Benchmark of structured machine learning methods for microbial identification from mass-spectrometry data

Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical classification where the proximity between species is generally measured in terms of evolutionary distances and/or clinical phenotypes. Surprisingly, the information provided by this well-known hierarchical structure is rarely used by machine learning-based automatic microbial identification systems. Structured machine learning methods were recently proposed for taking into account the structure embedded in a hierarchy and using it as additional a priori information, and could therefore allow to improve microbial identification systems. We test and compare several state-of-the-art machine learning methods for microbial identification on a new Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) dataset. We include in the benchmark standard and structured methods, that leverage the knowledge of the underlying hierarchical structure in the learning process. Our results show that although some methods perform better than others, structured methods do not consistently perform better than their "flat" counterparts. We postulate that this is partly due to the fact that standard methods already reach a high level of accuracy in this context, and that they mainly confuse species close to each other in the tree, a case where using the known hierarchy is not helpful

Evolving machine learning and deep learning models using evolutionary algorithms

Despite the great success in data mining, machine learning and deep learning models are yet subject to material obstacles when tackling real-life challenges, such as feature selection, initialization sensitivity, as well as hyperparameter optimization. The prevalence of these obstacles has severely constrained conventional machine learning and deep learning methods from fulfilling their potentials. In this research, three evolving machine learning and one evolving deep learning models are proposed to eliminate above bottlenecks, i.e. improving model initialization, enhancing feature representation, as well as optimizing model configuration, respectively, through hybridization between the advanced evolutionary algorithms and the conventional ML and DL methods. Specifically, two Firefly Algorithm based evolutionary clustering models are proposed to optimize cluster centroids in K-means and overcome initialization sensitivity as well as local stagnation. Secondly, a Particle Swarm Optimization based evolving feature selection model is developed for automatic identification of the most effective feature subset and reduction of feature dimensionality for tackling classification problems. Lastly, a Grey Wolf Optimizer based evolving Convolutional Neural Network-Long Short-Term Memory method is devised for automatic generation of the optimal topological and learning configurations for Convolutional Neural Network-Long Short-Term Memory networks to undertake multivariate time series prediction problems. Moreover, a variety of tailored search strategies are proposed to eliminate the intrinsic limitations embedded in the search mechanisms of the three employed evolutionary algorithms, i.e. the dictation of the global best signal in Particle Swarm Optimization, the constraint of the diagonal movement in Firefly Algorithm, as well as the acute contraction of search territory in Grey Wolf Optimizer, respectively. The remedy strategies include the diversification of guiding signals, the adaptive nonlinear search parameters, the hybrid position updating mechanisms, as well as the enhancement of population leaders. As such, the enhanced Particle Swarm Optimization, Firefly Algorithm, and Grey Wolf Optimizer variants are more likely to attain global optimality on complex search landscapes embedded in data mining problems, owing to the elevated search diversity as well as the achievement of advanced trade-offs between exploration and exploitation