In the last few decades, antimicrobial peptides (AMPs) have been explored as an alternative to classical antibiotics, which in turn motivated the development of machine learning models to predict antimicrobial activities in peptides. The first generation of these predictors was filled with what is now known as shallow learning-based models. These models require the computation and selection of molecular descriptors to characterize each peptide sequence and train the models. The second generation, known as deep learning-based models, which no longer requires the explicit computation and selection of those descriptors, started to be used in the prediction task of AMPs just four years ago. The superior performance claimed by deep models regarding shallow models has created a prevalent inertia to using deep learning to identify AMPs. However, methodological flaws and/or modeling biases in the building of deep models do not support such superiority. Here, we analyze the main pitfalls that led to establish biased conclusions on the leading performance of deep models. Also, we analyze whether deep models truly contribute to achieve better predictions than shallow models by performing fair studies on different state-of-the-art benchmarking datasets. The experiments reveal that deep models do not outperform shallow models in the classification of AMPs, and that both types of models codify similar chemical information since their predictions are highly similar. Thus, according to the currently available datasets, we conclude that the use of deep learning could not be the most suitable approach to develop models to identify AMPs, mainly because shallow models achieve comparable-to-superior performances and are simpler (Ockham’s razor principle). Even so, we suggest the use of deep learning only when its capabilities lead to obtaining significantly better performance gains worth the additional computational cost.

This paper presents the spectral gap-based topology control algorithm (SGTC) for wireless backhaul networks, a novel approach that employs the Laplacian Spectral Gap (LSG) to find expander-like graphs that optimize the topology of the network in terms of robustness, diameter, energy cost, and network entropy. The latter measures the network’s ability to promote seamless traffic offloading from the Macro Base Stations to smaller cells by providing a high diversity of shortest paths connecting all the stations. Given the practical constraints imposed by cellular technologies, the proposed algorithm uses simulated annealing to search for feasible network topologies with a large LSG. Then, it computes the Pareto front of the set of feasible solutions found during the annealing process when considering robustness, diameter, and entropy as objective functions. The algorithm’s result is the Pareto efficient solution that minimizes energy cost. A set of experimental results shows that by optimizing the LSG, the proposed algorithm simultaneously optimizes the set of desirable topological properties mentioned above. The results also revealed that generating networks with good spectral expansion is possible even under the restrictions imposed by current wireless technologies. This is a desirable feature because these networks have strong connectivity properties even if they do not have a large number of links.