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The phrase "compare the differences in" is correct and usable in written English.
You can use it any time you want to contrast two things by exploring the ways in which they differ. For example, "Let's compare the differences in the way that two different politicians responded to the same issue."
Exact(60)
(2) We will use other multi-objective optimization algorithms apart from NSGA-II to solve optional paths and compare the differences in performance between different algorithms.
An independent one-way ANOVA was used to compare the differences in functional fitness among the different groups.
I tried three or four types of bean from different producing countries to compare the differences in tastes and flavours.
The χ test was used to compare the differences in HPV genotype representation for different cytological grades.
The SES quintiles were used to compare the differences in level of acceptability and sources of the different contraceptives.
Shortest path analysis used for network comparison was performed to compare the differences in distance for each pair of metabolites, when different conditions are applied to the system.
To compare the differences in the survival between the groups, the chi-square test was used.
We compare the differences in the detection performance between the constant and the random cases.
To compare the differences in the hemodynamics between normal pregnancy and preeclampsia, using thoracic electrical bioimpedance.
In this article, I compare the differences in Scandinavian nationality law and the political processes that led to these changes.
Finally, the SD models are employed to compare the differences in the development of spatial patterns of waterway systems under two modes of governance and different investment structures.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com