One of the main challenges in applying machine learning algorithms to biological sequence data is how to numerically represent a sequence in a numeric input vector. Feature extraction techniques capable of extracting numerical information from biological sequences have been reported in the literature. However, many of these techniques are not available in existing packages, such as mathematical descriptors. This paper presents a new package, MathFeature, which implements mathematical descriptors able to extract relevant numerical information from biological sequences, i.e. DNA, RNA and proteins (prediction of structural features along the primary sequence of amino acids). MathFeature makes available 20 numerical feature extraction descriptors based on approaches found in the literature, e.g. multiple numeric mappings, genomic signal processing, chaos game theory, entropy and complex networks. MathFeature also allows the extraction of alternative features, complementing the existing packages. To ensure that our descriptors are robust and to assess their relevance, experimental results are presented in nine case studies. According to these results, the features extracted by MathFeature showed high performance (0.6350–0.9897, accuracy), both applying only mathematical descriptors, but also hybridization with well-known descriptors in the literature. Finally, through MathFeature, we overcame several studies in eight benchmark datasets, exemplifying the robustness and viability of the proposed package. MathFeature has advanced in the area by bringing descriptors not available in other packages, as well as allowing non-experts to use feature extraction techniques.

Recent technological advances have led to an exponential expansion of biological sequence data and extraction of meaningful information through Machine Learning (ML) algorithms. This knowledge has improved the understanding of mechanisms related to several fatal diseases, e.g. Cancer and coronavirus disease 2019, helping to develop innovative solutions, such as CRISPR-based gene editing, coronavirus vaccine and precision medicine. These advances benefit our society and economy, directly impacting people’s lives in various areas, such as health care, drug discovery, forensic analysis and food processing. Nevertheless, ML-based approaches to biological data require representative, quantitative and informative features. Many ML algorithms can handle only numerical data, and therefore sequences need to be translated into a numerical feature vector. This process, known as feature extraction, is a fundamental step for developing high-quality ML-based models in bioinformatics, by allowing the feature engineering stage, with design and selection of suitable features. Feature engineering, ML algorithm selection and hyperparameter tuning are often manual and time-consuming processes, requiring extensive domain knowledge. To deal with this problem, we present a new package: BioAutoML. BioAutoML automatically runs an end-to-end ML pipeline, extracting numerical and informative features from biological sequence databases, using the MathFeature package, and automating the feature selection, ML algorithm(s) recommendation and tuning of the selected algorithm(s) hyperparameters, using Automated ML (AutoML). BioAutoML has two components, divided into four modules: (1) automated feature engineering (feature extraction and selection modules) and (2) Metalearning (algorithm recommendation and hyper-parameter tuning modules). We experimentally evaluate BioAutoML in two different scenarios: (i) prediction of the three main classes of noncoding RNAs (ncRNAs) and (ii) prediction of the eight categories of ncRNAs in bacteria, including housekeeping and regulatory types. To assess BioAutoML predictive performance, it is experimentally compared with two other AutoML tools (RECIPE and TPOT). According to the experimental results, BioAutoML can accelerate new studies, reducing the cost of feature engineering processing and either keeping or improving predictive performance. BioAutoML is freely available at https://github.com/Bonidia/BioAutoML.

Recently, data mining studies are being successfully conducted to estimate several parameters in a variety of domains. Data mining techniques have attracted the attention of the information industry and society as a whole, due to a large amount of data and the imminent need to turn it into useful knowledge. However, the effective use of data in some areas is still under development, as is the case in sports, which in recent years, has presented a slight growth; consequently, many sports organizations have begun to see that there is a wealth of unexplored knowledge in the data extracted by them. Therefore, this article presents a systematic review of sports data mining. Regarding years 2010 to 2018, 31 types of research were found in this topic. Based on these studies, we present the current panorama, themes, the database used, proposals, algorithms, and research opportunities. Our findings provide a better understanding of the sports data mining potentials, besides motivating the scientific community to explore this timely and interesting topic.

Machine learning algorithms have been applied to numerous transcript datasets to identify Long non-coding RNAs (lncRNAs). Nevertheless, before these algorithms are applied to RNA data, features must be extracted from the original sequences. As many of these features can be redundant or irrelevant, the predictive performance of the algorithms can be improved by performing feature selection. However, the most current approaches usually select features independently, ignoring possible relations. In this paper, we propose a new model, which identifies the best subsets, removing unnecessary, irrelevant, and redundant predictive features, taking the importance of their co-occurrence into account. The proposed model is based on decomposing solutions and is called $k$ -rounds of decomposition features. In this model, the least relevant features are suppressed according to their contribution to a classification task. To evaluate our proposal, we extract from 5 plant species datasets, a set of features based on sequence structures, using GC content, k-mer (1-6), sequence length, and Open Reading Frame. Next, we apply 5 metaheuristics approaches (Genetic Algorithm, ($\mu + \lambda $ ) Evolutionary Algorithm, Artificial Bee Colony, Ant Colony Optimization, and Particle Swarm Optimization) to select the best feature subsets. The main contribution of this work was to include in each metaheuristic a decomposition model that uses round and voting scheme. To investigate its relevance, we select the REPTree classifier to assess the predictive capacity of each subset of features selected in 8 plant species. We identified that the inclusion of the proposed decomposition model significantly reduces the dimensions of the datasets and improves predictive performance, regardless of the metaheuristic. Furthermore, the resulting pipeline has been compared with five approaches in the literature, for lncRNA, when it also showed superior predictive performance. Finally, this study generated a new pipeline to find a minimum number of features in lncRNAs and biological sequences.

Machine Learning (ML) algorithms have been important tools for the extraction of useful knowledge from biological sequences, particularly in healthcare, agriculture, and the environment. However, the categorical and unstructured nature of these sequences requiring usually additional feature engineering steps, before an ML algorithm can be efficiently applied. The addition of these steps to the ML algorithm creates a processing pipeline, known as end-to-end ML. Despite the excellent results obtained by applying end-to-end ML to biotechnology problems, the performance obtained depends on the expertise of the user in the components of the pipeline. In this work, we propose an end-to-end ML-based framework called BioPrediction-RPI, which can identify implicit interactions between sequences, such as pairs of non-coding RNA and proteins, without the need for specialized expertise in end-to-end ML. This framework applies feature engineering to represent each sequence by structural and topological features. These features are divided into feature groups and used to train partial models, whose partial decisions are combined into a final decision, which, provides insights to the user by giving an interpretability report. In our experiments, the developed framework was competitive when compared with various expert-created models. We assessed BioPrediction-RPI with 12 datasets when it presented equal or better performance than all tools in 40% to 100% of cases, depending on the experiment. Finally, BioPrediction-RPI can fine-tune models based on new data and perform at the same level as ML experts, democratizing end-to-end ML and increasing its access to those working in biological sciences.