Making a high speed USB communication from STM32F4 and Java on Linux PC
USB protocol is divided into a number of classes , such as HID,Mass Storage,Audio etc.

1.You should try to look into a class that requires to transfer data at a high bit rate, examples of such classes would be Video or Mass Storage devices.
Classes which use bulk or isochronous packets to transfer data over the bus will have high bit rates,because they have a larger packet size and can have a bigger time slots to use the bus.

2.Then you should look at the code samples shipped with your board for the these above mentioned classes.

Could you give a little more insight on what data do you want to transfer between the board and the PC?