Deep Survival Analysis in Multimodal Medical Data: A Parametric and Probabilistic Approach with Competing Risks

Accurate survival prediction is critical in oncology for prognosis and treatment planning. Traditional approaches often rely on a single data modality, limiting their ability to capture the complexity of tumor biology. To address this challenge, we introduce a multimodal deep learning framework for survival analysis capable of modeling both single and competing risks scenarios, evaluating the impact of integrating multiple medical data sources on survival predictions. We propose SAMVAE (Survival Analysis Multimodal Variational Autoencoder), a novel deep learning architecture designed for survival prediction that integrates six data modalities: clinical variables, four molecular profiles, and histopathological images. SAMVAE leverages modality specific encoders to project inputs into a shared latent space, enabling robust survival prediction while preserving modality specific information. Its parametric formulation enables the derivation of clinically meaningful statistics from the output distributions, providing patient-specific insights through interactive multimedia that contribute to more informed clinical decision-making and establish a foundation for interpretable, data-driven survival analysis in oncology. We evaluate SAMVAE on two cancer cohorts breast cancer and lower grade glioma applying tailored preprocessing, dimensionality reduction, and hyperparameter optimization. The results demonstrate the successful integration of multimodal data for both standard survival analysis and competing risks scenarios across different datasets. Our model achieves competitive performance compared to state-of-the-art multimodal survival models. Notably, this is the first parametric multimodal deep learning architecture to incorporate competing risks while modeling continuous time to a specific event, using both tabular and image data.

DeCaFlow: A Deconfounding Causal Generative Model

Causal generative models (CGMs) have recently emerged as capable approaches to simulate the causal mechanisms generating our observations, enabling causal inference. Unfortunately, existing approaches either are overly restrictive, assuming the absence of hidden confounders, or lack generality, being tailored to a particular query and graph. In this work, we introduce DeCaFlow, a CGM that accounts for hidden confounders in a single amortized training process using only observational data and the causal graph. Importantly, DeCaFlow can provably identify all causal queries with a valid adjustment set or sufficiently informative proxy variables. Remarkably, for the first time to our knowledge, we show that a confounded counterfactual query is identifiable, and thus solvable by DeCaFlow, as long as its interventional counterpart is as well. Our empirical results on diverse settings (including the Ecoli70 dataset, with 3 independent hidden confounders, tens of observed variables and hundreds of causal queries) show that DeCaFlow outperforms existing approaches, while demonstrating its out-of-the-box flexibility.

Artificial Inductive Bias for Synthetic Tabular Data Generation in Data-Scarce Scenarios

While synthetic tabular data generation using Deep Generative Models (DGMs) offers a compelling solution to data scarcity and privacy concerns, their effectiveness relies on substantial training data, often unavailable in real-world applications. This paper addresses this challenge by proposing a novel methodology for generating realistic and reliable synthetic tabular data with DGMs in limited real-data environments. Our approach proposes several ways to generate an artificial inductive bias in a DGM through transfer learning and meta-learning techniques. We explore and compare four different methods within this framework, demonstrating that transfer learning strategies like pre-training and model averaging outperform meta-learning approaches, like Model-Agnostic Meta-Learning, and Domain Randomized Search. We validate our approach using two state-of-the-art DGMs, namely, a Variational Autoencoder and a Generative Adversarial Network, to show that our artificial inductive bias fuels superior synthetic data quality, as measured by Jensen-Shannon divergence, achieving relative gains of up to 50\% when using our proposed approach. This methodology has broad applicability in various DGMs and machine learning tasks, particularly in areas like healthcare and finance, where data scarcity is often a critical issue.

Synthetic Tabular Data Validation: A Divergence-Based Approach

The ever-increasing use of generative models in various fields where tabular data is used highlights the need for robust and standardized validation metrics to assess the similarity between real and synthetic data. Current methods lack a unified framework and rely on diverse and often inconclusive statistical measures. Divergences, which quantify discrepancies between data distributions, offer a promising avenue for validation. However, traditional approaches calculate divergences independently for each feature due to the complexity of joint distribution modeling. This paper addresses this challenge by proposing a novel approach that uses divergence estimation to overcome the limitations of marginal comparisons. Our core contribution lies in applying a divergence estimator to build a validation metric considering the joint distribution of real and synthetic data. We leverage a probabilistic classifier to approximate the density ratio between datasets, allowing the capture of complex relationships. We specifically calculate two divergences: the well-known Kullback-Leibler (KL) divergence and the Jensen-Shannon (JS) divergence. KL divergence offers an established use in the field, while JS divergence is symmetric and bounded, providing a reliable metric. The efficacy of this approach is demonstrated through a series of experiments with varying distribution complexities. The initial phase involves comparing estimated divergences with analytical solutions for simple distributions, setting a benchmark for accuracy. Finally, we validate our method on a real-world dataset and its corresponding synthetic counterpart, showcasing its effectiveness in practical applications. This research offers a significant contribution with applicability beyond tabular data and the potential to improve synthetic data validation in various fields.

An improved tabular data generator with VAE-GMM integration

The rising use of machine learning in various fields requires robust methods to create synthetic tabular data. Data should preserve key characteristics while addressing data scarcity challenges. Current approaches based on Generative Adversarial Networks, such as the state-of-the-art CTGAN model, struggle with the complex structures inherent in tabular data. These data often contain both continuous and discrete features with non-Gaussian distributions. Therefore, we propose a novel Variational Autoencoder (VAE)-based model that addresses these limitations. Inspired by the TVAE model, our approach incorporates a Bayesian Gaussian Mixture model (BGM) within the VAE architecture. This avoids the limitations imposed by assuming a strictly Gaussian latent space, allowing for a more accurate representation of the underlying data distribution during data generation. Furthermore, our model offers enhanced flexibility by allowing the use of various differentiable distributions for individual features, making it possible to handle both continuous and discrete data types. We thoroughly validate our model on three real-world datasets with mixed data types, including two medically relevant ones, based on their resemblance and utility. This evaluation demonstrates significant outperformance against CTGAN and TVAE, establishing its potential as a valuable tool for generating synthetic tabular data in various domains, particularly in healthcare.

SAVAE: Leveraging the variational Bayes autoencoder for survival analysis

As in many fields of medical research, survival analysis has witnessed a growing interest in the application of deep learning techniques to model complex, high-dimensional, heterogeneous, incomplete, and censored medical data. Current methods often make assumptions about the relations between data that may not be valid in practice. In response, we introduce SAVAE (Survival Analysis Variational Autoencoder), a novel approach based on Variational Autoencoders. SAVAE contributes significantly to the field by introducing a tailored ELBO formulation for survival analysis, supporting various parametric distributions for covariates and survival time (as long as the log-likelihood is differentiable). It offers a general method that consistently performs well on various metrics, demonstrating robustness and stability through different experiments. Our proposal effectively estimates time-to-event, accounting for censoring, covariate interactions, and time-varying risk associations. We validate our model in diverse datasets, including genomic, clinical, and demographic data, with varying levels of censoring. This approach demonstrates competitive performance compared to state-of-the-art techniques, as assessed by the Concordance Index and the Integrated Brier Score. SAVAE also offers an interpretable model that parametrically models covariates and time. Moreover, its generative architecture facilitates further applications such as clustering, data imputation, and the generation of synthetic patient data through latent space inference from survival data.