Preheat oven to 350 degrees F. and place paper baking cups in muffin pan. You will need 18.
In a medium bowl whisk together the flour, pumpkin pie spice, baking soda and salt and set aside.
In a separate bowl whisk together the can of pumpkin, sugar and brown sugar.
Beat in eggs, canola oil and vanilla extract.
Slowly stir in the flour mixture until there are no lumps. Fill muffin tins 3/4 full.
In a medium bowl beat cream cheese, sugar, egg yolk and vanilla until smooth.
Top each muffin with 1 Tbsp of cream cheese mixture; use a toothpick to swirl with the batter.
Bake muffins 20 - 22 minutes or until a toothpick inserted in the center comes out clean.
Store covered in the refrigerator.