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Multimodality Stacking with Blockwise missing values and application to the PIONeeR biomarkers study for prediction of resistance to immunotherapy
Boussena, Mohamed, Monville, Florence, Fieschi-Meric, Jacques, Vely, Frederic, Milpied, Pierre, Mazieres, Julien, Perol, Maurice, Vivier, Eric, Greillier, Laurent, Barlesi, Fabrice, Benzekry, Sebastien
Integrating multimodal datasets in clinical oncology is frequently hindered by high dimensionality and blockwise missingness, where entire data sources are unavailable for specific patient subsets. Standard survival models often struggle with these gaps, leading to biased results or patient exclusion. We introduce Multimodality Stacking with Blockwise missing values (MSB), a late-fusion framework for survival analysis that independently models modality-specific features before aggregating predictions via a cross-validated stacking meta-learner. MSB was validated on the PIONeeR study (n=443 patients, 378 biomarkers across eight heterogeneous sources) to predict progression-free survival in advanced non-small cell lung cancer patients receiving immunotherapy. MSB yielded higher predictive performance (C-index) than baseline algorithms. Improvements varied by baseline strength: linear models showed a 15.9% increase (p<0.001 for the Wilcoxon signed-rank test), random survival forests gained 5.4% (p=0.002), and gradient boosting methods improved by 2.1% (p=0.030). Beyond discrimination, MSB reduced the generalization gap (train-test difference in 5 folds cross-validation repeated 3 times: 0.055 vs 0.380 for linear models). Permutation importance analysis identified routine laboratory markers, clinical features, and PD-L1 expression as primary predictive drivers. Missing block indicators showed negligible importance, suggesting the model learned from biomarker values rather than data availability patterns. MSB provides a statistically validated framework for multimodal survival prediction with blockwise missingness. By enabling systematic biomarker evaluation without requiring complete data, MSB offers a practical tool for predictive modeling in biomedical research, pending external validation. Implementation is available at https://github.com/MohamedBoussena/MSB under Inria license.
MAGPI: Multifidelity-Augmented Gaussian Process Inputs for Surrogate Modeling from Scarce Data
Rex, Atticus, Qian, Elizabeth, Peterson, David
Supervised machine learning describes the practice of fitting a parameterized model to labeled input-output data. Supervised machine learning methods have demonstrated promise in learning efficient surrogate models that can (partially) replace expensive high-fidelity models, making many-query analyses, such as optimization, uncertainty quantification, and inference, tractable. However, when training data must be obtained through the evaluation of an expensive model or experiment, the amount of training data that can be obtained is often limited, which can make learned surrogate models unreliable. However, in many engineering and scientific settings, cheaper \emph{low-fidelity} models may be available, for example arising from simplified physics modeling or coarse grids. These models may be used to generate additional low-fidelity training data. The goal of \emph{multifidelity} machine learning is to use both high- and low-fidelity training data to learn a surrogate model which is cheaper to evaluate than the high-fidelity model, but more accurate than any available low-fidelity model. This work proposes a new multifidelity training approach for Gaussian process regression which uses low-fidelity data to define additional features that augment the input space of the learned model. The approach unites desirable properties from two separate classes of existing multifidelity GPR approaches, cokriging and autoregressive estimators. Numerical experiments on several test problems demonstrate both increased predictive accuracy and reduced computational cost relative to the state of the art.
WildfireSpreadTS: A dataset of multi-modal time series for wildfire spread prediction
We present a multi-temporal, multi-modal remote-sensing dataset for predicting how active wildfires will spread at a resolution of 24 hours. The dataset consists of 13 607 images across 607 fire events in the United States from January 2018 to October 2021. For each fire event, the dataset contains a full time series of daily observations, containing detected active fires and variables related to fuel, topography and weather conditions. The dataset is challenging due to: a) its inputs being multi-temporal, b) the high number of 23 multi-modal input channels, c) highly imbalanced labels and d) noisy labels, due to smoke, clouds, and inaccuracies in the active fire detection.