To operate an autonomous vehicle, a rail agent is detected in a vicinity of the autonomous vehicle using a detection system. One or more tracks are determined on which the detected rail agent is possibly traveling, and possible paths for the rail agent are predicted based on the determined one or more tracks. One or more motion paths are determined for one or more probable paths from the possible paths, and a likelihood for each of the one or more probable paths is determined based on each motion plan. A path for the autonomous vehicle is then determined based on a most probable path associated with a highest likelihood for the rail agent, and the autonomous vehicle is operated using the determined path.