Multitask Multimodal Fusion with Tabular Foundation Models for Peak and Durability Prediction of Pertussis Booster Response

TL;DR

This paper introduces a multi-task multimodal fusion model for predicting both peak and durability of immune responses to pertussis booster vaccination, addressing the challenge of heterogeneous data and biological dissociation.

Contribution

The authors develop a novel contrastive multimodal fusion architecture that jointly predicts two biologically distinct immune response phases using structured missingness handling.

Findings

Achieves AUROC of 0.797 for peak response and 0.755 for durability.

Model outperforms baselines with all 95% CIs above chance on both tasks.

Identifies task-specific modality contributions consistent with immunology.

Abstract

Pertussis booster vaccination produces immune responses that vary widely across individuals in both peak magnitude and long-term durability. These two phases are governed by partly distinct biological compartments:peak reflects acute B-cell activation and antibody secretion, while durability reflects the establishment of long-term humoral memory. Yet most computational models target only one, missing the full boost-and-wane trajectory. Jointly predicting both is non-trivial because the two endpoints are biologically dissociated rather than redundant; samples are small, modalities are heterogeneous with structured missingness, and the two tasks rely on different measurement windows. We propose a multi-task contrastive multimodal fusion architecture combining frozen TabPFN-v2 per-modality encoders, a dual-label supervised contrastive loss that treats two subjects as a positive pair if they agree on the Task 1 label or the Task 2 label, modality dropout calibrated to empirical missingness, and missingness-masked attention fusion. Applied to a curated subset of the CMI-PB pertussis booster dataset (n = 158 subjects, four modalities, 44.9% with at least one modality missing; Spearman r = -0.58 between peak and durability, n = 96), the model achieves test AUROC 0.797 (95% CI [0.621, 0.948]) for peak response and 0.755 (95% CI [0.519, 0.945]) for durability, with both significant under joint label permutation (N = 1000; p = 0.002 and p = 0.045). Across logistic regression, XGBoost, and MLP baselines on raw features and on TabPFN embeddings, the proposed model is the only one whose 95% CIs lie above chance on both tasks simultaneously. Per-modality contribution analyses recover task-specific modality contributions consistent with the underlying immunology: peak prediction is carried by cytokine signatures, while durability is carried by baseline antibody features.