Multitask Multimodal Fusion with Tabular Foundation Models for Peak and Durability Prediction of Pertussis Booster Response
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Computer Science > Machine Learning
arXiv:2605.12852 (cs)
[Submitted on 13 May 2026]
Title:Multitask Multimodal Fusion with Tabular Foundation Models for Peak and Durability Prediction of Pertussis Booster Response
Authors:Divya Sitani
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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.
| Comments: | 22 pages, 8 figures, 4 tables. Code available at this https URL |
| Subjects: | Machine Learning (cs.LG); Quantitative Methods (q-bio.QM) |
| Cite as: | arXiv:2605.12852 [cs.LG] |
| (or arXiv:2605.12852v1 [cs.LG] for this version) | |
| https://doi.org/10.48550/arXiv.2605.12852
arXiv-issued DOI via DataCite (pending registration)
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View a PDF of the paper titled Multitask Multimodal Fusion with Tabular Foundation Models for Peak and Durability Prediction of Pertussis Booster Response, by Divya Sitani
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