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Yes, you can file as Head of Household with a non-resident spouse.

In the My Info/Personal Info section, you can change your Filing Status by checking the box on that page.

On the next page, choose the option 'non-resident spouse'.

You will need to indicate that you provided over 50% of household support, and run through your Dependent's screens again to confirm them as your dependents. 

Here's more info on Filing as Head of Household if Married.