Abstract

In contrast to the well characterized mitotic machinery in eukaryotes it seems as if there is no universal mechanism organizing chromosome segregation in all bacteria. Apparently, some bacteria even use combinations of different segregation mechanisms such as protein machines or rely on physical forces. The identification of the relevant mechanisms is a difficult task. Here, we introduce a new machine learning approach to this problem. It is based on the analysis of trajectories of individual loci in the course of chromosomal segregation obtained by fluorescence microscopy. While machine learning approaches have already been applied successfully to trajectory classification in other areas, so far it has not been possible to use them to discriminate segregation mechanisms in bacteria. A main obstacle for this is the large number of trajectories required to train machine learning algorithms that we overcome here by using trajectories obtained from molecular dynamics simulations. We used these trajectories to train four different machine learning algorithms, two linear models and two tree-based classifiers, to discriminate segregation mechanisms and possible combinations of them. The classification was performed once using the complete trajectories as high-dimensional input vectors as well as on a set of features which were used to transform the trajectories into low-dimensional input vectors for the classifiers. Finally, we tested our classifiers on shorter trajectories with duration times comparable (or even shorter) than typical experimental trajectories and on trajectories measured with varying temporal resolutions. Our results demonstrate that machine learning algorithms are indeed capable of discriminating different segregation mechanisms in bacteria and to even resolve combinations of the mechanisms on rather short time scales. In this repository, the trained machine learning models and the corresponding data sets are stored. The code for evaluating the models can be found in the GitHub repository https://github.com/DavidGeisel/ML_Classification_MD_Trajectories.
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Date2021-09-11
AuthorsGeisel, David
LicenseCreative Commons Attribution 4.0
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README.txt .txt2.194Kb612bc2c4aae41f807deda84285c86bff
svm.tar .tar2.799Gb0d8e78b346140991a84bead019d15f6e
random-forest.tar .tar5.626Gb7c0c40333853c58411eb76d00e45cbca
logistic-regression.tar .tar2.568Gbbdd07c477bcf71fe6489eae868338ae0
gradient-boosting.tar .tar9.804Gb7e85f07c2a529b4112ab719db0216898
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Creative Commons Attribution 4.0
Except where otherwise noted, this item's license is described as Creative Commons Attribution 4.0