Modeling & Data Analysis

Systems Medicine

of Infectious Diseases

Research Group

Machine Learning Development and Applications

Overview: Machine learning is a growing field based on computational and statistical algorithms that are trained with experimental data to give computers the ability to learn specific tasks for prediction-making. On the other hand, data assimilation algorithms can help to forecast variables of complex systems as well as interpolate sparse observation data using knowledge a mathematical model based on observed data.


State of the art: At present, the use of neural networks for modeling and learning has rapidly increased in recent years. In addition, new training algorithms have been raising with different properties to tackle complex problems.

Our research in Machine Learning and Data Assimilation aims to:


  • machine learning algorithms will be used for the discovery of novel biomarker signatures and gene-regulatory networks


  • predicting disease progression with computational approaches


  • develop new algorithms for data assimilation, identification, and optimization


Relevant Publications in this Field:


  • Nicholas Tobias, Cesar Parra-Rojas, Yan-Ni Shi, Yi-Ming Shi, Svenja Simonyi, Aunchalee Thanwisai, Apichat Vitta, Narisara Chantratita, Esteban A Hernandez-Vargas, Helge B Bode. Focused natural product elucidation by prioritizing high-throughput metabolomic studies with machine learning. BioRxiv. 2019. [Link]


  • M. Hernandez-Gonzalez, E.A. Hernandez-Vargas, M.V. Basin. Discrete-time high order neural network identifier trained with cubature Kalman filter. Neurocomputing. 2018 [Link]
  • G. Hernandez-Mejia, A.Y. Alanis, E.A. Hernandez-Vargas. Neural inverse optimal control for discrete-time impulsive systems. Neurocomputing. 2018 [Link]


  • V.K. Nguyen, C. Parra-Rojas, E.A. Hernandez-Vargas. The 2017 plague outbreak in Madagascar: data descriptions and epidemic modelling. Epidemics. 2018 [Link]


  • C. Villaseñor, J.D. Rios, N. Arana-Daniel, A.Y. Alanis, C. Lopez-Franco, E.A. Hernandez-Vargas. Germinal Center Optimization Algorithm. International Journal of Computational Intelligence Systems, 12: 13-27, 2018 [Link]
  • E. Rangel-Carrillo, E.A. Hernandez-Vargas, N. Arana-Daniel, C. Lopez-Franco, and A.Y. Alanis. Particle swarm optimization algorithm with a bio-inspired aging model. Particle Swarm Optimizations, InTechOpen, 2018 [Link]
  • G. Hernandez-Mejia, N. Arana-Daniel, A.Y. Alanis, E.A. Hernandez-Vargas. Recurrent High Order Neural Networks Identification for Infectious Diseases. Proceedings in the IEEE World Congress on Computational Intelligence, Rio de Janeiro, Brazil. 2018


  • M. Samir, M. Hamed, F. Abdallah, V.K. Nguyen, E.A. Hernandez-Vargas, F. Seehusen, W. Baumgartner, A. Hussein, A.A. Ali, F. Pessler. An Egyptian HPAI H5N1 isolate from clade is highly pathogenic in an experimentally infected domestic duck breed (Sudani duck). Transboundary and Emerging Diseases. 1-15, 2018 [PDF]


  • C. Villaseñor, J.D. Rios, N. Arana-Daniel, A.Y. Alanis, C. Lopez-Franco, E.A. Hernandez-Vargas. Germinal Center Optimization Applied to Neural Inverse Optimal Control for an All-Terrain Tracked Robot. Applied Sciences. 8(1):1-16, 2017 [PDF]


  • C. E. Torres-Cerna, A. Y. Alanis, I. Poblete-Castro, M. Bermejo-Jambrina, E. A. Hernandez-Vargas. A Comparative Study of Differential Evolution Algorithms for Parameter Fitting Procedures. Proceedings in IEEE World Congress on Computational Intelligence. 2016 [PDF]
  • S. Jaafoura,M. G. de Goër de Herve, E.A. Hernandez-Vargas, H. Hendel-Chavez, M. Abdoh, M.C. Mateo, R. Krzysiek,M. Merad, R. Seng, M. Tardieu, J. F. Delfraissy, C. Goujard, Y. Taoufik. Progressive contraction of the latent HIV reservoir around a core of less-differentiated ​CD4+ memory T Cells. Nature Communications, Vol.5, 5407, 1-8, 2014 [PDF]


  • A.Y. Alanis, M. Hernandez-Gonzalez, E.A. Hernandez-Vargas. Observers for biological systems. Applied Soft Computing, Vol.24, 1175–1182, 2014 [PDF]
  • M. Hernandez-Gonzalez, A. Alanis, E.A. Hernandez-Vargas, Decentralized Discrete-Time Neural Control for a Quanser 2-DOF Helicopter. Applied Soft Computing, Vol. 12, 2462–2469, 2012 [PDF]
  • E.A. Hernandez-Vargas, P. Colaneri, R. Middleton, F. Blanchini. Dynamic optimization algorithms to mitigate HIV escape. Proceedings in the IEEE Conference on Decision Control, Atlanta, 2010 [PDF]


  • A. Alanis, E. N. Sanchez, A. Loukianov, E.A. Hernandez-Vargas. Discrete-time recurrent high order neural networks for nonlinear identification. Journal of the Franklin Institute, Vol. 347 (7), 1253-1265, 2010 [PDF]


  • E.A. Hernandez-Vargas, E. N. Sanchez, C. Cadet, J. F. Beteau. Neural observer based hybrid intelligent scheme for activated sludge wastewater treatment. Chemical and Biochemical Engineering Quarterly Journal, Vol. 23 (4), 2009 [PDF]