arXiv2025

Data Management System Analysis for Distributed Computing Workloads

Large-scale international collaborations such as ATLAS rely on globally distributed workflows and data management to process, move, and store vast volumes of data. ATLAS's Production and Distributed Analysis (PanDA) workflow system and the Rucio data management system are each highly optimized for their respective design goals. However, operating them together at global scale exposes systemic inefficiencies, including underutilized resources, redundant or unnecessary transfers, and altered error distributions. Moreover, PanDA and Rucio currently lack shared performance awareness and coordinated, adaptive strategies. This work charts a path toward co-optimizing the two systems by diagnosing data-management pitfalls and prioritizing end-to-end improvements. With the observation of spatially and temporally imbalanced transfer activities, we develop a metadata-matching algorithm that links PanDA jobs and Rucio datasets at the file level, yielding a complete, fine-grained view of data access and movement. Using this linkage, we identify anomalous transfer patterns that violate PanDA's data-centric job-allocation principle. We then outline mitigation strategies for these patterns and highlight opportunities for tighter PanDA-Rucio coordination to improve resource utilization, reduce unnecessary data movement, and enhance overall system resilience.

cs.DC↗

arXiv2025

TPCpp-10M: Simulated proton-proton collisions in a Time Projection Chamber for AI Foundation Models

Scientific foundation models hold great promise for advancing nuclear and particle physics by improving analysis precision and accelerating discovery. Yet, progress in this field is often limited by the lack of openly available large scale datasets, as well as standardized evaluation tasks and metrics. Furthermore, the specialized knowledge and software typically required to process particle physics data pose significant barriers to interdisciplinary collaboration with the broader machine learning community. This work introduces a large, openly accessible dataset of 10 million simulated proton-proton collisions, designed to support self-supervised training of foundation models. To facilitate ease of use, the dataset is provided in a common NumPy format. In addition, it includes 70,000 labeled examples spanning three well defined downstream tasks: track finding, particle identification, and noise tagging, to enable systematic evaluation of the foundation model's adaptability. The simulated data are generated using the Pythia Monte Carlo event generator at a center of mass energy of sqrt(s) = 200 GeV and processed with Geant4 to include realistic detector conditions and signal emulation in the sPHENIX Time Projection Chamber at the Relativistic Heavy Ion Collider, located at Brookhaven National Laboratory. This dataset resource establishes a common ground for interdisciplinary research, enabling machine learning scientists and physicists alike to explore scaling behaviors, assess transferability, and accelerate progress toward foundation models in nuclear and high energy physics. The complete simulation and reconstruction chain is reproducible with the sPHENIX software stack. All data and code locations are provided under Data Accessibility.

physics.data-an↗

arXiv2025

Resting-state fMRI Analysis using Quantum Time-series Transformer

Resting-state functional magnetic resonance imaging (fMRI) has emerged as a pivotal tool for revealing intrinsic brain network connectivity and identifying neural biomarkers of neuropsychiatric conditions. However, classical self-attention transformer models--despite their formidable representational power--struggle with quadratic complexity, large parameter counts, and substantial data requirements. To address these barriers, we introduce a Quantum Time-series Transformer, a novel quantum-enhanced transformer architecture leveraging Linear Combination of Unitaries and Quantum Singular Value Transformation. Unlike classical transformers, Quantum Time-series Transformer operates with polylogarithmic computational complexity, markedly reducing training overhead and enabling robust performance even with fewer parameters and limited sample sizes. Empirical evaluation on the largest-scale fMRI datasets from the Adolescent Brain Cognitive Development Study and the UK Biobank demonstrates that Quantum Time-series Transformer achieves comparable or superior predictive performance compared to state-of-the-art classical transformer models, with especially pronounced gains in small-sample scenarios. Interpretability analyses using SHapley Additive exPlanations further reveal that Quantum Time-series Transformer reliably identifies clinically meaningful neural biomarkers of attention-deficit/hyperactivity disorder (ADHD). These findings underscore the promise of quantum-enhanced transformers in advancing computational neuroscience by more efficiently modeling complex spatio-temporal dynamics and improving clinical interpretability.

eess.IV↗

arXiv2025

It's-A-Me, Quantum Mario: Scalable Quantum Reinforcement Learning with Multi-Chip Ensembles

Quantum reinforcement learning (QRL) promises compact function approximators with access to vast Hilbert spaces, but its practical progress is slowed by NISQ-era constraints such as limited qubits and noise accumulation. We introduce a multi-chip ensemble framework using multiple small Quantum Convolutional Neural Networks (QCNNs) to overcome these constraints. Our approach partitions complex, high-dimensional observations from the Super Mario Bros environment across independent quantum circuits, then classically aggregates their outputs within a Double Deep Q-Network (DDQN) framework. This modular architecture enables QRL in complex environments previously inaccessible to quantum agents, achieving superior performance and learning stability compared to classical baselines and single-chip quantum models. The multi-chip ensemble demonstrates enhanced scalability by reducing information loss from dimensionality reduction while remaining implementable on near-term quantum hardware, providing a practical pathway for applying QRL to real-world problems.

quant-ph↗

arXiv2025

FM4NPP: A Scaling Foundation Model for Nuclear and Particle Physics

Large language models have revolutionized artificial intelligence by enabling large, generalizable models trained through self-supervision. This paradigm has inspired the development of scientific foundation models (FMs). However, applying this capability to experimental particle physics is challenging due to the sparse, spatially distributed nature of detector data, which differs dramatically from natural language. This work addresses if an FM for particle physics can scale and generalize across diverse tasks. We introduce a new dataset with more than 11 million particle collision events and a suite of downstream tasks and labeled data for evaluation. We propose a novel self-supervised training method for detector data and demonstrate its neural scalability with models that feature up to 188 million parameters. With frozen weights and task-specific adapters, this FM consistently outperforms baseline models across all downstream tasks. The performance also exhibits robust data-efficient adaptation. Further analysis reveals that the representations extracted by the FM are task-agnostic but can be specialized via a single linear mapping for different downstream tasks.

cs.LG↗