Dataset Information

Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm.

ABSTRACT: Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate recombinants and parents, as well as appropriate statistical methods to correct for the large number of comparisons performed. In 2007, a computation was introduced for an exact nonparametric mosaicism statistic that gave high-precision P values for putative recombinants. This exact computation meant that multiple-comparisons corrected P values also had high precision, which is crucial when performing millions or billions of tests in large databases. Here, we introduce an improvement to the algorithmic complexity of this computation from O(mn3) to O(mn2), where m and n are the numbers of recombination-informative sites in the candidate recombinant. This new computation allows for recombination analysis to be performed in alignments with thousands of polymorphic sites. Benchmark runs are presented on viral genome sequence alignments, new features are introduced, and applications outside recombination analysis are discussed.

SUBMITTER: Lam HM

PROVIDER: S-EPMC5850291 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Publications

Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm.

Lam Ha Minh HM Ratmann Oliver O Boni Maciej F MF

Molecular biology and evolution 20180101 1

Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate recombinants and parents, as well as appropriate statistical methods to correct for the large number of comparisons performed. In 2007, a computation was introduced for an exact nonparametric mosaicism statistic that gave high-precision P values for putative recombinants. This exact computation meant that multiple-comparisons corrected P values also ha ...[more]

PMID: 29029186

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Project description:Object detection based on deep learning has made great progress in the past decade and has been widely used in various fields of daily life. Model lightweighting is the core of deploying target detection models on mobile or edge devices. Lightweight models have fewer parameters and lower computational costs, but are often accompanied by lower detection accuracy. Based on YOLOv5s, this article proposes an improved lightweight target detection model, which can achieve higher detection accuracy with smaller parameters. Firstly, utilizing the lightweight feature of the Ghost module, we integrated it into the C3 structure and replaced some of the C3 modules after the upsample layer on the neck network, thereby reducing the number of model parameters and expediting the model's inference process. Secondly, the coordinate attention (CA) mechanism was added to the neck to enhance the model's ability to pay attention to relevant information and improved detection accuracy. Finally, a more efficient Simplified Spatial Pyramid Pooling-Fast (SimSPPF) module was designed to enhance the stability of the model and shorten the training time of the model. In order to verify the effectiveness of the improved model, experiments were conducted using three datasets with different features. Experimental results show that the number of parameters of our model is significantly reduced by 28% compared with the original model, and mean average precision (mAP) is increased by 3.1%, 1.1% and 1.8% respectively. The model also performs better in terms of accuracy compared to existing lightweight state-of-the-art models. On three datasets with different features, mAP of the proposed model achieved 87.2%, 77.8% and 92.3%, which is better than YOLOv7tiny (81.4%, 77.7%, 90.3%), YOLOv8n (84.7%, 77.7%, 90.6%) and other advanced models. When achieving the decreased number of parameters, the improved model can successfully increase mAP, providing great reference for deploying the model on mobile or edge devices.

Dataset Information

Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm.

Publications

Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm.

Similar Datasets

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