Dataset Information

Multi-volume modeling of Eucalyptus trees using regression and artificial neural networks.

ABSTRACT: The stem volume of commercial trees is an important variable that assists in decision making and economic analysis in forest management. Wood from forest plantations can be used for several purposes, which makes estimating multi-volumes for the same tree a necessary task. Defining its exploitation and use potential, such as the total and merchantable volumes (up to a minimum diameter of interest), with or without bark, is a possible work. The goal of this study was to use different strategies to model multi-volumes of the stem of eucalyptus trees. The data came from rigorous scaling of 460 felled trees stems from four eucalyptus clones in high forest and coppice regimes. The diameters were measured at different heights, with the volume of the sections obtained by the Smalian method. Data were randomly separated into fit and validation data. The single multi-volume model, volume-specific models, and the training of artificial neural networks (ANNs) were fitted. The evaluation criteria of the models were: coefficient of determination, root mean square error, mean absolute error, mean bias error, as well as graphical analysis of observed and estimated values and distribution of residuals. Additionally, the t-test (? = 0.05) was performed between the volume obtained in the rigorous scaling and estimated by each strategy with the validation data. Results showed that the strategies used to model different tree stem volumes are efficient. The actual and estimated volumes showed no differences. The multi-volume model had the most considerable advantage in volume estimation practicality, while the volume-specific models were more efficient in the accuracy of estimates. Given the conditions of this study, the ANNs are more suitable than the regression models in the estimation of multi-volumes of eucalyptus trees, revealing greater accuracy and practicality.

SUBMITTER: de Azevedo GB

PROVIDER: S-EPMC7485850 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Multi-volume modeling of Eucalyptus trees using regression and artificial neural networks.

de Azevedo Gileno Brito GB Tomiazzi Heitor Vicensotto HV Azevedo Glauce Taís de Oliveira Sousa GTOS Teodoro Larissa Pereira Ribeiro LPR Teodoro Paulo Eduardo PE de Souza Marcos Talvani Pereira MTP Batista Tays Silva TS de Jesus Eufrade-Junior Humberto H Guerra Saulo Philipe Sebastião SPS

PloS one 20200911 9

The stem volume of commercial trees is an important variable that assists in decision making and economic analysis in forest management. Wood from forest plantations can be used for several purposes, which makes estimating multi-volumes for the same tree a necessary task. Defining its exploitation and use potential, such as the total and merchantable volumes (up to a minimum diameter of interest), with or without bark, is a possible work. The goal of this study was to use different strategies to ...[more]

PMID: 32915871

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Project description:Over the last decade, numerous computational methods have been developed in order to infer and model biological networks. Transcriptional networks in particular have attracted significant attention due to their critical role in cell survival. The majority of network inference methods use genome-wide experimental data to search for modules of genes with coherent expression profiles and common regulators, often ignoring the multi-layer structure of transcriptional cascades. Modeling methodologies on the other hand assume a given network structure and vary significantly in their algorithmic approach, ranging from over-simplified representations (e.g., Boolean networks) to detailed -but computationally expensive-network simulations (e.g., with differential equations). In this work we use Artificial Neural Networks (ANNs) to model transcriptional regulatory cascades that emerge during the stress response in Saccharomyces cerevisiae and extend in three layers. We confine the structure of the ANNs to match the structure of the biological networks as determined by gene expression, DNA-protein interaction and experimental evidence provided in publicly available databases. Trained ANNs are able to predict the expression profile of 11 target genes across multiple experimental conditions with a correlation coefficient >0.7. When time-dependent interactions between upstream transcription factors (TFs) and their indirect targets are also included in the ANNs, accurate predictions are achieved for 30/34 target genes. Moreover, heterodimer formation is taken into account. We show that ANNs can be used to (1) accurately predict the expression of downstream genes in a 3-layer transcriptional cascade based on the expression of their indirect regulators and (2) infer the condition- and time-dependent activity of various TFs as well as during heterodimer formation. We show that a three-layer regulatory cascade whose structure is determined by co-expressed gene modules and their regulators can successfully be modeled using ANNs with a similar configuration.

Project description:BackgroundNovel strategies are required in order to handle the huge amount of data produced by microarray technologies. To infer gene regulatory networks, the first step is to find direct regulatory relationships between genes building the so-called gene co-expression networks. They are typically generated using correlation statistics as pairwise similarity measures. Correlation-based methods are very useful in order to determine whether two genes have a strong global similarity but do not detect local similarities.ResultsWe propose model trees as a method to identify gene interaction networks. While correlation-based methods analyze each pair of genes, in our approach we generate a single regression tree for each gene from the remaining genes. Finally, a graph from all the relationships among output and input genes is built taking into account whether the pair of genes is statistically significant. For this reason we apply a statistical procedure to control the false discovery rate. The performance of our approach, named REGNET, is experimentally tested on two well-known data sets: Saccharomyces Cerevisiae and E.coli data set. First, the biological coherence of the results are tested. Second the E.coli transcriptional network (in the Regulon database) is used as control to compare the results to that of a correlation-based method. This experiment shows that REGNET performs more accurately at detecting true gene associations than the Pearson and Spearman zeroth and first-order correlation-based methods.ConclusionsREGNET generates gene association networks from gene expression data, and differs from correlation-based methods in that the relationship between one gene and others is calculated simultaneously. Model trees are very useful techniques to estimate the numerical values for the target genes by linear regression functions. They are very often more precise than linear regression models because they can add just different linear regressions to separate areas of the search space favoring to infer localized similarities over a more global similarity. Furthermore, experimental results show the good performance of REGNET.

Dataset Information

Multi-volume modeling of Eucalyptus trees using regression and artificial neural networks.

Publications

Multi-volume modeling of Eucalyptus trees using regression and artificial neural networks.

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