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Yuankai Huo

Publications and source records attributed to Yuankai Huo.

At least 19 recordsLinked to original sources
arXiv2026

From Cross-Section to Cross-Omics: Conditional Cell Nucleus Image Editing in Spatial Transcriptomics

Spatial transcriptomics (ST) platforms simultaneously measure gene expression and capture cell nucleus images at single-cell resolution. A fundamental property of tissue preparation introduces a confounding relationship between the two measurement modalities: sectioning a three-dimensional tissue into a thin slice produces a two-dimensional cross-section whose area depends on the cutting angle. Larger cross-sections expose more cytoplasm, yielding higher mRNA counts, while pathomics features such as nuclear area are measured directly from the same 2D boundary. This sectioning geometry creates an apparent correlation between gene expression and pathomics that reflects the measurement process rather than independent biology. Existing gene-to-image methods generate cell images from gene features but do not support condition-driven editing of existing images across both omics layers. We apply the Manifold-Aware Diffusion (MAD) framework to this dual-omics editing setting, enabling targeted modification of one feature group while preserving the other. Evaluated on podocyte cells from CosMx SMI kidney tissue, MAD achieves MAE=0.6636 and FID=25.19 for pathomics editing, outperforming all compared baselines. A controlled simulation study further confirms that the VAE component in MAD better preserves cross-group independence than CCDM (MAD without VAE).

cs.AI↗
arXiv2026

STRATA: Reinforcement-driven Active Sampling with Tri-paradigm Adaptation for Efficient 3D Spatial Transcriptomics

Spatial transcriptomics (ST) enables joint characterization of tissue morphology and gene expression. However, 3D volumetric ST acquisition remains expensive. AI-driven methods offer a low-cost alternative but remain limited in accuracy, while recent 2D section-wise ST acquisition still rely on dense grid sampling, resulting in redundant measurements and undersampling of biologically informative regions. To bridge the gap, we propose STRATA, a reinforcement-driven active sampling framework with tri-paradigm adaptation for reconstructing dense 3D transcriptomic maps from sparse voxel-wise ST acquisition. STRATA constructs a 3D graph integrating H&E morphology with single-cell priors and employs a reinforcement learning agent to estimate morphological sparsity and transcriptomic informativeness, enabling budget-aware selection of informative spots. Given these sparse measurements, an adaptive tri-paradigm predictor combines retrieval, regression, and cross-layer imputation through lightweight fusion, dynamically weighting their contributions. Experiments across datasets demonstrate improved sampling efficiency and accuracy, particularly under low-budget settings. Code is available at https://github.com/Junchao-Zhu/STRATA.

cs.CV↗
arXiv2026

MASC: Metal-Aware Sampling and Correction via Reinforcement Learning for Accelerated MRI

Metal implants in MRI cause severe artifacts that degrade image quality and hinder clinical diagnosis. Traditional approaches address metal artifact reduction (MAR) and accelerated MRI acquisition as separate problems. We propose MASC, a unified reinforcement learning framework that jointly optimizes metal-aware k-space sampling and artifact correction for accelerated MRI. To enable supervised training, we construct a paired MRI dataset using physics-based simulation, generating k-space data and reconstructions for phantoms with and without metal implants. This paired dataset provides simulated 3D MRI scans with and without metal implants, where each metal-corrupted sample has an exactly matched clean reference, enabling direct supervision for both artifact reduction and acquisition policy learning. We formulate active MRI acquisition as a sequential decision-making problem, where an artifact-aware Proximal Policy Optimization (PPO) agent learns to select k-space phase-encoding lines under a limited acquisition budget. The agent operates on undersampled reconstructions processed through a U-Net-based MAR network, learning patterns that maximize reconstruction quality. We further propose an end-to-end training scheme where the acquisition policy learns to select k-space lines that best support artifact removal while the MAR network simultaneously adapts to the resulting undersampling patterns. Experiments demonstrate that MASC's learned policies outperform conventional sampling strategies, and end-to-end training improves performance compared to using a frozen pre-trained MAR network, validating the benefit of joint optimization. Cross-dataset experiments on FastMRI with physics-based artifact simulation further confirm generalization to realistic clinical MRI data. The code and models of MASC have been made publicly available: https://github.com/hrlblab/masc

cs.CV↗
arXiv2026

PathLang: A Language-Centered Benchmark for Vision-Language Models in Computational Pathology

Pathology vision-language models (VLMs) have shown strong visual perception ability, but their robustness in the language domain remains poorly characterized. Existing pathology VLM benchmarks largely rely on canonical closed-set prompts or perturb only generic templates, treating language as a fixed evaluation component rather than a variable axis of model behavior. In clinical practice, however, diagnostic language varies across reports, institutions, and candidate diagnoses. We introduce PathLang, a language-centered and clinically grounded zero-shot benchmark. PathLang holds the underlying slides, ground-truth labels, and image-text evaluation direction fixed while systematically varying only the diagnostic language, so that performance differences reflect how a diagnosis is phrased rather than what is imaged. The language variation follows how pathologists actually rephrase diagnoses (terminology, specificity, and reporting style), and all prompts and candidate pools are validated by six board-certified pathologists. PathLang covers four task families: (1) zero-shot classification with image-text alignment analysis, (2) cross-modal retrieval, (3) paraphrase robustness, including semantic-equivalence paraphrases, length and reporting-style variation, and prompt ensembling, and (4) open-vocabulary diagnosis retrieval over four candidate pools with distinct forms of semantic competition. Across nine VLMs and five public datasets spanning four organs, we find that performance is highly sensitive to clinically equivalent paraphrases, varies substantially across forms of semantic competition, and that image-text alignment quality does not necessarily translate into inter-class separability. We release the prompt corpus, candidate pools, pre-computed text embeddings, and evaluation code at https://anonymous.4open.science/r/PathLang.

cs.CV↗
arXiv2026

Comprehensive Evaluation and Fine-Tuning of Foundational Cell Nuclei Segmentation Models in Renal Pathology

Accurate nuclei instance segmentation is essential for quantitative renal pathology, yet general-purpose models often struggle with low contrast, dense nuclei, complex morphology, and strong background staining. In this work, we extended a human-in-the-loop framework by combining 5,901 foundation-model-generated pseudo-labels from well-segmented cases (Easy), 860 newly expert-annotated unresolved challenging cases (Medium), and 198 expert-annotated consensus failure cases (Hard). These annotations, spanning different levels of segmentation difficulty, enabled the systematic evaluation of seven single-source and mixed-source fine-tuning strategies across nine cell segmentation model configurations. Fine-tuning improved all models, with Medium data included in seven of the nine best-performing strategies. LSP-DETR achieved the highest F1 score of 0.8725 with Hard-only fine-tuning, while StarDist showed the largest improvement, increasing from 0.7380 to 0.8332 with Medium-only fine-tuning. These findings show that annotations spanning multiple difficulty levels support effective model adaptation, although the optimal annotation composition remains model dependent.

cs.CV↗
arXiv2026

OpenMASC: An Open-Source Pipeline for Cross-Trajectory Metal-Aware Sampling and Correction in Accelerated MRI

Metal implants corrupt MRI measurements throughout $k$-space, yet existing accelerated MRI methods assume clean data and most metal artifact reduction approaches assume fully sampled acquisitions. No public dataset provides paired $k$-space and images with and without metal for the same anatomy, and no framework jointly addresses artifact-aware acquisition and reconstruction across sampling trajectories. We present OpenMASC, an open-source pipeline covering the full workflow from data generation to deployment. A physics-based data generation module converts public CT volumes into paired clean and metal-corrupted MRI data in both Cartesian and radial formats. MA-VarNet, an unrolled reconstruction network with a per-cascade DC Rectifier, corrects artifacts that data-consistency steps reintroduce from corrupted measurements. A reinforcement learning agent actively selects $k$-space readouts and co-trains with the reconstruction network through a decoupled three-stage procedure. The framework is trajectory-agnostic except for the data-consistency operator, supporting both Cartesian and radial acquisition without architectural changes. Experiments on two datasets at $4\times$ and $8\times$ acceleration demonstrate consistent improvements over conventional and learned baselines on both trajectories.

cs.CV↗
arXiv2026

Benchmarking Active Spot Selection for Cost-Efficient Spatial Transcriptomics

Spatial transcriptomics (ST) measures gene expression in tissue context, but dense capture grids can be costly and may repeatedly sample morphologically similar regions. Most active learning strategies were developed for categorical labels and independent samples. We conduct a retrospective pool-based benchmark of active learning versus uniform Random sampling for ST, where expression vectors are high-dimensional and continuous and candidates are spatially correlated. Using two fully profiled public ST cohorts, we mask candidate expression vectors and simulate multi-round selection with uncertainty-based Monte Carlo dropout (MC-dropout) and temporal output discrepancy (TOD), and diversity-based CoreSet and TypiClust-inspired selection. We compare 160 completed configurations at 5%, 10%, 30%, and 50% of the fold-wide training spot pool under patient-level cross-validation, with a separate full-label reference. Within each budget, strategies share the selection schedule, morphology-to-expression predictor, and optimization protocol. We assess mean per-gene within-slide Pearson correlation coefficient (PCC), expression-cluster agreement, and Moran's I fidelity. On HER2-positive breast cancer, pooled mean PCC differences from Random across the four active strategies were -0.0176, -0.0117, +0.0056, and +0.0057 at 5%, 10%, 30%, and 50%, respectively. On cutaneous squamous cell carcinoma (cSCC), three strategies were below Random at 5%, and all four were below Random at 10%. On HER2-positive breast cancer, CoreSet and MC-dropout had lower PCC but higher expression-cluster agreement than Random at the two smallest budgets; this pattern did not reproduce on cSCC. Under the reported fixed training horizons, the evaluated active strategies do not consistently improve on Random at small budgets, and rankings depend on the evaluation measure.

cs.CV↗
arXiv2026

PARAGraph: Pathology-Anatomy-Aware Hierarchical Graph for Diabetic Retinopathy Grading

Diabetic retinopathy (DR) remains a leading cause of vision loss among working-age adults worldwide, making reliable severity grading clinically important. Despite strong performance, most deep models formulate DR grading as image-level classification and do not explicitly model clinically grounded evidence, such as lesion types and spatial relations. In this paper, we propose PARAGraph, a Pathology-Anatomy-Aware Hierarchical Graph framework for DR grading. PARAGraph represents each image as a three-level hierarchical graph with lesion-level nodes, intermediate category and region nodes, and global anatomical and semantic nodes. To incorporate medical priors into nodes, we construct an optic disc-fovea-anchored coordinate frame that provides a scale- and rotation-normalized retinal reference system. Within this frame, lesion nodes are encoded with category, normalized area, and anatomical coordinates. To mitigate noisy lesion segmentation, PARAGraph uses a dual-fusion strategy that introduces global visual context into a graph semantic node and a decision-level prediction branch, improving robustness when lesion evidence is unreliable. Extensive experiments on Messidor-2, APTOS, and DDR show that PARAGraph achieves consistent DR grading performance over state-of-the-art methods. Interpretability and robustness analyses further demonstrate that its predictions are clinically grounded, closely associated with lesion evidence and robust to lesion segmentation noise.

cs.CV↗
arXiv2026

SAGEAgent: A Self-Evolving Agent for Cost-Aware Modality Acquisition in Multimodal Survival Prediction

Does every cancer patient truly need a complete diagnostic workup for accurate survival prediction? In multimodal clinical oncology, diagnostic modalities follow a clinically mandated order of escalating burden -- from demographics collected at intake to genomic profiling requiring specialized tissue analysis. Current multimodal survival methods either assume all modalities are available or passively handle missing data, but none actively reason about whether acquiring the next modality is justified for a given patient along this ordered workflow. We formulate this as a sequential decision problem and propose SAGEAgent (Sequential Acquisition Guided by Experience), a self-evolving LLM-based clinical agent that decides which diagnostic modalities to acquire for each patient, balancing predictive accuracy against clinical invasiveness. SAGEAgent reasons about each patient's evolving diagnostic state through clinical tools that translate numerical predictions into text, an episodic memory that retrieves similar past cases, and a semantic memory that accumulates reusable decision patterns from experience. Experiments on a glioma cohort combining TCGA-LGG, TCGA-GBM, and BraTS with four diagnostic modalities demonstrate that SAGEAgent achieves competitive survival prediction accuracy while reducing average acquisition burden by 55%.

cs.AI↗
arXiv2026

Fast Electromagnetic and RF Circuit Co-Simulation for Passive Resonator Field Calculation and Optimization in MRI

Passive resonators have been widely used in MRI to manipulate RF field distributions. However, optimizing these structures using full-wave electromagnetic simulations is computationally prohibitive, particularly for large passive resonator arrays with many degrees of freedom. This work presents a co-simulation framework tailored specifically for the analysis and optimization of passive resonators. The framework performs a single full-wave electromagnetic simulation in which the resonator's lumped components are replaced by ports, followed by circuit-level computations to evaluate arbitrary capacitor and inductor configurations. This allows integration with a genetic algorithm to rapidly optimize resonator parameters and enhance the B1 field in a targeted region of interest (ROI). We validated the method in three scenarios: (1) a single-loop passive resonator on a spherical phantom, (2) a two-loop array on a cylindrical phantom, and (3) a two-loop array on a human head model. In all cases, the co-simulation results showed excellent agreement with full-wave simulations, with relative errors below 1%. The genetic-algorithm-driven optimization, involving tens of thousands of capacitor combinations, completed in under 5 minutes, whereas equivalent full-wave EM sweeps would require an impractically long computation time. This work extends co-simulation methodology to passive resonator design for first time, enabling the fast, accurate, and scalable optimization. The approach significantly reduces computational burden while preserving full-wave accuracy, making it a powerful tool for passive RF structure development in MRI.

physics.med-ph↗
arXiv2026

MORI-Seg: Learning Morphological Geometry for Instance Segmentation without Instance Annotations

Instance-level quantification of kidney functional units is essential for morphometric analysis, yet most publicly available pathology datasets provide only semantic segmentation annotations, where adjacent structures of the same class are merged into single regions. This prevents reliable instance-level analysis and limits downstream quantitative studies. Existing heuristic post-processing methods often yield suboptimal instance separation, particularly in crowded and adherent regions, while deep learning-based instance segmentation approaches typically require intensive instance-level annotations that are costly and labor-intensive to obtain. We propose MORI-Seg, a deep learning framework that enables instance segmentation without requiring instance-level annotations. Instead of heuristic splitting or instance supervision, MORI-Seg learns morphology-aware geometric representations directly from semantic masks by jointly modeling object-centric distance fields and boundary-band representations to encode interior structure and contact interfaces. A class-conditioned feature disentanglement module further promotes intra-instance coherence and inter-instance separation. Under semantic-only supervision, MORI-Seg decomposes connected semantic regions into distinct instance masks in an end-to-end manner. Experiments demonstrate improved instance separation accuracy and more reliable morphometric quantification compared with classical post-processing pipelines and representative semantic-to-instance learning approaches. The official implementation is publicly available at https://github.com/ddrrnn123/MORI-Seg.

cs.CV↗
arXiv2026

DUET: Dual-Paradigm Adaptive Expert Triage with Single-cell Inductive Prior for Spatial Transcriptomics Prediction

Inferring spatially resolved gene expression from histology images offers a cost-effective complement to spatial transcriptomics (ST). However, existing methods reduce this task to a simple morphology-to-expression mapping, where visual similarity does not guarantee molecular consistency. Meanwhile, single-cell data has amassed rich resources far surpassing the scale of ST data, yet it remains underexplored in vision-omics modeling. Furthermore, current approaches commit to a monolithic paradigm with bottlenecks, unable to balance expressive flexibility with biological fidelity. To bridge these gaps, we propose DUET, a novel dual-paradigm framework that synergizes parametric prediction and memory-based retrieval under cellular inductive priors. DUET implements a parallel regression-retrieval paradigm, adaptively reconciling the outputs of its complementary pathways. To mitigate aleatoric vision ambiguity, we incorporate large-scale single-cell references to impose molecular states as biological constraints for faithful learning. Building upon structural refinement, we further design a lightweight adapter to dynamically assign branch preference across spatial contexts to achieve optimal performance. Extensive experiments on three public datasets across varied gene scales demonstrate that DUET achieves SOTA performance, with consistent gains contributed by each proposed component. Code is available at https://github.com/Junchao-Zhu/DUET

cs.CV↗
arXiv2026

Knowledge Transfer Scaling Laws for 3D Medical Imaging

Vision foundation models are increasingly moving beyond 2D to volumetric domains such as 3D medical imaging, where unified pretraining across different imaging modalities (i.e. CT, MRI, and PET) could provide foundational models for diverse clinical tasks. However, training such models requires mixing heterogeneous imaging domains, and current mixture strategies remain largely heuristic. In this work, we observe that different medical imaging domains scale at variable rates during pretraining, and knowledge transfer between domains is strongly asymmetric: training on one domain can substantially improve another, but the reverse may be much weaker. Interestingly, both MAE reconstruction loss and cross-domain transfer follow predictable power-law trends with domain-specific behaviors. Motivated by these findings, we formulate data allocation as a scaling-law optimization problem. The derived allocations reveal an interpretable hub-and-island structure: highly transferable domains emerge as hubs that benefit many others and deserve strategic allocation, while isolated domains act as islands requiring direct investment. Empirically, transfer-aware allocation outperforms data-proportional sampling by up to 58% and generalizes well to unseen budgets with r=0.989. Downstream validation on disease classification and organ/lesion segmentation further confirms that the derived transfer-aware mixtures provide stronger pretrained representations for clinical 3D medical imaging tasks.

cs.CV↗
arXiv2026

An Artifact-based Agent Framework for Adaptive and Reproducible Medical Image Processing

Medical imaging research is increasingly shifting from controlled benchmark evaluation toward real-world clinical deployment. In such settings, applying analytical methods extends beyond model design to require dataset-aware workflow configuration and provenance tracking. Two requirements therefore become central: \textbf{adaptability}, the ability to configure workflows according to dataset-specific conditions and evolving analytical goals; and \textbf{reproducibility}, the guarantee that all transformations and decisions are explicitly recorded and re-executable. Here, we present an artifact-based agent framework that introduces a semantic layer to augment medical image processing. The framework formalizes intermediate and final outputs through an artifact contract, enabling structured interrogation of workflow state and goal-conditioned assembly of configurations from a modular rule library. Execution is delegated to a workflow executor to preserve deterministic computational graph construction and provenance tracking, while the agent operates locally to comply with most privacy constraints. We evaluate the framework on real-world clinical CT and MRI cohorts, demonstrating adaptive configuration synthesis, deterministic reproducibility across repeated executions, and artifact-grounded semantic querying. These results show that adaptive workflow configuration can be achieved without compromising reproducibility in heterogeneous clinical environments.

cs.AI↗
arXiv2026

An Interpretable Vision Transformer as a Fingerprint-Based Diagnostic Aid for Kabuki and Wiedemann-Steiner Syndromes

Kabuki syndrome (KS) and Wiedemann-Steiner syndrome (WSS) are rare but distinct developmental disorders that share overlapping clinical features, including neurodevelopmental delay, growth restriction, and persistent fetal fingertip pads. While genetic testing remains the diagnostic gold standard, many individuals with KS or WSS remain undiagnosed due to barriers in access to both genetic testing and expertise. Dermatoglyphic anomalies, despite being established hallmarks of several genetic syndromes, remain an underutilized diagnostic signal in the era of molecular testing. This study presents a vision transformer-based deep learning model that leverages fingerprint images to distinguish individuals with KS and WSS from unaffected controls and from one another. We evaluate model performance across three binary classification tasks. Across the three classification tasks, the model achieved AUC scores of 0.80 (control vs. KS), 0.73 (control vs. WSS), and 0.85 (KS vs. WSS), with corresponding F1 scores of 0.71, 0.72, and 0.83, respectively. Beyond classification, we apply attention-based visualizations to identify fingerprint regions most salient to model predictions, enhancing interpretability. Together, these findings suggest the presence of syndrome-specific fingerprint features, demonstrating the feasibility of a fingerprint-based artificial intelligence (AI) tool as a noninvasive, interpretable, and accessible future diagnostic aid for the early diagnosis of underdiagnosed genetic syndromes.

cs.CV↗
arXiv2026

Explainable Pathomics Feature Visualization via Correlation-aware Conditional Feature Editing

Pathomics is a recent approach that offers rich quantitative features beyond what black-box deep learning can provide, supporting more reproducible and explainable biomarkers in digital pathology. However, many derived features (e.g., "second-order moment") remain difficult to interpret, especially across different clinical contexts, which limits their practical adoption. Conditional diffusion models show promise for explainability through feature editing, but they typically assume feature independence**--**an assumption violated by intrinsically correlated pathomics features. Consequently, editing one feature while fixing others can push the model off the biological manifold and produce unrealistic artifacts. To address this, we propose a Manifold-Aware Diffusion (MAD) framework for controllable and biologically plausible cell nuclei editing. Unlike existing approaches, our method regularizes feature trajectories within a disentangled latent space learned by a variational auto-encoder (VAE). This ensures that manipulating a target feature automatically adjusts correlated attributes to remain within the learned distribution of real cells. These optimized features then guide a conditional diffusion model to synthesize high-fidelity images. Experiments demonstrate that our approach is able to navigate the manifold of pathomics features when editing those features. The proposed method outperforms baseline methods in conditional feature editing while preserving structural coherence.

cs.CV↗
arXiv2026

Spatially-Adaptive Gradient Re-parameterization for 3D Large Kernel Optimization

Large kernel convolutions offer a scalable alternative to vision transformers for high-resolution 3D volumetric analysis, yet naively increasing kernel size often leads to optimization instability. Motivated by the spatial bias inherent in effective receptive fields (ERFs), we theoretically demonstrate that structurally re-parameterized blocks induce spatially varying learning rates that are crucial for convergence. Leveraging this insight, we introduce Rep3D, a framework that employs a lightweight modulation network to generate receptive-biased scaling masks, adaptively re-weighting kernel updates within a plain encoder architecture. This approach unifies spatial inductive bias with optimization-aware learning, avoiding the complexity of multi-branch designs while ensuring robust local-to-global convergence. Extensive evaluations on five 3D segmentation benchmarks demonstrate that Rep3D consistently outperforms state-of-the-art transformer and fixed-prior baselines. The source code is publicly available at https://github.com/leeh43/Rep3D.

cs.CV↗
arXiv2026

SCR2-ST: Combine Single Cell with Spatial Transcriptomics for Efficient Active Sampling via Reinforcement Learning

Spatial transcriptomics (ST) is an emerging technology that enables researchers to investigate the molecular relationships underlying tissue morphology. However, acquiring ST data remains prohibitively expensive, and traditional fixed-grid sampling strategies lead to redundant measurements of morphologically similar or biologically uninformative regions, thus resulting in scarce data that constrain current methods. The well-established single-cell sequencing field, however, could provide rich biological data as an effective auxiliary source to mitigate this limitation. To bridge these gaps, we introduce SCR2-ST, a unified framework that leverages single-cell prior knowledge to guide efficient data acquisition and accurate expression prediction. SCR2-ST integrates a single-cell guided reinforcement learning-based (SCRL) active sampling and a hybrid regression-retrieval prediction network SCR2Net. SCRL combines single-cell foundation model embeddings with spatial density information to construct biologically grounded reward signals, enabling selective acquisition of informative tissue regions under constrained sequencing budgets. SCR2Net then leverages the actively sampled data through a hybrid architecture combining regression-based modeling with retrieval-augmented inference, where a majority cell-type filtering mechanism suppresses noisy matches and retrieved expression profiles serve as soft labels for auxiliary supervision. We evaluated SCR2-ST on three public ST datasets, demonstrating SOTA performance in both sampling efficiency and prediction accuracy, particularly under low-budget scenarios. Code is publicly available at: https://github.com/hrlblab/SCR2ST

cs.CV↗