Carlos Sevilla-Salcedo

Alejandro Guerrero-López, Carlos Sevilla-Salcedo, Vanessa Gómez-Verdejo et al.

Purpose: Handling heterogeneous and mixed data types has become increasingly critical with the exponential growth in real-world databases. While deep generative models attempt to merge diverse data views into a common latent space, they often sacrifice interpretability, flexibility, and modularity. This study proposes a novel method to address these limitations by combining Variational AutoEncoders (VAEs) with a Factor Analysis latent space (FA-VAE). Methods: The proposed FA-VAE method employs multiple VAEs to learn a private representation for each heterogeneous data view in a continuous latent space. Information is shared between views using a low-dimensional latent space, generated via a linear projection matrix. This modular design creates a hierarchical dependency between private and shared latent spaces, allowing for the flexible addition of new views and conditioning of pre-trained models. Results: The FA-VAE approach facilitates cross-generation of data from different domains and enables transfer learning between generative models. This allows for effective integration of information across diverse data views while preserving their distinct characteristics. Conclusions: By overcoming the limitations of existing methods, the FA-VAE provides a more interpretable, flexible, and modular solution for managing heterogeneous data types. It offers a pathway to more efficient and scalable data-handling strategies, enhancing the potential for cross-domain data synthesis and model transferability.

Carlos Sevilla-Salcedo, Ascensión Gallardo-Antolín, Vanessa Gómez-Verdejo et al.

This paper introduces a novel approach for multi-task regression that connects Kernel Machines (KMs) and Extreme Learning Machines (ELMs) through the exploitation of the Random Fourier Features (RFFs) approximation of the RBF kernel. In this sense, one of the contributions of this paper shows that for the proposed models, the KM and the ELM formulations can be regarded as two sides of the same coin. These proposed models, termed RFF-BLR, stand on a Bayesian framework that simultaneously addresses two main design goals. On the one hand, it fits multitask regressors based on KMs endowed with RBF kernels. On the other hand, it enables the introduction of a common-across-tasks prior that promotes multioutput sparsity in the ELM view. This Bayesian approach facilitates the simultaneous consideration of both the KM and ELM perspectives enabling (i) the optimisation of the RBF kernel parameter $γ$ within a probabilistic framework, (ii) the optimisation of the model complexity, and (iii) an efficient transfer of knowledge across tasks. The experimental results show that this framework can lead to significant performance improvements compared to the state-of-the-art methods in multitask nonlinear regression.

Lucía González-Zamorano, Nuria Balbás-Esteban, Vanessa Gómez-Verdejo et al.

Multimodal clinical data are characterized by high dimensionality, heterogeneous representations, and structured missingness, posing significant challenges for predictive modeling, data integration, and interpretability. We propose BIONIC (Bayesian Integration of Nonlinear Incomplete Clinical data), a unified probabilistic framework that integrates heterogeneous multimodal data under missingness through a joint generative-discriminative latent architecture. BIONIC uses pretrained embeddings for complex modalities such as medical images and clinical text, while incorporating structured clinical variables directly within a Bayesian multimodal formulation. The proposed framework enables robust learning in partially observed and semi-supervised settings by explicitly modeling modality-level and variable-level missingness, as well as missing labels. We evaluate BIONIC on three multimodal clinical and biomedical datasets, demonstrating strong and consistent discriminative performance compared to representative multimodal baselines, particularly under incomplete data scenarios. Beyond predictive accuracy, BIONIC provides intrinsic interpretability through its latent structure, enabling population-level analysis of modality relevance and supporting clinically meaningful insight.

Albert Belenguer-Llorens, Carlos Sevilla-Salcedo, Janaina Mourao-Miranda et al.

Real-world clinical problems are often characterized by multimodal data, usually associated with incomplete views and limited sample sizes in their cohorts, posing significant limitations for machine learning algorithms. In this work, we propose a Bayesian approach designed to efficiently handle these challenges while providing interpretable solutions. Our approach integrates (1) a generative formulation to capture cross-view relationships with a semi-supervised strategy, and (2) a discriminative task-oriented formulation to identify relevant information for specific downstream objectives. This dual generative-discriminative formulation offers both general understanding and task-specific insights; thus, it provides an automatic imputation of the missing views while enabling robust inference across different data sources. The potential of this approach becomes evident when applied to the multimodal clinical data, where our algorithm is able to capture and disentangle the complex interactions among biological, psychological, and sociodemographic modalities.

Long Lin, Pablo Peiro-Corbacho, Pablo Ávila et al.

Intracavitary atrial electrograms (EGMs) provide high-resolution insights into cardiac electrophysiology but are often contaminated by noise and remain high-dimensional, limiting real-time analysis. We introduce CLARAE (CLArity-preserving Reconstruction AutoEncoder), a one-dimensional encoder--decoder designed for atrial EGMs, which achieves both high-fidelity reconstruction and a compact 64-dimensional latent representation. CLARAE is designed to preserve waveform morphology, mitigate reconstruction artifacts, and produce interpretable embeddings through three principles: downsampling with pooling, a hybrid interpolation--convolution upsampling path, and a bounded latent space. We evaluated CLARAE on 495,731 EGM segments (unipolar and bipolar) from 29 patients across three rhythm types (AF, SR300, SR600). Performance was benchmarked against six state-of-the-art autoencoders using reconstruction metrics, rhythm classification, and robustness across signal-to-noise ratios from -5 to 15 dB. In downstream rhythm classification, CLARAE achieved F1-scores above 0.97 for all rhythm types, and its latent space showed clear clustering by rhythm. In denoising tasks, it consistently ranked among the top performers for both unipolar and bipolar signals. In order to promote reproducibility and enhance accessibility, we offer an interactive web-based application. This platform enables users to explore pre-trained CLARAE models, visualize the reconstructions, and compute metrics in real time. Overall, CLARAE combines robust denoising with compact, discriminative representations, offering a practical foundation for clinical workflows such as rhythm discrimination, signal quality assessment, and real-time mapping.

Pablo Peiro-Corbacho, Long Lin, Pablo Ávila et al.

Atrial Fibrillation (AF) is the most prevalent sustained arrhythmia, yet current ablation therapies, including pulmonary vein isolation, are frequently ineffective in persistent AF due to the involvement of non-pulmonary vein drivers. This study proposes a deep learning framework using convolutional autoencoders for unsupervised feature extraction from unipolar and bipolar intracavitary electrograms (EGMs) recorded during AF in ablation studies. These latent representations of atrial electrical activity enable the characterization and automation of EGM analysis, facilitating the detection of AF drivers. The database consisted of 11,404 acquisitions recorded from 291 patients, containing 228,080 unipolar EGMs and 171,060 bipolar EGMs. The autoencoders successfully learned latent representations with low reconstruction loss, preserving the morphological features. The extracted embeddings allowed downstream classifiers to detect rotational and focal activity with moderate performance (AUC 0.73-0.76) and achieved high discriminative performance in identifying atrial EGM entanglement (AUC 0.93). The proposed method can operate in real-time and enables integration into clinical electroanatomical mapping systems to assist in identifying arrhythmogenic regions during ablation procedures. This work highlights the potential of unsupervised learning to uncover physiologically meaningful features from intracardiac signals.

Albert Belenguer-Llorens, Carlos Sevilla-Salcedo, Jussi Tohka et al.

We present BALDUR, a novel Bayesian algorithm designed to deal with multi-modal datasets and small sample sizes in high-dimensional settings while providing explainable solutions. To do so, the proposed model combines within a common latent space the different data views to extract the relevant information to solve the classification task and prune out the irrelevant/redundant features/data views. Furthermore, to provide generalizable solutions in small sample size scenarios, BALDUR efficiently integrates dual kernels over the views with a small sample-to-feature ratio. Finally, its linear nature ensures the explainability of the model outcomes, allowing its use for biomarker identification. This model was tested over two different neurodegeneration datasets, outperforming the state-of-the-art models and detecting features aligned with markers already described in the scientific literature.

Albert Belenguer-Llorens, Carlos Sevilla-Salcedo, Emilio Parrado-Hernández et al.

This paper presents the Relevance Feature and Vector Machine (RFVM), a novel model that addresses the challenges of the fat-data problem when dealing with clinical prospective studies. The fat-data problem refers to the limitations of Machine Learning (ML) algorithms when working with databases in which the number of features is much larger than the number of samples (a common scenario in certain medical fields). To overcome such limitations, the RFVM incorporates different characteristics: (1) A Bayesian formulation which enables the model to infer its parameters without overfitting thanks to the Bayesian model averaging. (2) A joint optimisation that overcomes the limitations arising from the fat-data characteristic by simultaneously including the variables that define the primal space (features) and those that define the dual space (observations). (3) An integrated prunning that removes the irrelevant features and samples during the training iterative optimization. Also, this last point turns out crucial when performing medical prospective studies, enabling researchers to exclude unnecessary medical tests, reducing costs and inconvenience for patients, and identifying the critical patients/subjects that characterize the disorder and, subsequently, optimize the patient recruitment process that leads to a balanced cohort. The model capabilities are tested against state-of-the-art models in several medical datasets with fat-data problems. These experimental works show that RFVM is capable of achieving competitive classification accuracies while providing the most compact subset of data (in both terms of features and samples). Moreover, the selected features (medical tests) seem to be aligned with the existing medical literature.

Vandad Imani, Elaheh Moradi, Carlos Sevilla-Salcedo et al.

Feature selection in noisy label scenarios remains an understudied topic. We propose a novel genetic algorithm-based approach, the Noise-Aware Multi-Objective Feature Selection Genetic Algorithm (NMFS-GA), for selecting optimal feature subsets in binary classification with noisy labels. NMFS-GA offers a unified framework for selecting feature subsets that are both accurate and interpretable. We evaluate NMFS-GA on synthetic datasets with label noise, a Breast Cancer dataset enriched with noisy features, and a real-world ADNI dataset for dementia conversion prediction. Our results indicate that NMFS-GA can effectively select feature subsets that improve the accuracy and interpretability of binary classifiers in scenarios with noisy labels.

Vandad Imani, Carlos Sevilla-Salcedo, Elaheh Moradi et al.

Multi-view datasets offer diverse forms of data that can enhance prediction models by providing complementary information. However, the use of multi-view data leads to an increase in high-dimensional data, which poses significant challenges for the prediction models that can lead to poor generalization. Therefore, relevant feature selection from multi-view datasets is important as it not only addresses the poor generalization but also enhances the interpretability of the models. Despite the success of traditional feature selection methods, they have limitations in leveraging intrinsic information across modalities, lacking generalizability, and being tailored to specific classification tasks. We propose a novel genetic algorithm strategy to overcome these limitations of traditional feature selection methods for multi-view data. Our proposed approach, called the multi-view multi-objective feature selection genetic algorithm (MMFS-GA), simultaneously selects the optimal subset of features within a view and between views under a unified framework. The MMFS-GA framework demonstrates superior performance and interpretability for feature selection on multi-view datasets in both binary and multiclass classification tasks. The results of our evaluations on three benchmark datasets, including synthetic and real data, show improvement over the best baseline methods. This work provides a promising solution for multi-view feature selection and opens up new possibilities for further research in multi-view datasets.

Carlos Sevilla-Salcedo, Vandad Imani, Pablo M. Olmos et al.

Machine learning techniques typically applied to dementia forecasting lack in their capabilities to jointly learn several tasks, handle time dependent heterogeneous data and missing values. In this paper, we propose a framework using the recently presented SSHIBA model for jointly learning different tasks on longitudinal data with missing values. The method uses Bayesian variational inference to impute missing values and combine information of several views. This way, we can combine different data-views from different time-points in a common latent space and learn the relations between each time-point while simultaneously modelling and predicting several output variables. We apply this model to predict together diagnosis, ventricle volume, and clinical scores in dementia. The results demonstrate that SSHIBA is capable of learning a good imputation of the missing values and outperforming the baselines while simultaneously predicting three different tasks.

Carlos Sevilla-Salcedo, Alejandro Guerrero-López, Pablo M. Olmos et al.

Multi-view problems can be faced with latent variable models since they are able to find low-dimensional projections that fairly capture the correlations among the multiple views that characterise each datum. On the other hand, high-dimensionality and non-linear issues are traditionally handled by kernel methods, inducing a (non)-linear function between the latent projection and the data itself. However, they usually come with scalability issues and exposition to overfitting. Here, we propose merging both approaches into single model so that we can exploit the best features of multi-view latent models and kernel methods and, moreover, overcome their limitations. In particular, we combine probabilistic factor analysis with what we refer to as kernelized observations, in which the model focuses on reconstructing not the data itself, but its relationship with other data points measured by a kernel function. This model can combine several types of views (kernelized or not), and it can handle heterogeneous data and work in semi-supervised settings. Additionally, by including adequate priors, it can provide compact solutions for the kernelized observations -- based in a automatic selection of Bayesian Relevance Vectors (RVs) -- and can include feature selection capabilities. Using several public databases, we demonstrate the potential of our approach (and its extensions) w.r.t. common multi-view learning models such as kernel canonical correlation analysis or manifold relevance determination.

Carlos Sevilla-Salcedo, Vanessa Gómez-Verdejo, Pablo M. Olmos

The Bayesian approach to feature extraction, known as factor analysis (FA), has been widely studied in machine learning to obtain a latent representation of the data. An adequate selection of the probabilities and priors of these bayesian models allows the model to better adapt to the data nature (i.e. heterogeneity, sparsity), obtaining a more representative latent space. The objective of this article is to propose a general FA framework capable of modelling any problem. To do so, we start from the Bayesian Inter-Battery Factor Analysis (BIBFA) model, enhancing it with new functionalities to be able to work with heterogeneous data, include feature selection, and handle missing values as well as semi-supervised problems. The performance of the proposed model, Sparse Semi-supervised Heterogeneous Interbattery Bayesian Analysis (SSHIBA) has been tested on 4 different scenarios to evaluate each one of its novelties, showing not only a great versatility and an interpretability gain, but also outperforming most of the state-of-the-art algorithms.