Is it valid to say 'in the presence of something' [closed]

Although "doing stuff" in a haystack sounds like much more fun, maybe you could get your point (the difficulty) across in your title by alluding to the haystack metaphor:

Finding synapses in an artifact stack/a stack of artifacts.

or to the “roses among the thorns” expression:

Finding synapses among the artifacts.

(Do you really need to use “data” in the title?) (and if you ever were seriously considering using “Doing stuff” in your title, using the above suggestions would be no less suitable, imo)

If the inclusion of the word “data” in the title is required (and if you were just using “doing stuff” as a place-filler for the sole purpose of this question) you could consider:

Finding synapses in artifact-ridden data

or

Finding synapses in [among] artifactual data [points].

(examples of usage from Google Books)

"Doing stuff in data in the presence of artifacts" is grammatical, but doesn't really mean what you intend.

"in the presence of X" is usually used with X being a person (though it could be something inanimate), and means more than just that X is present: it means that its presence is important for what you are doing, in the sense that if X were not present, it would not be proper, or not be official, or not be worthwhile. X being absent would not stop you doing it, but would render the whole activity less valuable in some way.

Here you mean almost the opposite: that X (the errors) being present makes the activity harder. I would say "Doing Stuff in Data with Artifacts Present". I would perhaps even omit the "Present", and say "with Artifacts" or "containing Artifacts". (These suggestions introduce a syntactic ambiguity which is not present in your original, because the "with/containing artifacts [present]" could attach to the Noun Phrase "Data" rather than to the verb "Doing"; but I don't think the meaning is much affected, so it doesn't matter.)