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Majority networks and local consensus algorithm.

ABSTRACT: In this paper, we study consensus behavior based on the local application of the majority consensus algorithm (a generalization of the majority rule) over four-connected bi-dimensional networks. In this context, we characterize theoretically every four-vicinity network in its capacity to reach consensus (every individual at the same opinion) for any initial configuration of binary opinions. Theoretically, we determine all regular grids with four neighbors in which consensus is reached and in which ones not. In addition, in those instances in which consensus is not reached, we characterize statistically the proportion of configurations that reach spurious fixed points from an ensemble of random initial configurations. Using numerical simulations, we also analyze two observables of the system to characterize the algorithm: (1) the quality of the achieved consensus, that is if it respects the initial majority of the network; and (2) the consensus time, measured as the average amount of steps to reach convergence.

SUBMITTER: Goles E

PROVIDER: S-EPMC9892600 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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Majority networks and local consensus algorithm.

Goles Eric E Medina Pablo P Santiváñez Julio J

Scientific reports 20230201 1

In this paper, we study consensus behavior based on the local application of the majority consensus algorithm (a generalization of the majority rule) over four-connected bi-dimensional networks. In this context, we characterize theoretically every four-vicinity network in its capacity to reach consensus (every individual at the same opinion) for any initial configuration of binary opinions. Theoretically, we determine all regular grids with four neighbors in which consensus is reached and in whi ...[more]

PMID: 36725907

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Project description:Motivation:Protein coding genes can be studied using long-read next generation sequencing. However, high rates of indel sequencing errors are problematic, corrupting the reading frame. Even the consensus of multiple independent sequence reads retains indel errors. To solve this problem, we introduce Reference-Informed Frame-Resolving multiple-Alignment Free template inference algorithm (RIFRAF), a sequence consensus algorithm that takes a set of error-prone reads and a reference sequence and infers an accurate in-frame consensus. RIFRAF uses a novel structure, analogous to a two-layer hidden Markov model: the consensus is optimized to maximize alignment scores with both the set of noisy reads and with a reference. The template-to-reads component of the model encodes the preponderance of indels, and is sensitive to the per-base quality scores, giving greater weight to more accurate bases. The reference-to-template component of the model penalizes frame-destroying indels. A local search algorithm proceeds in stages to find the best consensus sequence for both objectives. Results:Using Pacific Biosciences SMRT sequences from an HIV-1 env clone, NL4-3, we compare our approach to other consensus and frame correction methods. RIFRAF consistently finds a consensus sequence that is more accurate and in-frame, especially with small numbers of reads. It was able to perfectly reconstruct over 80% of consensus sequences from as few as three reads, whereas the best alternative required twice as many. RIFRAF is able to achieve these results and keep the consensus in-frame even with a distantly related reference sequence. Moreover, unlike other frame correction methods, RIFRAF can detect and keep true indels while removing erroneous ones. Availability and implementation:RIFRAF is implemented in Julia, and source code is publicly available at https://github.com/MurrellGroup/Rifraf.jl. Supplementary information:Supplementary data are available at Bioinformatics online.

Project description:AimConservation planning exercises increasingly rely on species distributions predicted either from one particular statistical model or, more recently, from an ensemble of models (i.e. ensemble forecasting). However, it has not yet been explored how different ways of summarizing ensemble predictions affect conservation planning outcomes. We evaluate these effects and compare commonplace consensus methods, applied before the conservation prioritization phase, to a novel method that applies consensus after reserve selection.LocationEurope.MethodsWe used an ensemble of predicted distributions of 146 Western Palaearctic bird species in alternative ways: four different consensus methods, as well as distributions discounted with variability, were used to produce inputs for spatial conservation prioritization. In addition, we developed and tested a novel method, in which we built 100 datasets by sampling the ensemble of predicted distributions, ran a conservation prioritization analysis on each of them and averaged the resulting priority ranks. We evaluated the conservation outcome against three controls: (i) a null control, based on random ranking of cells; (2) the reference solution, based on an expert-refined dataset; and (3) the independent solution, based on an independent dataset.ResultsNetworks based on predicted distributions were more representative of rare species than randomly selected networks. Alternative methods to summarize ensemble predictions differed in representativeness of resulting reserve networks. Our novel method resulted in better representation of rare species than pre-selection consensus methods.Main conclusionsRetaining information about the variation in the predicted distributions throughout the conservation prioritization seems to provide better results than summarizing the predictions before conservation prioritization. Our results highlight the need to understand and consider model-based uncertainty when using predicted distribution data in conservation prioritization.

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Majority networks and local consensus algorithm.

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Majority networks and local consensus algorithm.

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