José Luís Oliveira

h-index38
2papers
5,290citations

2 Papers

7.1LGMay 12, 2025Code
A Federated Random Forest Solution for Secure Distributed Machine Learning

Alexandre Cotorobai, Jorge Miguel Silva, Jose Luis Oliveira

Privacy and regulatory barriers often hinder centralized machine learning solutions, particularly in sectors like healthcare where data cannot be freely shared. Federated learning has emerged as a powerful paradigm to address these concerns; however, existing frameworks primarily support gradient-based models, leaving a gap for more interpretable, tree-based approaches. This paper introduces a federated learning framework for Random Forest classifiers that preserves data privacy and provides robust performance in distributed settings. By leveraging PySyft for secure, privacy-aware computation, our method enables multiple institutions to collaboratively train Random Forest models on locally stored data without exposing sensitive information. The framework supports weighted model averaging to account for varying data distributions, incremental learning to progressively refine models, and local evaluation to assess performance across heterogeneous datasets. Experiments on two real-world healthcare benchmarks demonstrate that the federated approach maintains competitive predictive accuracy - within a maximum 9\% margin of centralized methods - while satisfying stringent privacy requirements. These findings underscore the viability of tree-based federated learning for scenarios where data cannot be centralized due to regulatory, competitive, or technical constraints. The proposed solution addresses a notable gap in existing federated learning libraries, offering an adaptable tool for secure distributed machine learning tasks that demand both transparency and reliable performance. The tool is available at https://github.com/ieeta-pt/fed_rf.

1.0MLNov 12, 2017Code
A Sequence-Based Mesh Classifier for the Prediction of Protein-Protein Interactions

Edgar D. Coelho, Igor N. Cruz, André Santiago et al.

The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and pathogenic processes, thus being a priority for the identification of vital components and mechanisms in pathogens. Despite the advances of laboratorial techniques, computational models allow the screening of protein interactions between entire proteomes in a fast and inexpensive manner. Here, we present a supervised machine learning model for the prediction of PPIs based on the protein sequence. We cluster amino acids regarding their physicochemical properties, and use the discrete cosine transform to represent protein sequences. A mesh of classifiers was constructed to create hyper-specialised classifiers dedicated to the most relevant pairs of molecular function annotations from Gene Ontology. Based on an exhaustive evaluation that includes datasets with different configurations, cross-validation and out-of-sampling validation, the obtained results outscore the state-of-the-art for sequence-based methods. For the final mesh model using SVM with RBF, a consistent average AUC of 0.84 was attained.