arXiv subjects

Sangyoon Bae

Publications and source records attributed to Sangyoon Bae.

11 recordsLinked to original sources

arXiv2026

PIMSM: Physics-Informed Multi-Scale Mamba for Stable Neural Representations under Distribution Shift

Scientific foundation models are expected to reuse representations under changes in dataset, acquisition protocol, and deployment domain, yet many sequence backbones treat scientific temporal structure as an unconstrained pattern to be fitted. We argue that this misses a central property of natural dynamical systems: neural and atmospheric time series are organized by interacting processes across multiple physical timescales, and failure to preserve this multiscale structure contributes to brittleness under distribution shift. We formalize this failure mode as temporal kernel mismatch, where a model fits in-distribution dynamics with an effective memory policy that is not anchored to the signal's physical timescales, leading to representation drift and degraded transfer. We propose Physics-Informed Multi-Scale Mamba (PIMSM), a state-space architecture that maps spectrum-estimated transition points between frequency regimes (knee frequencies) to scale-specific discretization parameters and anchors them to acquisition time units. On Human Connectome Project fMRI, PIMSM improves robustness and representation stability under severe temporal-context truncation, extreme low-resource transfer, and resting-state-to-task-state generalization. Without modality-specific adaptation, the same architecture also attains the lowest variable-wise MAE across all reported horizons and variables on Weather-5K held-out-station spatial out-of-distribution forecasting. These results support temporal-scale alignment as a practical inductive bias for scientific foundation models that must preserve structure, not only fit correlations, under deployment shift.

cs.LG↗

arXiv2026

Latent-Space Causal Discovery from Indirect Neuroimaging Observations

Neuroimaging does not observe causal variables directly: hemodynamics and volume conduction distort signals so that statistical dependence need not reflect latent neural influence. Before estimating graphs, one must specify under what assumptions delayed directed structure can be studied from such indirect observations. We formalize a conditional setting - recoverable inversion under modality physics together with nonstationary latent dynamics - and derive an inversion-error propagation bound under explicit assumptions. Building on this framing, we propose INCAMA (INdirect CAusal MAmba): physics-aware inversion coupled with a delay-aware Mamba encoder that uses mechanism shifts as informative variation for directed graph scoring. We use controlled simulations for quantitative validation and HCP motor-task fMRI as a zero-shot external transfer check based on anatomical and task-network consistency. Across TVB simulations, INCAMA improves directed-structure recovery by 2-3x in F1 over observation-space and two-stage baselines, and on HCP motor-task fMRI it produces sparse directed estimates concentrated in canonical visuo-motor pathways.

q-bio.NC↗

arXiv2026

Attention-space Contrastive Guidance for Efficient Hallucination Mitigation in LVLMs

Hallucinations in large vision--language models (LVLMs) often arise when language priors dominate over visual evidence, leading to object misidentification and visually inconsistent descriptions. We address this problem by framing hallucination mitigation as contrastive guidance that steers generation toward visually grounded and semantically faithful text. We propose Attention-space Contrastive Guidance (ACG), a training-free, single-pass method that operates directly in self-attention layers, where hallucination-inducing cross-modal biases emerge. ACG constructs both image-conditioned and approximate text-only attention paths within a single forward pass, enabling efficient guidance before errors accumulate at the output layer. Because this masking-based surrogate can introduce approximation bias, we further apply a lightweight orthogonal projection that suppresses components aligned with the text-only path, yielding a more visually grounded correction. Experiments on CHAIR and POPE show that ACG improves faithfulness over existing training-free baselines while maintaining caption quality, reducing latency by up to $2\times$ compared to multi-pass contrastive decoding methods.

cs.CV↗

arXiv2025

Transformer-Based Sleep Stage Classification Enhanced by Clinical Information

Manual sleep staging from polysomnography (PSG) is labor-intensive and prone to inter-scorer variability. While recent deep learning models have advanced automated staging, most rely solely on raw PSG signals and neglect contextual cues used by human experts. We propose a two-stage architecture that combines a Transformer-based per-epoch encoder with a 1D CNN aggregator, and systematically investigates the effect of incorporating explicit context: subject-level clinical metadata (age, sex, BMI) and per-epoch expert event annotations (apneas, desaturations, arousals, periodic breathing). Using the Sleep Heart Health Study (SHHS) cohort (n=8,357), we demonstrate that contextual fusion substantially improves staging accuracy. Compared to a PSG-only baseline (macro-F1 0.7745, micro-F1 0.8774), our final model achieves macro-F1 0.8031 and micro-F1 0.9051, with event annotations contributing the largest gains. Notably, feature fusion outperforms multi-task alternatives that predict the same auxiliary labels. These results highlight that augmenting learned representations with clinically meaningful features enhances both performance and interpretability, without modifying the PSG montage or requiring additional sensors. Our findings support a practical and scalable path toward context-aware, expert-aligned sleep staging systems.

cs.LG↗

arXiv2025

Decoding Dynamic Visual Experience from Calcium Imaging via Cell-Pattern-Aware Pretraining

Neural recordings exhibit a distinctive form of heterogeneity rooted in differences in cell types, intrinsic circuit dynamics, and stochastic stimulus-response variability that goes beyond ordinary dataset variability, mixing statistically regular neurons with highly stochastic, stimulus-contingent ones within the same dataset. This heterogeneity poses a challenge for self-supervised learning (SSL) -- learnable statistical regularity -- thereby destabilizing representation learning and limiting reliable scaling. We introduce POYO-CAP (Cell-pattern Aware Pretraining), a biologically grounded hybrid pretraining strategy that first trains with masked reconstruction plus lightweight auxiliary supervision on statistically regular neurons -- identified via skewness and kurtosis -- and then fine-tunes on more stochastic populations. On the Allen Brain Observatory dataset, this curriculum yields 12--13\% relative improvements over from-scratch training and enables smooth, monotonic scaling with model size, whereas baselines trained on mixed populations plateau or destabilize. By making statistical predictability an explicit data-selection criterion, POYO-CAP turns neural heterogeneity into a scalable learning advantage for robust neural decoding.

q-bio.NC↗

arXiv2025

CausalMamba: Scalable Conditional State Space Models for Neural Causal Inference

We introduce CausalMamba, a scalable framework that addresses fundamental limitations in fMRI-based causal inference: the ill-posed nature of inferring neural causality from hemodynamically distorted BOLD signals and the computational intractability of existing methods like Dynamic Causal Modeling (DCM). Our approach decomposes this complex inverse problem into two tractable stages: BOLD deconvolution to recover latent neural activity, followed by causal graph inference using a novel Conditional Mamba architecture. On simulated data, CausalMamba achieves 37% higher accuracy than DCM. Critically, when applied to real task fMRI data, our method recovers well-established neural pathways with 88% fidelity, whereas conventional approaches fail to identify these canonical circuits in over 99% of subjects. Furthermore, our network analysis of working memory data reveals that the brain strategically shifts its primary causal hub-recruiting executive or salience networks depending on the stimulus-a sophisticated reconfiguration that remains undetected by traditional methods. This work provides neuroscientists with a practical tool for large-scale causal inference that captures both fundamental circuit motifs and flexible network dynamics underlying cognitive function.

cs.CV↗

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

Spatiotemporal Learning of Brain Dynamics from fMRI Using Frequency-Specific Multi-Band Attention for Cognitive and Psychiatric Applications

Understanding how the brain's complex nonlinear dynamics give rise to cognitive function remains a central challenge in neuroscience. While brain functional dynamics exhibits scale-free and multifractal properties across temporal scales, conventional neuroimaging analytics assume linearity and stationarity, failing to capture frequency-specific neural computations. Here, we introduce Multi-Band Brain Net (MBBN), the first transformer-based framework to explicitly model frequency-specific spatiotemporal brain dynamics from fMRI. MBBN integrates biologically-grounded frequency decomposition with multi-band self-attention mechanisms, enabling discovery of previously undetectable frequency-dependent network interactions. Trained on 49,673 individuals across three large-scale cohorts (UK Biobank, ABCD, ABIDE), MBBN sets a new state-of-the-art in predicting psychiatric and cognitive outcomes (depression, ADHD, ASD), showing particular strength in classification tasks with up to 52.5\% higher AUROC and provides a novel framework for predicting cognitive intelligence scores. Frequency-resolved analyses uncover disorder-specific signatures: in ADHD, high-frequency fronto-sensorimotor connectivity is attenuated and opercular somatosensory nodes emerge as dynamic hubs; in ASD, orbitofrontal-somatosensory circuits show focal high-frequency disruption together with enhanced ultra-low-frequency coupling between the temporo-parietal junction and prefrontal cortex. By integrating scale-aware neural dynamics with deep learning, MBBN delivers more accurate and interpretable biomarkers, opening avenues for precision psychiatry and developmental neuroscience.

q-bio.NC↗

arXiv2024

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↗

arXiv2024

Quantum Privacy Aggregation of Teacher Ensembles (QPATE) for Privacy-preserving Quantum Machine Learning

The utility of machine learning has rapidly expanded in the last two decades and presents an ethical challenge. Papernot et. al. developed a technique, known as Private Aggregation of Teacher Ensembles (PATE) to enable federated learning in which multiple teacher models are trained on disjoint datasets. This study is the first to apply PATE to an ensemble of quantum neural networks (QNN) to pave a new way of ensuring privacy in quantum machine learning (QML) models.

quant-ph↗

arXiv2023

SwiFT: Swin 4D fMRI Transformer

Modeling spatiotemporal brain dynamics from high-dimensional data, such as functional Magnetic Resonance Imaging (fMRI), is a formidable task in neuroscience. Existing approaches for fMRI analysis utilize hand-crafted features, but the process of feature extraction risks losing essential information in fMRI scans. To address this challenge, we present SwiFT (Swin 4D fMRI Transformer), a Swin Transformer architecture that can learn brain dynamics directly from fMRI volumes in a memory and computation-efficient manner. SwiFT achieves this by implementing a 4D window multi-head self-attention mechanism and absolute positional embeddings. We evaluate SwiFT using multiple large-scale resting-state fMRI datasets, including the Human Connectome Project (HCP), Adolescent Brain Cognitive Development (ABCD), and UK Biobank (UKB) datasets, to predict sex, age, and cognitive intelligence. Our experimental outcomes reveal that SwiFT consistently outperforms recent state-of-the-art models. Furthermore, by leveraging its end-to-end learning capability, we show that contrastive loss-based self-supervised pre-training of SwiFT can enhance performance on downstream tasks. Additionally, we employ an explainable AI method to identify the brain regions associated with sex classification. To our knowledge, SwiFT is the first Swin Transformer architecture to process dimensional spatiotemporal brain functional data in an end-to-end fashion. Our work holds substantial potential in facilitating scalable learning of functional brain imaging in neuroscience research by reducing the hurdles associated with applying Transformer models to high-dimensional fMRI.

cs.CV↗