Calibrating Multi-modal Representations: A Pursuit of Group Robustness without Annotations

Fine-tuning pre-trained vision-language models, like CLIP, has yielded success on diverse downstream tasks. However, several pain points persist for this paradigm: (i) directly tuning entire pre-trained models becomes both time-intensive and computationally costly. Additionally, these tuned models tend to become highly specialized, limiting their practicality for real-world deployment; (ii) recent studies indicate that pre-trained vision-language classifiers may overly depend on spurious features -- patterns that correlate with the target in training data, but are not related to the true labeling function; and (iii) existing studies on mitigating the reliance on spurious features, largely based on the assumption that we can identify such features, does not provide definitive assurance for real-world applications. As a piloting study, this work focuses on exploring mitigating the reliance on spurious features for CLIP without using any group annotation. To this end, we systematically study the existence of spurious correlation on CLIP and CILP+ERM. We first, following recent work on Deep Feature Reweighting (DFR), verify that last-layer retraining can greatly improve group robustness on pretrained CLIP. In view of them, we advocate a lightweight representation calibration method for fine-tuning CLIP, by first generating a calibration set using the pretrained CLIP, and then calibrating representations of samples within this set through contrastive learning, all without the need for group labels. Extensive experiments and in-depth visualizations on several benchmarks validate the effectiveness of our proposals, largely reducing reliance and significantly boosting the model generalization.

Robust automated calcification meshing for biomechanical cardiac digital twins

Calcification has significant influence over cardiovascular diseases and interventions. Detailed characterization of calcification is thus desired for predictive modeling, but calcified heart meshes for physics-driven simulations are still often reconstructed using manual operations. This poses a major bottleneck for large-scale adoption of computational simulations for research or clinical use. To address this, we propose an end-to-end automated meshing algorithm that enables robust incorporation of patient-specific calcification onto a given heart mesh. The algorithm provides a substantial speed-up from several hours of manual meshing to $\sim$1 minute of automated computation, and it solves an important problem that cannot be addressed with recent template registration-based heart meshing techniques. We validated our final calcified heart meshes with extensive simulations, demonstrating our ability to accurately model patient-specific aortic stenosis and Transcatheter Aortic Valve Replacement. Our method may serve as an important tool for accelerating the development and usage of physics-driven simulations for cardiac digital twins.

POUR-Net: A Population-Prior-Aided Over-Under-Representation Network for Low-Count PET Attenuation Map Generation

Low-dose PET offers a valuable means of minimizing radiation exposure in PET imaging. However, the prevalent practice of employing additional CT scans for generating attenuation maps (u-map) for PET attenuation correction significantly elevates radiation doses. To address this concern and further mitigate radiation exposure in low-dose PET exams, we propose POUR-Net - an innovative population-prior-aided over-under-representation network that aims for high-quality attenuation map generation from low-dose PET. First, POUR-Net incorporates an over-under-representation network (OUR-Net) to facilitate efficient feature extraction, encompassing both low-resolution abstracted and fine-detail features, for assisting deep generation on the full-resolution level. Second, complementing OUR-Net, a population prior generation machine (PPGM) utilizing a comprehensive CT-derived u-map dataset, provides additional prior information to aid OUR-Net generation. The integration of OUR-Net and PPGM within a cascade framework enables iterative refinement of $\mu$-map generation, resulting in the production of high-quality $\mu$-maps. Experimental results underscore the effectiveness of POUR-Net, showing it as a promising solution for accurate CT-free low-count PET attenuation correction, which also surpasses the performance of previous baseline methods.

Dual-Domain Coarse-to-Fine Progressive Estimation Network for Simultaneous Denoising, Limited-View Reconstruction, and Attenuation Correction of Cardiac SPECT

Single-Photon Emission Computed Tomography (SPECT) is widely applied for the diagnosis of coronary artery diseases. Low-dose (LD) SPECT aims to minimize radiation exposure but leads to increased image noise. Limited-view (LV) SPECT, such as the latest GE MyoSPECT ES system, enables accelerated scanning and reduces hardware expenses but degrades reconstruction accuracy. Additionally, Computed Tomography (CT) is commonly used to derive attenuation maps ($\mu$-maps) for attenuation correction (AC) of cardiac SPECT, but it will introduce additional radiation exposure and SPECT-CT misalignments. Although various methods have been developed to solely focus on LD denoising, LV reconstruction, or CT-free AC in SPECT, the solution for simultaneously addressing these tasks remains challenging and under-explored. Furthermore, it is essential to explore the potential of fusing cross-domain and cross-modality information across these interrelated tasks to further enhance the accuracy of each task. Thus, we propose a Dual-Domain Coarse-to-Fine Progressive Network (DuDoCFNet), a multi-task learning method for simultaneous LD denoising, LV reconstruction, and CT-free $\mu$-map generation of cardiac SPECT. Paired dual-domain networks in DuDoCFNet are cascaded using a multi-layer fusion mechanism for cross-domain and cross-modality feature fusion. Two-stage progressive learning strategies are applied in both projection and image domains to achieve coarse-to-fine estimations of SPECT projections and CT-derived $\mu$-maps. Our experiments demonstrate DuDoCFNet's superior accuracy in estimating projections, generating $\mu$-maps, and AC reconstructions compared to existing single- or multi-task learning methods, under various iterations and LD levels. The source code of this work is available at https://github.com/XiongchaoChen/DuDoCFNet-MultiTask.

Heteroscedastic Uncertainty Estimation for Probabilistic Unsupervised Registration of Noisy Medical Images

This paper proposes a heteroscedastic uncertainty estimation framework for unsupervised medical image registration. Existing methods rely on objectives (e.g. mean-squared error) that assume a uniform noise level across the image, disregarding the heteroscedastic and input-dependent characteristics of noise distribution in real-world medical images. This further introduces noisy gradients due to undesired penalization on outliers, causing unnatural deformation and performance degradation. To mitigate this, we propose an adaptive weighting scheme with a relative $\gamma$-exponentiated signal-to-noise ratio (SNR) for the displacement estimator after modeling the heteroscedastic noise using a separate variance estimator to prevent the model from being driven away by spurious gradients from error residuals, leading to more accurate displacement estimation. To illustrate the versatility and effectiveness of the proposed method, we tested our framework on two representative registration architectures across three medical image datasets. Our proposed framework consistently outperforms other baselines both quantitatively and qualitatively while also providing accurate and sensible uncertainty measures. Paired t-tests show that our improvements in registration accuracy are statistically significant. The code will be publicly available at \url{https://voldemort108x.github.io/hetero_uncertainty/}.

An Adaptive Correspondence Scoring Framework for Unsupervised Image Registration of Medical Images

We propose an adaptive training scheme for unsupervised medical image registration. Existing methods rely on image reconstruction as the primary supervision signal. However, nuisance variables (e.g. noise and covisibility) often cause the loss of correspondence between medical images, violating the Lambertian assumption in physical waves (e.g. ultrasound) and consistent imaging acquisition. As the unsupervised learning scheme relies on intensity constancy to establish correspondence between images for reconstruction, this introduces spurious error residuals that are not modeled by the typical training objective. To mitigate this, we propose an adaptive framework that re-weights the error residuals with a correspondence scoring map during training, preventing the parametric displacement estimator from drifting away due to noisy gradients, which leads to performance degradations. To illustrate the versatility and effectiveness of our method, we tested our framework on three representative registration architectures across three medical image datasets along with other baselines. Our proposed adaptive framework consistently outperforms other methods both quantitatively and qualitatively. Paired t-tests show that our improvements are statistically significant. The code will be publicly available at \url{https://voldemort108x.github.io/AdaCS/}.

Preserved Edge Convolutional Neural Network for Sensitivity Enhancement of Deuterium Metabolic Imaging (DMI)

Purpose: Common to most MRSI techniques, the spatial resolution and the minimal scan duration of Deuterium Metabolic Imaging (DMI) are limited by the achievable SNR. This work presents a deep learning method for sensitivity enhancement of DMI. Methods: A convolutional neural network (CNN) was designed to estimate the 2H-labeled metabolite concentrations from low SNR and distorted DMI FIDs. The CNN was trained with synthetic data that represent a range of SNR levels typically encountered in vivo. The estimation precision was further improved by fine-tuning the CNN with MRI-based edge-preserving regularization for each DMI dataset. The proposed processing method, PReserved Edge ConvolutIonal neural network for Sensitivity Enhanced DMI (PRECISE-DMI), was applied to simulation studies and in vivo experiments to evaluate the anticipated improvements in SNR and investigate the potential for inaccuracies. Results: PRECISE-DMI visually improved the metabolic maps of low SNR datasets, and quantitatively provided higher precision than the standard Fourier reconstruction. Processing of DMI data acquired in rat brain tumor models resulted in more precise determination of 2H-labeled lactate and glutamate + glutamine levels, at increased spatial resolution (from >8 to 2 $\mu$L) or shortened scan time (from 32 to 4 min) compared to standard acquisitions. However, rigorous SD-bias analyses showed that overuse of the edge-preserving regularization can compromise the accuracy of the results. Conclusion: PRECISE-DMI allows a flexible trade-off between enhancing the sensitivity of DMI and minimizing the inaccuracies. With typical settings, the DMI sensitivity can be improved by 3-fold while retaining the capability to detect local signal variations.

Learning Sequential Information in Task-based fMRI for Synthetic Data Augmentation

Insufficiency of training data is a persistent issue in medical image analysis, especially for task-based functional magnetic resonance images (fMRI) with spatio-temporal imaging data acquired using specific cognitive tasks. In this paper, we propose an approach for generating synthetic fMRI sequences that can then be used to create augmented training datasets in downstream learning tasks. To synthesize high-resolution task-specific fMRI, we adapt the $\alpha$-GAN structure, leveraging advantages of both GAN and variational autoencoder models, and propose different alternatives in aggregating temporal information. The synthetic images are evaluated from multiple perspectives including visualizations and an autism spectrum disorder (ASD) classification task. The results show that the synthetic task-based fMRI can provide effective data augmentation in learning the ASD classification task.

Copy Number Variation Informs fMRI-based Prediction of Autism Spectrum Disorder

The multifactorial etiology of autism spectrum disorder (ASD) suggests that its study would benefit greatly from multimodal approaches that combine data from widely varying platforms, e.g., neuroimaging, genetics, and clinical characterization. Prior neuroimaging-genetic analyses often apply naive feature concatenation approaches in data-driven work or use the findings from one modality to guide posthoc analysis of another, missing the opportunity to analyze the paired multimodal data in a truly unified approach. In this paper, we develop a more integrative model for combining genetic, demographic, and neuroimaging data. Inspired by the influence of genotype on phenotype, we propose using an attention-based approach where the genetic data guides attention to neuroimaging features of importance for model prediction. The genetic data is derived from copy number variation parameters, while the neuroimaging data is from functional magnetic resonance imaging. We evaluate the proposed approach on ASD classification and severity prediction tasks, using a sex-balanced dataset of 228 ASD and typically developing subjects in a 10-fold cross-validation framework. We demonstrate that our attention-based model combining genetic information, demographic data, and functional magnetic resonance imaging results in superior prediction performance compared to other multimodal approaches.

Rapid Brain Meninges Surface Reconstruction with Layer Topology Guarantee

The meninges, located between the skull and brain, are composed of three membrane layers: the pia, the arachnoid, and the dura. Reconstruction of these layers can aid in studying volume differences between patients with neurodegenerative diseases and normal aging subjects. In this work, we use convolutional neural networks (CNNs) to reconstruct surfaces representing meningeal layer boundaries from magnetic resonance (MR) images. We first use the CNNs to predict the signed distance functions (SDFs) representing these surfaces while preserving their anatomical ordering. The marching cubes algorithm is then used to generate continuous surface representations; both the subarachnoid space (SAS) and the intracranial volume (ICV) are computed from these surfaces. The proposed method is compared to a state-of-the-art deformable model-based reconstruction method, and we show that our method can reconstruct smoother and more accurate surfaces using less computation time. Finally, we conduct experiments with volumetric analysis on both subjects with multiple sclerosis and healthy controls. For healthy and MS subjects, ICVs and SAS volumes are found to be significantly correlated to sex (p<0.01) and age (p<0.03) changes, respectively.