arXiv subjects

Pedro Henrique da Costa Avelar

Publications and source records attributed to Pedro Henrique da Costa Avelar.

6 recordsLinked to original sources

arXiv2026

Biologically Informed Deep Neural Networks for Multi-Omic Integration, Pathway Activity Inference and Risk Stratification in Cancer

Integrating complex, multi-omics data presents significant challenges. Existing approaches often face a trade-off between model interpretability and representational capacity, with most either relying on post-hoc interpretation or use linear models that may overlook complex interactions. We report Pathway Activity Autoencoders for the multi-omics setting, which embed prior knowledge via pathway-informed architectural constraints, fostering interpretability, while preserving representational power. Our multi-omic framework is applied in the context of breast cancer and is evaluated in survival prediction and subtype classification with results indicating a positive effect of integration. We conduct analysis of individual omics layer impact on end-task performance, revealing that gene, protein, and microRNA expression layers provide the strongest contribution. Repeatability studies indicate that, while dropout improves model robustness and consistency, excessive regularisation can reduce predictive performance. Finally, visualizations of the learned feature space illustrate the framework's intrinsic transparency and clinical relevance. The results underscore the value of multi-omic integration and delineate the impact of individual omics layers, establishing practical guidelines for integration within our framework. Overall, our pathway activity autoencoder frameworks yield superior latent representations that are biologically meaningful and are directly translatable into clinically relevant insights.

cs.LG↗

arXiv2026

Is an Image Also Worth 16x16=256 Superpixels? A Framework for Attentional Image Classification

Superpixel-based image classification has traditionally leveraged graph neural networks (GNNs) for processing irregular image representations. Recent advances in computer vision, driven by Vision Transformers (ViTs), have introduced new paradigms in self-attentional models, surpassing convolutional neural networks (CNNs) in various tasks. However, a synergistic connection between GNNs, superpixels, and transformers remains unexplored. In this work, we propose Superpixel Transformers (SPT), a novel framework that unifies superpixel-based image classification and ViTs. SPT generalizes the Superpixel Image Classification with Graph Attention Networks (SICGAT) model and ViT to support arbitrary superpixel-based chunking strategies, connectivity graphs, and positional encodings. We introduce refinements including a multidimensional sine-cosine positional encoding and an enriched patch data structure that fully incorporates superpixel shape and color information. By testing SPT across datasets such as CIFAR10, FashionMNIST, and Imagenette, with various superpixel generation and graph connectivity strategies, we demonstrate that SPT achieves superior performance compared to previous superpixel-based GNN methods and remains competitive with ViTs. Notably, our approach addresses the limitations of SICGAT, such as information loss during pixel aggregation, and shows how constrained graph connectivity can enhance ViT performance. SPT bridges the gap between superpixel-based and transformer models, opening avenues for cross-domain generalization and future innovations in hybrid attentional frameworks, and showing that an image can also be worth $16\times16$ superpixels.

cs.CV↗

arXiv2025

Subset-Contrastive Multi-Omics Network Embedding

Motivation: Network-based analyses of omics data are widely used, and while many of these methods have been adapted to single-cell scenarios, they often remain memory- and space-intensive. As a result, they are better suited to batch data or smaller datasets. Furthermore, the application of network-based methods in multi-omics often relies on similarity-based networks, which lack structurally-discrete topologies. This limitation may reduce the effectiveness of graph-based methods that were initially designed for topologies with better defined structures. Results: We propose Subset-Contrastive multi-Omics Network Embedding (SCONE), a method that employs contrastive learning techniques on large datasets through a scalable subgraph contrastive approach. By exploiting the pairwise similarity basis of many network-based omics methods, we transformed this characteristic into a strength, developing an approach that aims to achieve scalable and effective analysis. Our method demonstrates synergistic omics integration for cell type clustering in single-cell data. Additionally, we evaluate its performance in a bulk multi-omics integration scenario, where SCONE performs comparable to the state-of-the-art despite utilising limited views of the original data. We anticipate that our findings will motivate further research into the use of subset contrastive methods for omics data.

cs.LG↗

arXiv2023

Incorporating Prior Knowledge in Deep Learning Models via Pathway Activity Autoencoders

Motivation: Despite advances in the computational analysis of high-throughput molecular profiling assays (e.g. transcriptomics), a dichotomy exists between methods that are simple and interpretable, and ones that are complex but with lower degree of interpretability. Furthermore, very few methods deal with trying to translate interpretability in biologically relevant terms, such as known pathway cascades. Biological pathways reflecting signalling events or metabolic conversions are Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. Determining which pathways are implicated in disease and incorporating such pathway data as prior knowledge may enhance predictive modelling and personalised strategies for diagnosis, treatment and prevention of disease. Results: We propose a novel prior-knowledge-based deep auto-encoding framework, PAAE, together with its accompanying generative variant, PAVAE, for RNA-seq data in cancer. Through comprehensive comparisons among various learning models, we show that, despite having access to a smaller set of features, our PAAE and PAVAE models achieve better out-of-set reconstruction results compared to common methodologies. Furthermore, we compare our model with equivalent baselines on a classification task and show that they achieve better results than models which have access to the full input gene set. Another result is that using vanilla variational frameworks might negatively impact both reconstruction outputs as well as classification performance. Finally, our work directly contributes by providing comprehensive interpretability analyses on our models on top of improving prognostication for translational medicine.

cs.LG↗

arXiv2022

Multi-Omic Data Integration and Feature Selection for Survival-based Patient Stratification via Supervised Concrete Autoencoders

Cancer is a complex disease with significant social and economic impact. Advancements in high-throughput molecular assays and the reduced cost for performing high-quality multi-omics measurements have fuelled insights through machine learning . Previous studies have shown promise on using multiple omic layers to predict survival and stratify cancer patients. In this paper, we developed a Supervised Autoencoder (SAE) model for survival-based multi-omic integration which improves upon previous work, and report a Concrete Supervised Autoencoder model (CSAE), which uses feature selection to jointly reconstruct the input features as well as predict survival. Our experiments show that our models outperform or are on par with some of the most commonly used baselines, while either providing a better survival separation (SAE) or being more interpretable (CSAE). We also perform a feature selection stability analysis on our models and notice that there is a power-law relationship with features which are commonly associated with survival. The code for this project is available at: https://github.com/phcavelar/coxae

cs.LG↗

arXiv2022

Weekly sequential Bayesian updating improves prediction of deaths at an early epidemic stage

Background: Following the outbreak of the coronavirus epidemic in early 2020, municipalities, regional governments and policymakers worldwide had to plan their Non-Pharmaceutical Interventions (NPIs) amidst a scenario of great uncertainty. At this early stage of an epidemic, where no vaccine or medical treatment is in sight, algorithmic prediction can become a powerful tool to inform local policymaking. However, when we replicated one prominent epidemiological model to inform health authorities in a region in the south of Brazil, we found that this model relied too heavily on manually predetermined covariates and was too reactive to changes in data trends. Methods: Our four proposed variations of the original method allow accessing data of daily reported infections and take into account the under-reporting of cases more explicitly. Two of the proposed versions also attempt to model the delay in test reporting. We simulated weekly forecasting of deaths from the period from 31/05/2020 until 31/01/2021. That workflow allowed us to run a lighter version of the model after the first calibration week. Google Mobility data, weekly updated, were used as covariates to the model at each simulated run. Findings: The changes made the model significantly less reactive and more rapid in adapting to scenarios after a peak in deaths is observed. Assuming that reported cases were under-reported greatly benefited the model in its stability, and modelling retroactively-added data (due to the "hot" nature of the data used) had a negligible impact on performance. Interpretation: Although not as reliable as death statistics, case statistics, when modelled in conjunction with an "overestimate" parameter, provide a good alternative for improving the forecasting of models, especially in long-range predictions and after the peak of an infection wave.

stat.AP↗