Evaporative cooling feature selection for genotypic data involving interactions
Evaporative cooling feature selection for genotypic data involving interactions
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DOI：
10.1093/bioinformatics/btm317
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发表时间：
2007-08-15
期刊：
影响因子：
5.8
通讯作者：
Moore, J. H.
中科院分区：
文献类型：
--
作者：
McKinney, B. A.;Reif, D. M.;Moore, J. H.
动机：基因分型的全基因组能力的发展导致了识别与表型分类相关的最小遗传变异子集的实际问题。在存在属性交互、噪声和小样本量的情况下，这一挑战尤其困难。方法：与蒸发的物理机制类似，我们引入了一种蒸发冷却（EC）特征选择算法，该算法寻求获得具有最佳信息温度（即最小噪声）的属性子集。EC使用类似于热力学自由能的属性质量度量，结合了Relief-F和互信息来蒸发（即去除）噪声特征，留下包含与给定表型相关的DNA序列变化的属性子集。结果：EC能够识别涉及影响其与表型关联的其他序列变异之间的相互作用（上位）的功能序列变异。这种能力在具有属性相互作用的模拟基因型数据和来自经历过天花疫苗接种后不良事件的个体的真实基因型数据上得到了证明。EC形式化允许我们将信息熵、能量和温度组合成一个单一的信息自由能属性质量度量，以平衡交互作用和主要影响。可用性：用Java编写的开源软件，可根据要求免费提供。联系人:brett.mckinney@gmail.com
Motivation: The development of genome-wide capabilities for genotyping has led to the practical problem of identifying the minimum subset of genetic variants relevant to the classification of a phenotype. This challenge is especially difficult in the presence of attribute interactions, noise and small sample size.Methods: Analogous to the physical mechanism of evaporation, we introduce an evaporative cooling (EC) feature selection algorithm that seeks to obtain a subset of attributes with the optimum information temperature (i. e. the least noise). EC uses an attribute quality measure analogous to thermodynamic free energy that combines Relief-F and mutual information to evaporate ( i. e. remove) noise features, leaving behind a subset of attributes that contain DNA sequence variations associated with a given phenotype.Results: EC is able to identify functional sequence variations that involve interactions ( epistasis) between other sequence variations that influence their association with the phenotype. This ability is demonstrated on simulated genotypic data with attribute interactions and on real genotypic data from individuals who experienced adverse events following smallpox vaccination. The EC formalism allows us to combine information entropy, energy and temperature into a single information free energy attribute quality measure that balances interaction and main effects.Availability: Open source software, written in Java, is freely available upon request.Contact: brett.mckinney@gmail.com