Disentangling Shared and Task-Specific Representations from Multi-Modal Clinical Data
Authors: He Lyu, Huolin Zeng, Junren Wang, Huazhen Yang, Linchao He, Yong Chen, Zhirui Li, Andreas Maier, +2 more
Organizations: Department of Anesthesiology and West China Biomedical Big Data Center West China Hospital, Sichuan University, Chengdu, China · Med-X Center for Informatics, Sichuan University, Chengdu, China · Department of National Key Laboratory of Fundamental Science on Synthetic Vision, Sichuan University, Chengdu, China · Sichuan University, Chengdu, China · Pattern Recognition Lab, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany · Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden · Center of Public Health Sciences, Faculty of Medicine, University of Iceland, Reykjav´ık, Iceland
Real-world clinical data is inherently multimodal, providing complementary evidence that mirrors the practical necessity of jointly assessing multiple related outcomes. Although multi-task learning can improve efficiency by sharing information across outcomes, existing approaches often fail to balance shared representation learning with outcome-specific modeling. Hard parameter sharing can trigger negative transfer when task gradients conflict, while flexible sharing may still entangle shared and task-specific signals. To address this, we propose a multi-task framework built on a unified Transformer for multimodal fusion, augmented with Orthogonal Task Decomposition (OrthTD) to split patient representations into shared and task-specific subspaces and impose a geometric orthogonality constraint to reduce redundancy and isolate task-specific signals. We evaluated OrthTD on a real-world cohort of 12,430 surgical patients for predicting four outcomes. OrthTD achieved average AUC (area under the receiver operating characteristic curve) of 87.5% and average AUPRC (area under the precision-recall curve) of 37.2%, consistently outperformed advanced tabular and multi-task methods. Notably, OrthTD achieves substantial gains in AUPRC, indicating superior performance in identifying rare events within imbalanced clinical data. These results suggest that enforcing non-redundant shared and task-specific representations can improve multi-outcome prediction from multimodal clinical data.
Most existing multitask learning approaches are limited by their reliance on task-specific loss functions tailored to the scale and type of each outcome. When outcomes differ across tasks, these losses are generally not directly comparable, which makes it difficult to formulate a unified objective and may limit information sharing across tasks. We propose a multitask transformation framework in which task-specific responses may differ through unknown monotone transformations. Motivated by high-dimensional biological applications in which the predictor dimension may diverge with the sample size while only a common subset of predictors is informative, we consider shared sparsity across tasks. Under this framework, we estimate the target functions and identify important predictors by optimizing a smoothed rank-based criterion with a group-Lasso penalty, implemented through a multitask deep neural network with a shared first layer. We establish the nonasymptotic excess-risk bounds, and variable-selection consistency for the proposed estimator. Simulation studies show that the proposed method achieves competitive prediction and variable-selection performance compared with competing approaches. Analyses of gene-expression studies with continuous, binary, and mixed outcomes further illustrate that the proposed method improves prediction and identifies biologically meaningful shared predictors.
Multimodal fusion learning (MFL) has shown great potential in the medical domain, where we are faced with disparate data modalities such as imaging, clinical records, and omics. However, existing MFL strategies face several major challenges. First, they struggle to capture complex cross-modal interactions effectively, which in turn limits performance improvements. Second, they incur high computational costs, restricting their applicability in resource-constrained healthcare AI applications. Finally, they are often designed and evaluated for narrow, fixed modality configurations (e.g., imaging-only, or specific pairs such as image and omics), which limits evidence of their adaptability and generalizability to broader collections of heterogeneous medical modalities. To address these challenges, we propose a novel MFL framework - Cascaded Unified Representation Learning for Efficient Fusion Network (CURE) - a lightweight and scalable framework that progressively integrates various modalities through a novel efficient Hybrid Geometry Aware Fusion layer (HyFuse), where each HyFuse layer is sequentially learned for each modality, making the framework adaptable and generalizable. Within HyFuse, an efficient residual convolution module captures rich multi-scale features to ensure cost-effective learning, while a hybrid-space aware attention mixer learns coarse-to-fine structural cues to better preserve cross-modal relationships. Complementary learnable late-fusion and shared information refinement modules are then employed to learn robust modality-order-invariant shared representations, which in turn yields consistent performance improvements. Extensive evaluations on 16 public datasets show that CURE outperforms leading multimodal fusion methods, boosting performance by up to 3.97% and lowering computational costs by up to 87.8%, ensuring more effective and reliable predictions.
Accurate time-to-event (TTE) prediction from multimodal clinical data remains challenging due to modality imbalance and distribution shift. We introduce a foundation model-driven framework for cross-modal representation alignment between CT imaging and longitudinal EHR data, designed to generalize across tasks and institutions. CT and EHR modalities are encoded independently using domain-specific foundation models and aligned in a shared latent space through four principled fusion strategies: late fusion, contrastive alignment, cross-attention, and co-attention. We evaluate two clinically distinct TTE tasks: pulmonary embolism (PE) mortality and cardiovascular disease (CVD) outcomes, on large-scale multi-institutional cohorts (PE: N=3,099 train; 1,098 internal; 435 external; CVD: N=2,951 train; 837 internal; 682 external). Fusion consistently improves concordance index by 1.5-5.4% over unimodal baselines when modalities contribute comparably. Overall, contrastive multimodal fusion, particularly with CLMBR representations, provided the most consistent and statistically robust improvements, especially for PE mortality prediction. For MACE, cross-attention (one-hot) achieved the highest internal performance and image-guided co-attention achieved the best external performance. We therefore introduce a generalizable foundation model-based cross-modal alignment framework and provide the first systematic analysis of fusion behavior under modality imbalance in TTE prediction. Our results establish task-aware multimodal alignment as a necessary design principle for robust generalization and scalable clinical deployment.