The basic meaning of with is "with", there is a concept of accompaniment, or denotes the use of some kind of tangible tool, usually made of accompaniment. The nouns that follow with it generally have an article.
Example Sentence 1: I come into the classroom with a bag. I walked into the classroom with my bag. (Table with)
Example Sentence 2: Tom cleaned the room with a broom. Tom cleans the room with a broom (the table uses some kind of tangible tool)
The basic meaning of By is "pass", which means the use of a certain means or means, and the nouns that follow by by by are all without an article.
Example Sentence 1: I go to school by bus. I took the bus to school. (Table by some means)
Example Sentence 2: They made the car by hand. They built this car by hand. (by some means)
Example Sentence 3: I reach you by radio. I contact you by radio. (by some means)
In addition to the basic usage mentioned above, by can also be used in the passive voice to mean "be", which is used to connect the person who sent the action.
Example Sentence 4: The house was bought by her yesterday. She bought the house yesterday.