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Preheat oven to 350 degrees Fahrenheit. Line 12 muffin cups with foil liners or butter 12 6-ounce ramekins. Sift together the flour, baking soda, pumpkin pie spice, and salt.
Using an electric mixer, beat the cream cheese with the sugar and vanilla, then spoon into a small bowl and set aside.
Without washing the mixing bowl, cream the butter and sugar until fluffy. Add the eggs and vanilla and mix to combine, then beat in the pumpkin. With the mixer on low, add the flour mixture and stir just to combine. Fold in the chocolate chunks.
Divide the batter among the muffin cups. Dollop a spoonful of the cream cheese mixture among the muffin cups.
Bake for 20 minutes, or until puffed and set, just browning around the edges but not too brown on top. (It’s okay for these to be a bit underbaked.) Serve slightly warm or at room temperature.