The documentation for `rsync` (see `man rsync`) has the `--exclude-from` parameter that will allow you to specify a list of exclusions in a file.
With regard to your set of example exclusions, the directories should be followed with `/` to show they are directories rather than unspecified files or directories, and those that are only in your home directory itself should be prefixed with `/` so that they don't match anywhere else.
In an exclusions file they could be listed like this
# Directories found anywhere
__pycache__/
checkpoints/
logs/
plot/
# Directories found only in HOME
/.git/