Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease it.

In a large bowl, whisk together the flour, granulated sugar, brown sugar, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon.

In a separate bowl, whisk the pumpkin puree, vegetable oil, eggs, vanilla extract, and milk until smooth.

Add the wet ingredients to the dry ingredients and stir just until combined. Do not overmix.

In another bowl, beat the cream cheese, sugar, egg yolk, vanilla extract, and flour until smooth and creamy.

Divide the pumpkin batter evenly among the muffin cups, filling each about 2/3 full.

Spoon about 1 tablespoon of the cream cheese filling into the center of each muffin. Gently press it down slightly into the batter.

Sprinkle pumpkin seeds over the tops of the muffins.

Bake for 18 to 22 minutes, or until the muffins are set and a toothpick inserted into the pumpkin portion comes out clean or with a few moist crumbs.

Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.