OCL: Ordinal Contrastive Learning for Imputating Features with Progressive Labels

Accurately discriminating progressive stages of Alzheimer's Disease (AD) is crucial for early diagnosis and prevention. It often involves multiple imaging modalities to understand the complex pathology of AD, however, acquiring a complete set of images is challenging due to high cost and burden for subjects. In the end, missing data become inevitable which lead to limited sample-size and decrease in precision in downstream analyses. To tackle this challenge, we introduce a holistic imaging feature imputation method that enables to leverage diverse imaging features while retaining all subjects. The proposed method comprises two networks: 1) An encoder to extract modality-independent embeddings and 2) A decoder to reconstruct the original measures conditioned on their imaging modalities. The encoder includes a novel {\em ordinal contrastive loss}, which aligns samples in the embedding space according to the progression of AD. We also maximize modality-wise coherence of embeddings within each subject, in conjunction with domain adversarial training algorithms, to further enhance alignment between different imaging modalities. The proposed method promotes our holistic imaging feature imputation across various modalities in the shared embedding space. In the experiments, we show that our networks deliver favorable results for statistical analysis and classification against imputation baselines with Alzheimer's Disease Neuroimaging Initiative (ADNI) study.

Modality-Agnostic Style Transfer for Holistic Feature Imputation

Characterizing a preclinical stage of Alzheimer's Disease (AD) via single imaging is difficult as its early symptoms are quite subtle. Therefore, many neuroimaging studies are curated with various imaging modalities, e.g., MRI and PET, however, it is often challenging to acquire all of them from all subjects and missing data become inevitable. In this regards, in this paper, we propose a framework that generates unobserved imaging measures for specific subjects using their existing measures, thereby reducing the need for additional examinations. Our framework transfers modality-specific style while preserving AD-specific content. This is done by domain adversarial training that preserves modality-agnostic but AD-specific information, while a generative adversarial network adds an indistinguishable modality-specific style. Our proposed framework is evaluated on the Alzheimer's Disease Neuroimaging Initiative (ADNI) study and compared with other imputation methods in terms of generated data quality. Small average Cohen's $d$ $< 0.19$ between our generated measures and real ones suggests that the synthetic data are practically usable regardless of their modality type.

Augmented Intelligence for Multimodal Virtual Biopsy in Breast Cancer Using Generative Artificial Intelligence

Full-Field Digital Mammography (FFDM) is the primary imaging modality for routine breast cancer screening; however, its effectiveness is limited in patients with dense breast tissue or fibrocystic conditions. Contrast-Enhanced Spectral Mammography (CESM), a second-level imaging technique, offers enhanced accuracy in tumor detection. Nonetheless, its application is restricted due to higher radiation exposure, the use of contrast agents, and limited accessibility. As a result, CESM is typically reserved for select cases, leaving many patients to rely solely on FFDM despite the superior diagnostic performance of CESM. While biopsy remains the gold standard for definitive diagnosis, it is an invasive procedure that can cause discomfort for patients. We introduce a multimodal, multi-view deep learning approach for virtual biopsy, integrating FFDM and CESM modalities in craniocaudal and mediolateral oblique views to classify lesions as malignant or benign. To address the challenge of missing CESM data, we leverage generative artificial intelligence to impute CESM images from FFDM scans. Experimental results demonstrate that incorporating the CESM modality is crucial to enhance the performance of virtual biopsy. When real CESM data is missing, synthetic CESM images proved effective, outperforming the use of FFDM alone, particularly in multimodal configurations that combine FFDM and CESM modalities. The proposed approach has the potential to improve diagnostic workflows, providing clinicians with augmented intelligence tools to improve diagnostic accuracy and patient care. Additionally, as a contribution to the research community, we publicly release the dataset used in our experiments, facilitating further advancements in this field.

SatFlow: Generative model based framework for producing High Resolution Gap Free Remote Sensing Imagery

Frequent, high-resolution remote sensing imagery is crucial for agricultural and environmental monitoring. Satellites from the Landsat collection offer detailed imagery at 30m resolution but with lower temporal frequency, whereas missions like MODIS and VIIRS provide daily coverage at coarser resolutions. Clouds and cloud shadows contaminate about 55\% of the optical remote sensing observations, posing additional challenges. To address these challenges, we present SatFlow, a generative model-based framework that fuses low-resolution MODIS imagery and Landsat observations to produce frequent, high-resolution, gap-free surface reflectance imagery. Our model, trained via Conditional Flow Matching, demonstrates better performance in generating imagery with preserved structural and spectral integrity. Cloud imputation is treated as an image inpainting task, where the model reconstructs cloud-contaminated pixels and fills gaps caused by scan lines during inference by leveraging the learned generative processes. Experimental results demonstrate the capability of our approach in reliably imputing cloud-covered regions. This capability is crucial for downstream applications such as crop phenology tracking, environmental change detection etc.,

MIND: Modality-Informed Knowledge Distillation Framework for Multimodal Clinical Prediction Tasks

Multimodal fusion leverages information across modalities to learn better feature representations with the goal of improving performance in fusion-based tasks. However, multimodal datasets, especially in medical settings, are typically smaller than their unimodal counterparts, which can impede the performance of multimodal models. Additionally, the increase in the number of modalities is often associated with an overall increase in the size of the multimodal network, which may be undesirable in medical use cases. Utilizing smaller unimodal encoders may lead to sub-optimal performance, particularly when dealing with high-dimensional clinical data. In this paper, we propose the Modality-INformed knowledge Distillation (MIND) framework, a multimodal model compression approach based on knowledge distillation that transfers knowledge from ensembles of pre-trained deep neural networks of varying sizes into a smaller multimodal student. The teacher models consist of unimodal networks, allowing the student to learn from diverse representations. MIND employs multi-head joint fusion models, as opposed to single-head models, enabling the use of unimodal encoders in the case of unimodal samples without requiring imputation or masking of absent modalities. As a result, MIND generates an optimized multimodal model, enhancing both multimodal and unimodal representations. It can also be leveraged to balance multimodal learning during training. We evaluate MIND on binary and multilabel clinical prediction tasks using time series data and chest X-ray images. Additionally, we assess the generalizability of the MIND framework on three non-medical multimodal multiclass datasets. Experimental results demonstrate that MIND enhances the performance of the smaller multimodal network across all five tasks, as well as various fusion methods and multimodal architectures, compared to state-of-the-art baselines.

Generalized Least Squares Kernelized Tensor Factorization

Real-world datasets often contain missing or corrupted values. Completing multidimensional tensor-structured data with missing entries is essential for numerous applications. Smoothness-constrained low-rank factorization models have shown superior performance with reduced computational costs. While effective at capturing global and long-range correlations, these models struggle to reproduce short-scale, high-frequency variations in the data. In this paper, we introduce the \Generalized Least Squares Kernelized Tensor Factorization (GLSKF) framework for tensor completion. GLSKF integrates smoothness-constrained low-rank factorization with a locally correlated residual process; the resulting additive structure can effectively characterize both global dependencies and local variations. In particular, we define the covariance norm to enforce the smoothness of factor matrices in the global low-rank factorization, and use structured covariance/kernel functions to model the local processes. For model estimation, we develop an alternating least squares (ALS) procedure with closed-form solutions for each subproblem. To efficiently handle missing data, GLSKF utilizes projection matrices that preserve the Kronecker structure of covariances, facilitating fast computations through conjugate gradient (CG) and preconditioned conjugate gradient (PCG) algorithms. The proposed framework is evaluated on four real-world datasets across diverse tasks: traffic speed imputation, color image inpainting, video completion, and MRI image reconstruction. Experimental results confirm that GLSKF delivers superior effectiveness and scalability, establishing it as a robust solution for multidimensional tensor completion.

VIPaint: Image Inpainting with Pre-Trained Diffusion Models via Variational Inference

Diffusion probabilistic models learn to remove noise that is artificially added to the data during training. Novel data, like images, may then be generated from Gaussian noise through a sequence of denoising operations. While this Markov process implicitly defines a joint distribution over noise-free data, it is not simple to condition the generative process on masked or partial images. A number of heuristic sampling procedures have been proposed for solving inverse problems with diffusion priors, but these approaches do not directly approximate the true conditional distribution imposed by inference queries, and are often ineffective for large masked regions. Moreover, many of these baselines cannot be applied to latent diffusion models which use image encodings for efficiency. We instead develop a hierarchical variational inference algorithm that analytically marginalizes missing features, and uses a rigorous variational bound to optimize a non-Gaussian Markov approximation of the true diffusion posterior. Through extensive experiments with both pixel-based and latent diffusion models of images, we show that our VIPaint method significantly outperforms previous approaches in both the plausibility and diversity of imputations, and is easily generalized to other inverse problems like deblurring and superresolution.

ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics

Spatial transcriptomics (ST) is an emerging technology that enables medical computer vision scientists to automatically interpret the molecular profiles underlying morphological features. Currently, however, most deep learning-based ST analyses are limited to two-dimensional (2D) sections, which can introduce diagnostic errors due to the heterogeneity of pathological tissues across 3D sections. Expanding ST to three-dimensional (3D) volumes is challenging due to the prohibitive costs; a 2D ST acquisition already costs over 50 times more than whole slide imaging (WSI), and a full 3D volume with 10 sections can be an order of magnitude more expensive. To reduce costs, scientists have attempted to predict ST data directly from WSI without performing actual ST acquisition. However, these methods typically yield unsatisfying results. To address this, we introduce a novel problem setting: 3D ST imputation using 3D WSI histology sections combined with a single 2D ST slide. To do so, we present the Anatomy-aware Spatial Imputation Graph Network (ASIGN) for more precise, yet affordable, 3D ST modeling. The ASIGN architecture extends existing 2D spatial relationships into 3D by leveraging cross-layer overlap and similarity-based expansion. Moreover, a multi-level spatial attention graph network integrates features comprehensively across different data sources. We evaluated ASIGN on three public spatial transcriptomics datasets, with experimental results demonstrating that ASIGN achieves state-of-the-art performance on both 2D and 3D scenarios. Code is available at https://github.com/hrlblab/ASIGN.

Federated Foundation Models on Heterogeneous Time Series

Training a general-purpose time series foundation models with robust generalization capabilities across diverse applications from scratch is still an open challenge. Efforts are primarily focused on fusing cross-domain time series datasets to extract shared subsequences as tokens for training models on Transformer architecture. However, due to significant statistical heterogeneity across domains, this cross-domain fusing approach doesn't work effectively as the same as fusing texts and images. To tackle this challenge, this paper proposes a novel federated learning approach to address the heterogeneity in time series foundation models training, namely FFTS. Specifically, each data-holding organization is treated as an independent client in a collaborative learning framework with federated settings, and then many client-specific local models will be trained to preserve the unique characteristics per dataset. Moreover, a new regularization mechanism will be applied to both client-side and server-side, thus to align the shared knowledge across heterogeneous datasets from different domains. Extensive experiments on benchmark datasets demonstrate the effectiveness of the proposed federated learning approach. The newly learned time series foundation models achieve superior generalization capabilities on cross-domain time series analysis tasks, including forecasting, imputation, and anomaly detection.

Online learning in motion modeling for intra-interventional image sequences

Image monitoring and guidance during medical examinations can aid both diagnosis and treatment. However, the sampling frequency is often too low, which creates a need to estimate the missing images. We present a probabilistic motion model for sequential medical images, with the ability to both estimate motion between acquired images and forecast the motion ahead of time. The core is a low-dimensional temporal process based on a linear Gaussian state-space model with analytically tractable solutions for forecasting, simulation, and imputation of missing samples. The results, from two experiments on publicly available cardiac datasets, show reliable motion estimates and an improved forecasting performance using patient-specific adaptation by online learning.