Preheat oven to 375, and place cupcake liners into a muffin pan.
In a medium bowl combine the flour, pumpkin spice, baking soda, and salt. Whisk until combined and set aside.
In a large bowl combine pumpkin puree, sugar and the brown sugar. Stir until combined and slowly beat in the eggs, vegetable oil, and vanilla extract.
Slowly stir the flour mixture you set aside into the pumpkin mixture, until well combined with no lumps.
Fill muffin liners about 3/4 of the way full, they don't rise too much.
Again use the bowl from the flour mixture, to make the cream cheese mixture. For this, beat together the cream cheese, sugar, egg yolk and vanilla extract. Stop when it's well combined with no lumps.
Top each liner filled with pumpkin mixture with about 2 tbsp of cream cheese mixture. Use a toothpick or knife to swirl the two mixtures together, making sure you don't puncture the cupcake liner.
Bake muffins for 17-19 minutes. They are done when an inserted toothpick comes out clean.
Enjoy warm or slightly chilled, refrigerate to store as they can become tacky when left out.