We examine the electromagnetic (EM) and gravitational wave (GW) signatures of stellar-mass compact objects (COs) spiraling into a supermassive black hole (extreme mass-ratio inspirals or EMRIs), embedded in a thin, radiation-pressure dominated, accretion disk. At large separations, the tidal effect of the secondary CO clears a gap. We show that the gap refills during the late GW-driven phase of the inspiral, leading to a sudden EM brightening of the source. The accretion disk leaves an imprint

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... n the GW through its angular momentum exchange with the binary, the mass increase of the binary members due to accretion, and its gravity. We compute the disk-modified GWs both in an analytical Newtonian approximation and in a numerical effective-one-body approach. We find that disk-induced migration provides the dominant perturbation to the inspiral, with weaker effects from the mass accretion onto the CO and hydrodynamic drag. Depending on whether a gap is present, the perturbation of the GW phase is between 10 and 1000 radians per year, detectable with the future Laser Interferometer Space Antenna (LISA) at high significance. The Fourier transform of the disk-modified GW in the stationary phase approximation is sensitive to disk parameters with a frequency trend different from post-Newtonian vacuum corrections. Our results suggest that observations of EMRIs may place new sensitive constraints on the physics of accretion disks.