EigenWorms

秀丽隐杆线虫是一种蛔虫，通常用作遗传学研究中的模式生物。众所周知，这些蠕虫的运动是了解行为遗传学的有用指标。 Brown {\em 等人}[1] 描述了一种系统，用于记录蠕虫在琼脂板上的运动并测量一系列人类定义的特征[2]。已经表明，秀丽隐杆线虫在琼脂板上采用的形状空间可以用六种基本形状或特征虫的组合来表示。一旦提取了蠕虫轮廓，当形状投影到六个特征蠕虫上时，每个蠕虫运动帧都可以由六个标量捕获，这些标量表示沿每个维度的幅度。使用为 [1] 中描述的工作收集的数据，我们解决了根据时间序列将单个蠕虫分类为野生型或突变体的问题。数据是从秀丽隐杆线虫行为数据库中提取的[3]。我们有 259 个案例，我们拆分了 131 个训练和 128 个测试。我们已将每个系列截断为可用的最短时间。每个系列有 17984 个观测值。每个蠕虫被分类为野生型（N2 参考株）或四种突变类型之一：goa-1； UNC-1； unc-38 和 unc-63。 [1] A. Brown、E. Yemini、L. Grundy、T. Jucikas 和 W. Schafer，行为基序词典揭示了影响秀丽隐杆线虫运动的基因簇，美国国家科学院院刊美国（PNAS），第一卷。 10，没有。 2, pp. 791 796, 2013. [2] E. Yemini、T. Jucikas、L. Grundy、A. Brown 和 W. Schafer，秀丽隐杆线虫行为表型数据库，自然方法，第一卷。 10, pp. 877 879, 2013. [3] 秀丽隐杆线虫行为数据库

Caenorhabditis elegans is a species of nematode commonly used as a model organism in genetic research. It is well-known that the locomotion of these worms serves as a valuable indicator for understanding behavioral genetics. Brown et al. [1] described a system for recording the locomotion of worms on agar plates and measuring a set of human-defined features [2]. It has been demonstrated that the shape space adopted by C. elegans on agar plates can be represented by a combination of six basic shapes, or "feature worms". Once the worm contour is extracted, each worm locomotion frame can be captured by six scalar values representing the magnitude along each dimension when the shape is projected onto the six feature worms. Using the data collected for the work described in [1], we address the problem of classifying individual worms as either wild-type or mutant based on their time-series data. The data were extracted from the Caenorhabditis elegans Behavior Database [3]. We have a total of 259 cases, which we split into 131 training samples and 128 test samples. We truncated each time series to match the length of the shortest available one; each series contains 17,984 observations. Each worm is classified as either wild-type (N2 reference strain) or one of four mutant types: goa-1, UNC-1, unc-38, and unc-63.
[1] A. Brown, E. Yemini, L. Grundy, T. Jucikas, and W. Schafer. "A dictionary of behavioral motifs reveals clusters of genes affecting Caenorhabditis elegans locomotion". Proceedings of the National Academy of Sciences of the United States of America (PNAS), vol. 10, no. 2, pp. 791–796, 2013.
[2] E. Yemini, T. Jucikas, L. Grundy, A. Brown, and W. Schafer. "Caenorhabditis elegans behavioral phenotype database". Nature Methods, vol. 10, pp. 877–879, 2013.
[3] Caenorhabditis elegans Behavior Database

搜集汇总

背景与挑战

背景概述

EigenWorms数据集是一个用于时间序列分类的数据集，包含259个秀丽隐杆线虫的运动行为案例，用于区分野生型和四种突变类型。数据集由伦敦大学学院于2018年发布，适用于遗传学和行为学研究。