Let's rephrase it into something that will give the meaning more clearly.
The study has taken that option because a single relationship often enhances computational efficiency in resolving ambiguities, although the result is an incomplete graph representation.
You're weighing positive and negative factors, to make a decision.
decision because positives, although negatives.
Now, English allows a lot of flexibility, so you can reshuffle these freely.
Because a single relationship often enhances computational efficiency in resolving ambiguities, the study has taken that option, although the result is an incomplete graph representation.
Although the result is an incomplete graph representation, because a single relationship often enhances computational efficiency in resolving ambiguities, the study has taken that option.
The study has taken that option, although the result is an incomplete graph representation, because a single relationship often enhances computational efficiency in resolving ambiguities.
It's best to keep the positives before the negatives though - in the latter two examples the reader may wrongly conclude the 'because' is continuation of the 'although' clause, strengthening it instead of opposing it ('the incomplete representation being a result of the enhanced computational efficiency...'). Still, it's all grammatically correct.