arXiv subjects

Yonggang Shi

Publications and source records attributed to Yonggang Shi.

10 recordsLinked to original sources

arXiv2026

M$^2$PFN: End-to-End Disentangled Alignment for Generalizable Multimodal In-Context Learning in Alzheimer's Disease

While various multimodal methods combining imaging and tabular data for Alzheimer's disease (AD) diagnosis were proposed, they are often limited in generalization across cohorts. In-context learning (ICL) has demonstrated excellent generalization performances and high flexibility in foundational tabular models such as TabPFN. To extend TabPFN's ICL to multimodal AD analysis, the main obstacle is that TabPFN is meta-trained on synthetic tabular priors that do not naturally match the statistical structure of image-derived features. We propose M$^2$PFN, an end-to-end framework that turns this tabular foundation model into a multimodal AD predictor. M$^2$PFN (i) performs differentiable inference through TabPFN's transformer, back-propagating task gradients into 3D-MRI and tabular encoders; (ii) aligns the two modalities into a shared subspace, via disentanglement and a contrastive objective, matched to the ICL engine's prior; and (iii) folds in a frozen tabular-only prediction through a learnable gated shortcut. Because the ICL engine stays frozen, its in-context mechanism is preserved for test-time generalization, while end-to-end training shapes the encoders into features it can exploit. On ADNI ($n=2240$, three-class CN/MCI/AD), M$^2$PFN attains $65.55\%$ macro-F1 and $82.21\%$ macro-AUC, surpassing a comprehensive set of unimodal and multimodal baselines. By swapping only the head for a TabPFN regressor, the same architecture regresses baseline MMSE on a $1250$-subject sub-cohort to test MAE $1.743$, outperforming every multimodal baseline. On two external cohorts (OASIS-3 and SCAN) with no retraining, M$^2$PFN achieves the best AUC and the lowest MMSE MAE across all baselines, and transfers even when the cognitive instrument changes.

cs.CV↗

arXiv2026

When Is a Conformal Guarantee Fair? Auditing Silent Subgroup Under-Coverage in Alzheimer's Disease Longitudinal Prediction

Longitudinal prediction of Alzheimer's disease biomarkers increasingly informs clinical decisions, and a forecast is only useful if it also reports how much to trust it. Conformal prediction supplies this by wrapping any forecaster in a prediction band with a finite-sample coverage guarantee under exchangeability. However, standard population-level conformal prediction guarantees only marginal coverage and may mask substantial under-coverage within clinically important subgroups. We introduce a general mechanism-driven framework for auditing and repairing such subgroup under-coverage. Across two cohorts (ADNI, OASIS-3), two base forecasters, and nine attributes spanning genetic risk, demographics, and clinical severity, we find that population-level bands under-cover high-risk subgroups in 57 of 68 audited combinations, despite achieving nominal marginal coverage. We trace these failures to two mechanisms: (A) \emph{rarity}, where a group-conditional band calibrated on only $n$ patients covers at most $k/(n+1)$; and (B) \emph{tail-heaviness}, where a population-wide band is too narrow for a heavy-tailed subgroup and additional data cannot close the gap. Under-coverage falls disproportionately on patients with high genetic risk and disease severity (6.1 pp mean deficit, 95\% CI [3.3, 8.9]), while demographic groups remain at the target level on average (0.0 pp, CI [$-1.9$, 1.7]). We pair each mechanism with a corresponding conformal correction: cross-conformal pooling for rarity, per-subgroup calibration for tail-heaviness, and a coverage-safe marginal floor when both arise. Together, these corrections restore target coverage for nearly every high-risk subgroup across both cohorts and forecasters.

stat.ME↗

arXiv2026

Feynman Kac Reweighted Schrödinger Bridge Matching for Surface-Based Tau PET Harmonization

Tau positron emission tomography (PET) is widely used for the in vivo characterization of disease stage and progression in Alzheimer's disease (AD). With the adoption of multiple tau PET tracers including AV-1451, PI-2620, MK-6240 with different binding behaviors in various large-scale studies, there is a great need of effective harmonization methods to enable the cross-tracer integration of tau PET datasets. While previous methods such as CenTauR were proposed to standardize scalar tau PET measures, they are limited in accounting for the heterogeneity of tau pathology. In this work, we propose Feynman-Kac Reweighted Schrödinger Bridge Matching (FKRSBM), a surface-based framework for cross-tracer tau PET harmonization. FKRSBM learns a direct stochastic transport between tracer domains using Schrödinger Bridge matching, avoiding the Gaussian-prior routing used in diffusion-based translation. To promote biologically consistent transport, FKRSBM introduces an endpoint penalty favoring bridge pairings with matched tau-pathology status and implements it through a Feynman-Kac reweighted endpoint proposal. To preserve cortical organization, FKRSBM uses a spherical convolutional network for vertex-level harmonization on cortical surface meshes. In our experiments, we demonstrate our method by harmonizing Tau PET images acquired with the AV-1451 (n=1480) and PI-2620 (n=2458) tracers from two large-scale datasets. Compared to previous methods including ComBat, CycleGAN, Diffusion Model(DF), and unregularized Schrödinger Bridge Model(DSBM), the proposed FKRSBM method outperforms these baselines in subgroup-level alignment, tau-positivity consistency, and diagnostic classification while preserving subject-specific cortical topography of tau pathology. The code is available at: https://github.com/jianweizhang17/FKRSBM.

eess.IV↗

arXiv2026

A Surface-based Multimodal Framework for Multitask Analysis in Alzheimer's Disease

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder, and longitudinal analysis is critical for early detection and effective intervention. Developing models capable of multimodal and multitask analysis enables a more comprehensive understanding of AD progression. However, multimodal learning remains challenged by cross-modal misalignment, non-Euclidean surface representations of cortical data, and limited data availability in small-sample clinical settings. In this work, we propose an augmented spherical data-driven multimodal framework for multitask AD analysis. A spherical diffusion model is first trained to generate paired cortical thickness and Tau PET Standardized Uptake Value Ratio (SUVR) data, enabling structurally consistent multimodal augmentation on cortical surfaces while preserving anatomical correspondence. The augmented data are subsequently used to train a contrastive learning model that learns aligned and fused cross-modal representations. This design strengthens multimodal integration and encourages more balanced representation learning. The learned imaging features are further integrated with tabular cognitive assessments and demographic variables, and processed using an in-context learning model to perform both classification and regression tasks without task-specific fine-tuning. Experiments on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset ($n = 802$) demonstrate consistent performance improvements across five diagnostic and longitudinal tasks, outperforming six baseline models.

eess.IV↗

arXiv2026

PromptDx: Differentiable Prompt Tuning for Multimodal In-Context Alzheimer's Diagnosis

Deep learning models in medical imaging typically operate as parametric memory, diagnosing patients by recalling fixed knowledge learned during training. This contrasts sharply with clinical practice, where physicians employ analogical reasoning to diagnose new cases by referencing similar records from past exemplars. While In-Context Learning (ICL) frameworks such as Tabular Prior-Fitted Networks (TabPFN) offer a promising diagnosis-by-reference paradigm, they are designed with tabular-specific inductive priors and rely on non-differentiable preprocessing pipelines, leading to manifold mismatch and gradient fracture when applied to heterogeneous multimodal data. To address these limitations, we propose PromptDx, a novel diagnosis-by-reference framework that leverages a pre-trained TabPFN as an ICL engine while enabling seamless integration with multimodal representations. Our core contribution is a Differentiable Prompt Tuning (DPT) mechanism that aligns a Masked Multimodal Modeling module with the pre-trained ICL engine. By training a lightweight adapter as a differentiable surrogate for the engine's non-differentiable preprocessors, we enable an end-to-end optimization of multimodal prompts within the ICL paradigm. We validate our method on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset using 3D MRI and tabular biomarkers. Experiments demonstrate that our approach outperforms traditional parametric baselines. Notably, our method achieves superior performance using only 1% context samples compared to 30% in standard ICL, demonstrating exceptional manifold condensation ability. We further validate the generalizability of our DPT framework across six tabular datasets with diverse scales. Overall, our method offers a more data-efficient and clinically aligned paradigm for Alzheimer's Disease diagnosis.

cs.CV↗

arXiv2026

NeuroAgent: LLM Agents for Multimodal Neuroimaging Analysis and Research

Multimodal neuroimaging analysis often involves complex, modality-specific preprocessing workflows that require careful configuration, quality control, and coordination across heterogeneous toolchains. Beyond preprocessing, downstream statistical analysis and disease classification commonly require task-specific code, evaluation protocols, and data-format conventions, creating additional barriers between raw acquisitions and reproducible scientific analysis. We present NeuroAgent, an LLM-driven agentic framework that automates key preprocessing and analysis steps for heterogeneous neuroimaging data, including sMRI, fMRI, dMRI, and PET, and supports interactive downstream analysis through natural-language queries. NeuroAgent employs a hierarchical multi-agent architecture with a feedback-driven Generate-Execute-Validate engine: agents autonomously generate executable preprocessing code, detect and recover from runtime errors, and validate output integrity. We evaluate the system on 1,470 subjects pooled across all ADNI phases (CN=1,000, AD=470), where all subjects have sMRI and tabular data, with subsets also having Tau-PET (n=469), fMRI (n=278), and DTI ($n=620$). Pipeline ablation studies across multiple LLM backends show that capable models reach up to 100% intent-parsing accuracy, with the strongest backend (Qwen3.5-27B) reaching 84.8% end-to-end preprocessing step correctness. Automated recovery limits manual intervention to edge cases where human review is required via the Human-In-The-Loop interface. For Alzheimer's Disease classification using automatically preprocessed multimodal data, our agent ensemble achieves an AUC of 0.9518 with four modalities, outperforming all single-modality baselines. These results show that NeuroAgent can reduce the manual effort required for neuroimaging preprocessing and enable end-to-end automated analysis pipelines for neuroimaging research.

cs.AI↗

arXiv2025

Tau Anomaly Detection in PET Imaging via Bilateral-Guided Deterministic Diffusion Model

The emergence of tau PET imaging over the last decade has enabled Alzheimer's disease (AD) researchers to examine tau pathology in vivo and more effectively characterize the disease trajectories of AD. Current tau PET analysis methods, however, typically perform inferences on large cortical ROIs and are limited in the detection of localized tau pathology that varies across subjects. In this work, we propose a novel bilateral-guided deterministic diffusion sampling method to perform anomaly detection from tau PET imaging data. By including individualized brain structure and cognitively normal (CN) template conditions, our model computes a voxel-level anomaly map based on the deterministically sampled pseudo-healthy reconstruction. We train our model on ADNI CN subjects (n=380) and evaluate anomaly localization performance on the left MCI/AD subjects (n=154) and the preclinical subjects of the A4 clinical trial (n=447). We further train a CNN classifier on the derived 3D anomaly maps from ADNI, including CN and MCI/AD, to classify subjects into two groups and test classification performance on A4. We demonstrate that our method outperforms baselines in anomaly localization. Additionally, we show that our method can successfully group preclinical subjects with significantly different cognitive functions, highlighting the potential of our approach for application in preclinical screening tests. The code will be publicly available.

eess.IV↗

arXiv2024

ssProp: Energy-Efficient Training for Convolutional Neural Networks with Scheduled Sparse Back Propagation

Recently, deep learning has made remarkable strides, especially with generative modeling, such as large language models and probabilistic diffusion models. However, training these models often involves significant computational resources, requiring billions of petaFLOPs. This high resource consumption results in substantial energy usage and a large carbon footprint, raising critical environmental concerns. Back-propagation (BP) is a major source of computational expense during training deep learning models. To advance research on energy-efficient training and allow for sparse learning on any machine and device, we propose a general, energy-efficient convolution module that can be seamlessly integrated into any deep learning architecture. Specifically, we introduce channel-wise sparsity with additional gradient selection schedulers during backward based on the assumption that BP is often dense and inefficient, which can lead to over-fitting and high computational consumption. Our experiments demonstrate that our approach reduces 40\% computations while potentially improving model performance, validated on image classification and generation tasks. This reduction can lead to significant energy savings and a lower carbon footprint during the research and development phases of large-scale AI systems. Additionally, our method mitigates over-fitting in a manner distinct from Dropout, allowing it to be combined with Dropout to further enhance model performance and reduce computational resource usage. Extensive experiments validate that our method generalizes to a variety of datasets and tasks and is compatible with a wide range of deep learning architectures and modules. Code is publicly available at https://github.com/lujiazho/ssProp.

cs.LG↗

arXiv2024

Diffusion Model-based FOD Restoration from High Distortion in dMRI

Fiber orientation distributions (FODs) is a popular model to represent the diffusion MRI (dMRI) data. However, imaging artifacts such as susceptibility-induced distortion in dMRI can cause signal loss and lead to the corrupted reconstruction of FODs, which prohibits successful fiber tracking and connectivity analysis in affected brain regions such as the brain stem. Generative models, such as the diffusion models, have been successfully applied in various image restoration tasks. However, their application on FOD images poses unique challenges since FODs are 4-dimensional data represented by spherical harmonics (SPHARM) with the 4-th dimension exhibiting order-related dependency. In this paper, we propose a novel diffusion model for FOD restoration that can recover the signal loss caused by distortion artifacts. We use volume-order encoding to enhance the ability of the diffusion model to generate individual FOD volumes at all SPHARM orders. Moreover, we add cross-attention features extracted across all SPHARM orders in generating every individual FOD volume to capture the order-related dependency across FOD volumes. We also condition the diffusion model with low-distortion FODs surrounding high-distortion areas to maintain the geometric coherence of the generated FODs. We trained and tested our model using data from the UK Biobank (n = 1315). On a test set with ground truth (n = 43), we demonstrate the high accuracy of the generated FODs in terms of root mean square errors of FOD volumes and angular errors of FOD peaks. We also apply our method to a test set with large distortion in the brain stem area (n = 1172) and demonstrate the efficacy of our method in restoring the FOD integrity and, hence, greatly improving tractography performance in affected brain regions.

eess.IV↗

arXiv2024

Anatomy-Guided Surface Diffusion Model for Alzheimer's Disease Normative Modeling

Normative modeling has emerged as a pivotal approach for characterizing heterogeneity and individual variance in neurodegenerative diseases, notably Alzheimer's disease(AD). One of the challenges of cortical normative modeling is the anatomical structure mismatch due to folding pattern variability. Traditionally, registration is applied to address this issue and recently many studies have utilized deep generative models to generate anatomically align samples for analyzing disease progression; however, these models are predominantly applied to volume-based data, which often falls short in capturing intricate morphological changes on the brain cortex. As an alternative, surface-based analysis has been proven to be more sensitive in disease modeling such as AD, yet, like volume-based data, it also suffers from the mismatch problem. To address these limitations, we proposed a novel generative normative modeling framework by transferring the conditional diffusion generative model to the spherical non-Euclidean domain. Additionally, this approach generates normal feature map distributions by explicitly conditioning on individual anatomical segmentation to ensure better geometrical alignment which helps to reduce anatomical variance between subjects in analysis. We find that our model can generate samples that are better anatomically aligned than registered reference data and through ablation study and normative assessment experiments, the samples are able to better measure individual differences from the normal distribution and increase sensitivity in differentiating cognitively normal (CN), mild cognitive impairment (MCI), and Alzheimer's disease (AD) patients.

eess.IV↗