arXiv subjects

Shinjae Yoo

Publications and source records attributed to Shinjae Yoo.

At least 19 recordsLinked to original sources

arXiv2026

Inverse mask design for interference lithography using automatic differentiable wave propagation

Interference lithography (IL) is powerful for fabricating high-resolution periodic nanostructures, but designing masks to produce non-periodic patterns remains challenging. We introduce a gradient-based optimization framework for binary IL mask design using automatic differentiation. The forward model is implemented using the differentiable angular spectrum method (ASM). The inverse mask design is formulated as an optimization problem, where the mask logits are updated through backpropagation of the loss between the simulated field amplitude and the target pattern. We optimize a mask that reproduces a target pattern with only 0.1% isolated pixel-level defects, resolving features at half the mask pixel pitch. To scale mask optimization, we employ the shifted ASM, which partitions the mask into patches that are propagated independently and summed at the image plane. For a 3.84 mm$\times$3.84 mm mask, shifted ASM with 16 patches reduces peak GPU memory by 3.8$\times$ at only 1.3$\times$ runtime cost relative to standard ASM. With gradient checkpointing, peak memory is reduced by 7.4$\times$ at 2$\times$ runtime. Distributing across multiple GPUs further accelerates the optimization. This work establishes a physics-informed, machine learning-driven approach for IL mask design, moving a step further towards complex, non-periodic patterns. The source code is available at https://github.com/chuntian236/holography-optimization.git .

physics.optics↗

arXiv2026

Quasi-polar Decomposition of Quantum Neural Networks via Adaptive Non-local Observables

We use Diagonal Adaptive Non-local Observables (DANO) as a canonical decomposition for studying Variational Quantum Circuit model evolution. Separating each learned observable into a diagonal spectrum and a unitary basis gives a quasi-polar description: the spectral weights are viewed as radial coordinates, while the unitary circuit serves as angular coordinates through Lie group identifications. This turns the training process into a trajectory in spectral and Lie-algebra space. Experiments on two classification tasks show that DANO radial spectral expansion correlates with accuracy. DANO angle coordinates reveal a dominant accuracy-correlated component. The framework provides a different perspective to characterize quantum model behavior.

quant-ph↗

arXiv2026

Observable Geometry for Effective Quantum Circuits

We study redundancy and effectiveness of Variational Quantum Circuits via algebraic and geometric views of Lie groups. Considering unitary transformations acting on Hermitian observables, a stabilizer group decomposition is given. Subsequently, we identify the Hermitian orbit with a quotient space of a symmetric space. Through this connection, we characterize the effective circuit degrees of freedom. Our approach of spectral decompositions and homogeneous spaces yields tractable calculation criteria, which are verified by numerical experiments.

quant-ph↗

arXiv2026

Auditing Retrieval-Augmented LLM Hypotheses for Longitudinal Cell Painting Morphology

High-content morphological profiling (Cell Painting) yields sensitive, high-dimensional signatures of cellular state, but translating longitudinal morphology trajectories into interpretable biology remains difficult, especially for weak, chronic perturbations such as low-dose-rate ionizing radiation. Large language models (LLMs) can synthesize heterogeneous evidence into biological narratives, yet their scientific use requires quantitative auditing. We present an evaluation-first, retrieval-augmented interpretation framework for longitudinal Cell Painting morphology, applied to a 9-week RPE-1 time course across five dose rates (0.003--6.0 mGy/hr). Week-matched treated-control morphology deltas are combined with retrieved perturbation neighbors, pathway context, and literature evidence through stable evidence identifiers, enabling an LLM to generate structured, evidence-linked hypotheses that are hierarchically summarized while preserving provenance. We introduce two quantitative auditing tests: V1 citation validity, which verifies that cited evidence identifiers exist in the prompt, and V2 proxy-based morphology compatibility, which evaluates consistency between predicted biological processes and the most altered morphology features. In our experiments, V1 detected no invalid evidence references, while V2 showed meaningful morphology compatibility that increased with perturbation strength and was positively associated with an independent morphology drift summary. The framework produces auditable, falsifiable biological hypotheses, including an adaptive phenotype involving metabolic reprogramming and proteostatic stress at lower dose rates (0.003--0.3 mGy/hr). Current limitations include proxy-based evaluation and the lack of ground-truth mechanism labels.

q-bio.QM↗

arXiv2026

Stable Self-Modulating Quantum Fast-Weight Programmers with Bounded Memory Gates

Quantum Fast-Weight Programmers (QFWPs) store temporal information in dynamically programmed variational-circuit parameters rather than in nonlinear recurrent hidden states, offering a practical route to quantum sequence modeling. Self-Modulating QFWP improves this framework by using input-dependent gates for both new fast-weight updates and the accumulated fast-weight state, but its unbounded old-state multiplier can diverge in long-sequence regimes. We propose a bounded old-state modulation rule that applies a sign-preserving tanh gate only to the recurrent memory branch while leaving the additive update and new-update modulation unchanged. We evaluate standard QFWP, full Self-Modulating QFWP, Only-New, and Only-Old variants on two CUDA-Q quantum-dynamics forecasting tasks and on Milan SMS telecommunication activity prediction. The quantum-dynamics results show that old-state modulation is the most consistent source of improvement over Standard QFWP, and that bounding the old-state gate removes long-sequence divergence while improving aggregate robustness. On Milan SMS forecasting, the original unbounded Self-Modulating QFWP converges across the tested grid and shows its clearest gains at longer input windows, with behavior close to the Only-Old ablation. These findings identify accumulated-memory modulation as the key mechanism of Self-Modulating QFWP and bounded old-state gating as a targeted stabilization strategy.

quant-ph↗

arXiv2026

Recursive QLSTM with Dynamic Variational Quantum Circuit Adaptation

Recent advances in quantum computing and machine learning have motivated the development of quantum models for sequential data processing. In this paper, we propose a Recursive Quantum Long Short-Term Memory model, or Recursive QLSTM, which extends QLSTM through metacore-based recursive constructions. We numerically test the model under different input sequence lengths, metacore designs, and recursive rules, and identify the best-performing architecture among these variants. For this selected model, we further provide theoretical arguments explaining why its recursive structure improves temporal information propagation and enhances learning performance. Our results suggest that Recursive QLSTM offers a flexible and effective framework for quantum recurrent learning over input time series of various lengths.

quant-ph↗

arXiv2026

Self-Modulating Quantum Fast-Weight Programmers for Efficient Adaptive Sequential Learning

Recent advances in quantum machine learning have motivated efficient models for sequential data processing. In this paper, we propose Self-Modulating Quantum Fast Weight Programmers, or Self-Modulating QFWP, which extends Quantum Fast Weight Programmers by introducing adaptive modulation over both newly generated fast-weight updates and historical fast-weight memory. Numerical results show that the proposed mechanism improves convergence stability and prediction performance across varying model settings, including different numbers of qubits and input sequence lengths. We further provide theoretical arguments explaining how self-modulation balances new information injection with memory retention, thereby enhancing temporal information propagation. These results suggest that Self-Modulating QFWP is a compact and effective framework for quantum machine learning on time-series data.

quant-ph↗

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

A Mixture of Experts Foundation Model for Scanning Electron Microscopy Image Analysis

Scanning Electron Microscopy (SEM) is indispensable in modern materials science, enabling high-resolution imaging across a wide range of structural, chemical, and functional investigations. However, SEM imaging remains constrained by task-specific models and labor-intensive acquisition processes that limit its scalability across diverse applications. Here, we introduce the first foundation model for SEM images, pretrained on a large corpus of multi-instrument, multi-condition scientific micrographs, enabling generalization across diverse material systems and imaging conditions. Leveraging a self-supervised transformer architecture, our model learns rich and transferable representations that can be fine-tuned or adapted to a wide range of downstream tasks. As a compelling demonstration, we focus on defocus-to-focus image translation-an essential yet underexplored challenge in automated microscopy pipelines. Our method not only restores focused detail from defocused inputs without paired supervision but also outperforms state-of-the-art techniques across multiple evaluation metrics. This work lays the groundwork for a new class of adaptable SEM models, accelerating materials discovery by bridging foundational representation learning with real-world imaging needs.

cs.LG↗

arXiv2026

Substrate-Mediated Evaporation and Stochastic Evolution of Supported Au Nanoparticles

We use in situ transmission electron microscopy with automated tracking to study supported gold nanoparticles (NPs) during high-temperature vacuum annealing. \rev{The average mass loss per NP is governed by a flat, nearly size-independent substrate-mediated evaporation profile.} On top of \rev{this mean shrinkage}, individual NPs show significant fluctuations in apparent growth or shrinkage, and NP volume follows a \rev{random-walk-like trajectory. To rationalize both the ensemble-mean behavior and the particle-resolved variability, we develop a self-consistent theory that couples substrate-mediated evaporation to collective 2D Ostwald-type mass exchange through a shared adatom field, described in terms of a renormalized screening length and background concentration. In the experimentally relevant regime, the theory predicts an approximately size-independent mean shrinkage rate and clarifies how net mass loss suppresses classical coarsening.} \rev{Superimposed on this deterministic drift, we quantify stochastic volume trajectories and capture their fluctuation spectrum with a minimal Langevin description consistent with intermittent adatom attachment and detachment events.} In addition, we characterize the lateral diffusive motion of NPs, which is responsible for their coalescence. Altogether, our results highlight that stochasticity is intrinsic at the nanoscale \rev{and that predicting the evolution of supported NPs at early and intermediate times requires a unified framework combining substrate-mediated evaporation, collective mass exchange, and stochastic fluctuations.

cond-mat.mtrl-sci↗

arXiv2026

Hybrid Quantum Temporal Convolutional Networks

Quantum machine learning models for sequential data face scalability challenges with complex multivariate signals. We introduce the Hybrid Quantum Temporal Convolutional Network (HQTCN), which combines classical temporal windowing with a quantum convolutional neural network core. By applying a shared quantum circuit across temporal windows, HQTCN captures long-range dependencies while achieving significant parameter reduction. Evaluated on synthetic NARMA sequences and high-dimensional EEG time-series, HQTCN performs competitively with classical baselines on univariate data and outperforms all baselines on multivariate tasks. The model demonstrates particular strength under data-limited conditions, maintaining high performance with substantially fewer parameters than conventional approaches. These results establish HQTCN as a parameter-efficient approach for multivariate time-series analysis.

cs.LG↗

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

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

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

DIVER-1: Scaling Intracranial EEG Foundation Models for Transferable Representations

Intracranial EEG (iEEG) provides direct, millisecond-scale recordings of human neural activity, but reusable representation learning is difficult because electrode layouts, anatomical coverage, referencing schemes, and recording conditions vary across patients and centers. We introduce DIVER-1, a self-supervised iEEG foundation model for variable-input recordings that combines any-variate electrode-time attention, spatio-temporal resampling, input-conditioned positional embeddings, and multi-domain masked reconstruction without assuming a fixed electrode montage. We pretrain two variants, DIVER-1-0.1s and DIVER-1-1s, on 5,310 hours of ECoG and SEEG spanning 352k channel-hours, roughly 54x the BrainTreeBank-based pretraining volume. We evaluate DIVER-1 on two held-out benchmarks: Neuroprobe for naturalistic cognitive decoding and MAYO for seizure detection. On leakage-aware Neuroprobe, DIVER-1-0.1s outperforms prior evaluated iEEG foundation models despite using no BrainTreeBank recordings, the corpus underlying Neuroprobe, during pretraining; it also exceeds the linear spectrogram decoder in mean AUROC and remains competitive with stronger nonlinear baselines, a level prior evaluated iEEG foundation models did not reach. DIVER-1-1s also achieves the top AUROC on MAYO seizure detection. Finally, we conduct, to our knowledge, the first controlled compute-aware scaling study for self-supervised iEEG pretraining, sweeping data scale, subject count, training duration, and model size up to 1.8B parameters. Our results indicate a data-constrained regime: expanding unique recordings and training sufficiently long are more reliable scaling axes than increasing parameter count alone. Code is available at link.

cs.LG↗

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↗