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.

In multi-modal biomedical research, integrating high-dimensional genomic data with clinical baselines is essential for precision medicine. However, standard deep neural network approaches often entangle these modalities, obscuring the specific predictive impact of genetic features and leading to possibly suboptimal predictive performance. Motivated by the landmark METABRIC cohort primary breast tumors study, we propose the Stein-Encoder, a white-box supervised framework designed to isolate the genetic signal driving clinical outcomes conditional on nuisance covariates. By leveraging Stein's method and residualization techniques, our approach constructs an interpretable single index that summarizes relevant biological heterogeneity while flexibly incorporating clinical factors and can be used to improve downstream prediction. We establish theoretical guarantees for identification, consistency and efficiency improvement. Applied to the METABRIC cohort, the Stein-Encoder outperforms unsupervised benchmarks in predictive accuracy. Crucially, it achieves structural disentanglement by revealing response-specific biological mechanisms: we find that tumor size is driven primarily by mitotic networks, whereas prognostic indices rely on a distinct proliferation-versus-immune axis. This work contributes a unified, computationally efficient framework that bridges statistical rigor with the representational power of neural networks, enabling interpretable, task-specific and efficient compression of multi-modal health data for a wide range of precision medicine applications, beyond biomarker discovery.

Generative models can produce nonsensical text, unrealistic images, and unstable materials faster than simulation or human review can absorb; without per-sample confidence, trust erodes. Existing fixes run $k$ ensembles or stochastic trajectories at $k\times$ compute, measuring variability between models, not model confidence. We propose Flow Matching with Confidence (FMwC). FMwC injects input-dependent multiplicative noise at selected layers, propagates its variance through the network in closed form, and integrates it along the ODE trajectory, yielding a per-sample confidence score at standard sampling cost. The score supports multiple uses: filtering improves image quality and thermodynamic stability of crystals; editing rewinds trajectories to the points where the model commits and redirects them; and adaptive stepping concentrates ODE compute where the flow is ambiguous. We find that the confidence score correlates with the magnitude of the divergence of the learned velocity field, which gives us a window to understand the generative process, opening up surgical forms of guidance that target the moments that matter, new sampling algorithms and interpretability of generative models.

As datasets continue to expand in size and complexity, these models have become increasingly sophisticated, with deeper architectures and greater expressive power. Despite these advances, DNNs trained on imbalanced class distributions often exhibit a tendency to favor majority classes, leading to degraded performance on underrepresented classes [18, 39, 27, 17]. Because many real-world datasets follow long-tailed distributions in which minority classes can contain critical and informative patterns, developing methods that enable DNNs to learn effectively from imbalanced data is essential to prevent the loss of valuable information from these rare classes [26, 34, 16]. Moreover, data encountered in real-world applications are frequently multi-modal, meaning that observations originate from heterogeneous sources [6, 29, 7, 35]. To make effective use of such heterogeneous inputs, a wide range of multi-modal learning approaches have been proposed that exploit complementary information across modalities to enhance predictive performance [10, 5]. Common strategies integrate multiple modalities into a unified representation, using techniques that span from straightforward feature-level concatenation [19, 11, 12] to more sophisticated neural architectures that learn joint representations in an end-to-end manner [20, 32]. Although prior research has extensively studied class imbalance and multi-modal data separately, relatively little attentionhas beengiven to settings where bothchallenges arise si2 multaneously. Developing methods that can effectively handle long-tailed class distributions in conjunction with multi-modal inputs is therefore essential in many real-world applications. In the medical domain, for instance, datasets often contain far more samples from healthy individuals than from patients with specific conditions, while also encompassing diverse datatypes such asimagingdata(e.g., X-rays)alongsideauxiliary informationincluding demographics and clinical histories.

When modeling class-imbalanced data, it is crucial to address the imbalance, as models trained on such data tend to be biased towards the majority classes. This problem is amplified under partial supervision, where pseudo-labels for unlabeled data are predicted based on imbalanced labeled data, propagating the bias. While recent semi-supervised models address class imbalance, they typically assume single-modal input data. However, with the growing availability of multimodal data, it is essential to leverage complementary modalities. In this article, we propose a multimodal deep generative model for semi-supervised learning under class imbalance. Our approach uses separate encoders for each modality, sharing latent variables across modalities, and simplifies joint posterior computation with a product-of-experts method. To further address class imbalance, we replace typical Gaussian distributions with Student's t-distributions for the prior, encoder, and decoder, better capturing the heavy-tailed latent distributions in imbalanced data. We derive a new objective function for training the proposed model on both labeled and unlabeled data using $γ$-power divergence. Empirical results on benchmark and real-world datasets demonstrate that our model outperforms baseline methods in generalization, achieving superior classification performance for partially labeled multimodal data with imbalanced class distributions.

Encoding models have been used to assess how the human brain represents concepts in language and vision. While language and vision rely on similar concept representations, current encoding models are typically trained and tested on brain responses to each modality in isolation. Recent advances in multimodal pretraining have produced transformers that can extract aligned representations of concepts in language and vision. In this work, we used representations from multimodal transformers to train encoding models that can transfer across fMRI responses to stories and movies. We found that encoding models trained on brain responses to one modality can successfully predict brain responses to the other modality, particularly in cortical regions that represent conceptual meaning. Further analysis of these encoding models revealed shared semantic dimensions that underlie concept representations in language and vision. Comparing encoding models trained using representations from multimodal and unimodal transformers, we found that multimodal transformers learn more aligned representations of concepts in language and vision. Our results demonstrate how multimodal transformers can provide insights into the brain's capacity for multimodal processing.

Videos are a rich source of multi-modal supervision. In this work, we learn representations using self-supervision by leveraging three modalities naturally present in videos: visual, audio and language streams. To this end, we introduce the notion of a multimodal versatile network - a network that can ingest multiple modalities and whose representations enable downstream tasks in multiple modalities. In particular, we explore how best to combine the modalities, such that fine-grained representations of the visual and audio modalities can be maintained, whilst also integrating text into a common embedding. Driven by versatility, we also introduce a novel process of deflation, so that the networks can be effortlessly applied to the visual data in the form of video or a static image. We demonstrate how such networks trained on large collections of unlabelled video data can be applied on video, video-text, image and audio tasks. Equipped with these representations, we obtain state-of-the-art performance on multiple challenging benchmarks including UCF101, HMDB51, Kinetics600, AudioSet and ESC-50 when compared to previous self-supervised work. Our models are publicly available .

It takes image, video, audio and text as inputs to the encoder and produces their feature embeddings as outputs.