Showing papers by "Jesús Alcalá-Fdez published in 2020"
TL;DR: A novel rule-based XAI strategy (including pre-processing, knowledge-extraction and functional validation) for finding biologically relevant sequential patterns from longitudinal human gene expression data (GED) and proves the goodness of this strategy for the mining of biologically relevant gene-gene temporal relations.
Abstract: Until date, several machine learning approaches have been proposed for the dynamic modeling of temporal omics data. Although they have yielded impressive results in terms of model accuracy and predictive ability, most of these applications are based on "Black-box" algorithms and more interpretable models have been claimed by the research community. The recent eXplainable Artificial Intelligence (XAI) revolution offers a solution for this issue, were rule-based approaches are highly suitable for explanatory purposes. The further integration of the data mining process along with functional-annotation and pathway analyses is an additional way towards more explanatory and biologically soundness models. In this paper, we present a novel rule-based XAI strategy (including pre-processing, knowledge-extraction and functional validation) for finding biologically relevant sequential patterns from longitudinal human gene expression data (GED). To illustrate the performance of our pipeline, we work on in vivo temporal GED collected within the course of a long-term dietary intervention in 57 subjects with obesity (GSE77962). As validation populations, we employ three independent datasets following the same experimental design. As a result, we validate primarily extracted gene patterns and prove the goodness of our strategy for the mining of biologically relevant gene-gene temporal relations. Our whole pipeline has been gathered under open-source software and could be easily extended to other human temporal GED applications.
39 citations
TL;DR: A two‐level taxonomy is proposed according to whether the time variable is considered to provide order to the data collection and to locate some temporal constraints, or whether it is considered as an attribute within the learning process.
Abstract: Association rules are commonly used to provide decision‐makers with knowledge that helps them to make good decisions. Most of the published proposals mine association rules without paying particular attention to temporal information. However, in real‐life applications data usually change over time or presenting different temporal situations. Therefore, the extracted knowledge may not be useful, since we may not know whether the rules are currently applicable or whether they will be applicable in the future. For this reason, in recent years, many methods have been proposed in the literature for mining temporal association rules, which introduce a greater predictive and descriptive power providing an additional degree of interestingness. One of the main problems in this research field is the lack of visibility most works suffer since there is no standard terminology to refer to it, making it difficult to find and compare proposals and studies in the field. This contribution attempts to offer a well‐defined framework that allows researchers both to easily locate the previous proposals and to propose well‐grounded methods in the future. To accomplish both objectives, a two‐level taxonomy is proposed according to whether the time variable is considered to provide order to the data collection and to locate some temporal constraints, or whether it is considered as an attribute within the learning process. Some recent applications, available software tools, and a bibliographical analysis in accordance with the Web of Science are also shown. Finally, some critical considerations and potential further directions are discussed.
10 citations
TL;DR: It is demonstrated that the pGRS is strongly associated with childhood BMI Z-Score, and that it could be used as a good predictor of obesity longitudinal trajectories during puberty, and it was shown that certain environmental factors interact with the genetic predisposition to the disease.
Abstract: Polygenetic risk scores (pGRSs) consisting of adult body mass index (BMI) genetic variants have been widely associated with obesity in children populations. The implication of such obesity pGRSs in the development of cardio-metabolic alterations during childhood as well as their utility for the clinical prediction of pubertal obesity outcomes has been barely investigated otherwise. In the present study, we evaluated the utility of an adult BMI predisposing pGRS for the prediction and pharmacological management of obesity in Spanish children, further investigating its implication in the appearance of cardio-metabolic alterations. For that purpose, we counted on genetics data from three well-characterized children populations (composed of 574, 96 and 124 individuals), following both cross-sectional and longitudinal designs, expanding childhood and puberty. As a result, we demonstrated that the pGRS is strongly associated with childhood BMI Z-Score (B = 1.56, SE = 0.27 and p-value = 1.90 × 10-8), and that could be used as a good predictor of obesity longitudinal trajectories during puberty. On the other hand, we showed that the pGRS is not associated with cardio-metabolic comorbidities in children and that certain environmental factors interact with the genetic predisposition to the disease. Finally, according to the results derived from a weight-reduction metformin intervention in children with obesity, we discarded the utility of the pGRS as a pharmacogenetics marker of metformin response.
1 citations