Dataset Information

Networks of plants: how to measure similarity in vegetable species.

ABSTRACT: Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome similar problems and to exploit possibilities from environment. In this paper we introduce various quantitative measures based on recent advancements in complex network theory that allow to measure the effective similarities of various species. By using this approach on the similarity in fruit-typology ecological traits we obtain a clear plant classification in a way similar to traditional taxonomic classification. This result is not trivial, since a similar analysis done on the basis of diaspore morphological properties do not provide any clear parameter to classify plants species. Complex network theory can then be used in order to determine which feature amongst many can be used to distinguish scope and possibly evolution of plants. Future uses of this approach range from functional classification to quantitative determination of plant communities in nature.

SUBMITTER: Vivaldo G

PROVIDER: S-EPMC4895227 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Networks of plants: how to measure similarity in vegetable species.

Vivaldo Gianna G Masi Elisa E Pandolfi Camilla C Mancuso Stefano S Caldarelli Guido G

Scientific reports 20160607

Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome similar problems and to exploit possibilities from environment. In this paper we introduce various quantitative measures based on recent advancements in complex network theory that allow to measure the effective similarities of various species. By using this approach o ...[more]

PMID: 27271207

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Project description:This paper proposes a tuning method based on the Pythagorean fuzzy similarity measure and multi-criteria decision-making to determine the most suitable controller parameters for Fractional-order Proportional Integral Derivative (FOPID) and Integer-order Proportional Integral-Proportional Derivative (PI-PD) controllers. Due to the power of the Pythagorean fuzzy approach to evaluate a phenomenon with two memberships known as membership and non-membership, a multi-objective cost function based on the Pythagorean similarity measure is defined. The transient and steady-state properties of the system output were used for the multi-objective cost function. Thus, the determination of the controller parameters was considered a multi-criteria decision-making problem. Ant colony optimization for continuous domains (ACOR) and artificial bee colony (ABC) optimization are utilized to minimize multi-objective cost functions. The proposed method in the study was applied to three different systems: a second-order non-minimum phase stable system, a first-order unstable system with time delay, and a fractional-order unstable system with time delay, to validate its effectiveness. The cost function utilized in the proposed method is compared with the performance measures widely used in the literature based on the integral of the error, such as IAE (Integral Absolute Error), ITAE (Integral Time Absolute Error), ISE (Integral Square Error), and ITSE (Integral Time Square Error). The proposed method provides a more effective control performance by improving the system response characteristics compared to other cost functions. With the proposed method, the undershoot rate could be significantly reduced in the non-minimum phase system. In the other two systems, significant improvements were achieved compared to other methods by reducing the overshoot rate and oscillation. The proposed method does not require knowing the mathematical model of the system and offers a solution that does not require complex calculations. The proposed method can be used alone. Or it can be used as a second and fine-tuning method after a tuning process.

Project description:BackgroundBiological knowledge, and therefore Gene Ontology annotation sets, for human genes is incomplete. Recent studies have reported that biases in available GO annotations result in biased estimates of functional similarities of genes, but it is still unclear what the effect of incompleteness itself may be, even in the absence of bias. Pairwise gene similarities are used in a number of contexts, including gene "functional similarity" clustering and the related problem of functional ontology structure inference, but it is not known how different similarity measures or clustering methods perform on this task, and how the clusters are affected by annotation completeness.ResultsWe developed representations of both "complete" and "incomplete" GO annotation datasets based on experimentally-supported annotations from the GO database-specifically designed to model the incompleteness of human gene annotations-and computed semantic similarities for each set using a variety of different published measures. We then assessed the clusters derived from these measures using two different clustering methods: hierarchical clustering, and the CliXO algorithm. We find the CliXO algorithm, combined with appropriate measures, performs better than hierarchical clustering in reconstructing GO both when the data are complete, and incomplete. Some measures, particularly those that create a pairwise gene similarity by averaging over all pairwise annotation similarities, had consistently poor performance, and a few measures, such as Lin best-matched average and Relevance maximum, were generally among the best performers for a broad range in annotation completeness and types of GO classes. Finally, we show that for semantic similarity-based clustering, the multicellular organism process branch of the GO biological process ontology is more challenging to represent than the cellular process branch.ConclusionsWe assessed the effects of annotation completeness on the distribution of pairwise gene semantic similarity scores, and subsequent effects on the clusters derived from these scores. Our results suggest combinations of semantic similarity measures, gene-level scoring methods and clustering method that perform best for functional gene clustering using annotation sets of varying completeness. Overall, our results underscore the importance of increasing the completeness of GO annotations to for supporting computational analyses of gene function.

Project description:Single-cell analysis of the transcriptome deepens our understanding of an individual cell's contribution to its microenvironment. Using single-cell analysis to study complex biological processes requires state-of-the-art computational tools. Assessing similarity is highly important for bioinformatics algorithms in order to determine correlations between biological information. Similarity can appear by chance, particularly for low expressed entities. This is especially relevant in single cell RNA-seq (scRNA-seq) because the read counts obtained are lower compared to bulk RNA-sequencing and therefore classic bioinformatics tools are insufficient to obtain reproducible results. Recently, a Bayesian correlation scheme, that assigns low correlation values to correlations coming from low expressed genes, has been proposed to assess similarity for bulk RNA-seq and miRNA. This Bayesian method uses a prior distribution before using empirical evidence. Our goal was to extend the properties of this Bayesian correlation scheme to scRNA-seq data. We assessed 3 ways to compute similarity. First, we computed the similarity of each pair of genes over all cells. Second, we identified specific cell populations and computed the correlation in those specific cells. Third, we computed the similarity of each pair of genes over all clusters, by including the total mRNA expression in those cells. To study the effect of the number of cells on the method, we did not rely on simulated data, we generated 4 scRNA-seq mouse liver cell libraries with a varying number of input cells. Results: We show that Bayesian correlations are more reproducible than Pearson correlations in all the scenarios studied. Compared to Pearson correlations, Bayesian correlations have a smaller dependence on the number of input cells. We demonstrate that the Bayesian correlation algorithm assigns high similarity values to genes with a biological relevance in a specific population. Significance: Our results demonstrate that Bayesian correlation is a robust similarity measure for scRNA-seq datasets. The Bayesian method allows researchers to study similarity between pairs of genes without discarding low expressed entities and to minimize biasing the results by fake correlations. Taken together, using our method of Bayesian correlation the reproducibility of scRNA-seq experiments is increased significantly.

Dataset Information

Networks of plants: how to measure similarity in vegetable species.

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Networks of plants: how to measure similarity in vegetable species.

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