How you analyze this depends on which grammatical sect you adhere to, but adopting your very traditional terms the core sentence is
[Subject Our method] [Verb cannot achieve] [Direct Object 100% accuracy]
The 'Verb' can be further analyzed as
[Finite modal can] [Negator not] [Infinitive complement achieve]
What's left are two adjuncts, pieces which modify or qualify the core meaning:
[Participial phrase compared to the DART method]
This doesn't really belong anywhere in this sentence—you're not performing a comparison but stating an absolute (albeit vague) value—but you may understand it as a Sentence Adjunct modifier on the entire sentence, something which puts the sentence in context.
[Prepositional phrase due to the imprecise modeling]
Due to is best understood as a compound preposition taking the imprecise modeling as its object. This, too, may be understood as a Sentence Adjunct; it explains why your method cannot achieve 100% accuracy.
Because they are sentence adjuncts, these two phrases can fall at lots of ▼ places in the sentence, though the fact that there are two of them imposes some constraints.
▼ [Subject] ▼ [Finite modal can] [Negator not] ▼ [Infinitive complement achieve] [Direct Object 100% accuracy] ▼
Compared to the DART method, our method cannot achieve 100 percent accuracy due to the imprecise modeling.
Due to the imprecise modeling, our method cannot achieve 100 percent accuracy, compared to the DART method.
Our method, compared to the DART method, cannot, due to the imprecise modeling, achieve 100 percent accuracy.
Compared to the DART method, our method, due to the imprecise modeling, cannot achieve 100 percent accuracy.
They're all pretty awful, frankly.