Preheat oven to 425 degrees and line a muffin pan with 18 liners. Set pan aside.

In a large bowl, whisk together flour, spices, baking powder, baking soda and salt until well combined. Set aside.

In a medium bowl, whisk together pumpkin, 1 cup granulated sugar and brown sugar. Mix in melted butter, eggs and vanilla extract. Pour wet ingredients over dry ingredients and mix until just combined. Fill muffin cups about ¾ of the way full.

In a small bowl, beat together cream cheese, ¼ cup granulated sugar, egg yolk and 2 teaspoons vanilla extract until well blended.

Top muffins with 1 tablespoon of cream cheese mixture, swirling into batter using a toothpick or a spoon.

Bake at 425 degrees for five minutes. Reduce heat to 375 degrees and continue to bake for an additional 10-13 minutes or until a toothpick comes out clean.