I have read a sentence that is The soup base is usually made from soybean paste.
1. Can I use made by?-- No. 'By' refers to the agent: 'The soup base is made by the assistant chef'.' 2. What is the difference between those two?-- See #1
No -- the soup base can be made of soybean paste or made from soybean paste.
The soup is made by the chef. Or, The soup is made by adding soup base and chopped vegetables to boiling water.
Sometimes "made of" and "made from" can be used interchangeably. In general, though, the difference between being made of something and being made from