For pasta - it is always dry weight due to the differences in cooking. The longer you cook pasta, the softer it gets and the more water it soaks up. So it would weigh heavier than pasta cooked for less time.
Other items, like meats can be done either way, just make sure that the calorie count you use is for either raw or cooked. In general 4 oz of raw meat cooks down to 3 oz.
I don't think it matters with soy, though.
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