Advanced Systems works on applied physics (plasma weaponry and teleportation), as well as other special projects, such as the Institute's reactor. The area also contains Madison Li's laboratory and a shooting range.
Advanced Systems has two sections, the main lab with a shooting range where iterative improvements to the Institute laser and pistol are being tested. This room also contains a forcefield-blocked access portal to the Institute reactor (an old CIT experimental nuclear reactor), with Madison Li's office in the adjacent room, complete with a bed.
The Institute Advanced Systems appears only in Fallout 4.