Deep Learning Architecture Optimization with Metaheuristic Algorithms for Predicting BRCA1/BRCA2 Pathogenicity NGS Analysis


  • Pellegrino Eric
  • Brunet Theo
  • Pissier Christel
  • Camilla Clara
  • Abbou Norman
  • Beaufils Nathalie
  • Nanni-Metellus Isabelle
  • Métellus Philippe
  • Ouafik L'Houcine


  • Deep learning
  • Genetic algorithm
  • Particle swarm optimization
  • BRCA1 and BRCA2 genes
  • New generation sequencing
  • Ngs analysis
  • Neural network optimization
  • Genes prediction
  • Bioinformatics


Motivation, BRCA1 and BRCA2 are genes with tumor suppressor activity. They are involved in a considerable number of biological processes. To help the biologist in tumor classification, we developed a deep learning algorithm. The question when we want to construct a neural network is how many hidden layers and neurons should we use. If the number of inputs and outputs is defined by the problem, the number of hidden layers and neurons is difficult to define. Hidden layers and neurons that make up each layer of the neural network influence the performance of system predictions. There are different methods for finding the optimal architecture. In this paper, we present the two packages that we have developed, the genetic algorithm (GA) and the particle swarm optimization (PSO) to optimize the parameters of the neural network for predicting BRCA1 and BRCA2 pathogenicity; Results, we will compare the results obtained by the two algorithms. We used datasets collected from our NGS analysis of BRCA1 and BRCA2 genes to train deep learning models. It represents a data collection of 11,875 BRCA1 and BRCA2 variants. Our preliminary results show that the PSO provided the most significant architecture of hidden layers and the number of neurons compared to grid search and GA; Conclusions, the optimal architecture found by the PSO algorithm is composed of 6 hidden layers with 275 hidden nodes with an accuracy of 0.98, precision 0.99, recall 0.98, and a specificity of 0.99.

more information