Preheat oven to 375 F. Line 12 medium muffin cups with paper liners or spray bottoms with cooking spray. In a food processor, combine flours, brown sugar, cocoa powder, baking powder, baking soda, and salt. Pulse a few times to mix. Transfer mixture to a large mixing bowl. In food processor, process soy milk, soy yogurt, oil, and vanilla until smooth. Add wet ingredients to dry ingredients and stir by hand, quickly and lightly, until just mixed. Divide batter evenly between prepared muffin cups. Sprinkle with sliced almonds, if desired. Bake for 20 to 25 minutes.