I have been trying to solve this problem for over a year without much progress. It is part of a research project I'm doing, but I will illustrate it with a story example I made up, because the actual domain of the problem is a bit confusing (eye-tracking).
You are a plane tracking an enemy ship that travels across the ocean, so you have collected a series of (x,y,time) coordinates of the ship. You know that a hidden submarine travels with the ship to protect it, but while there is a correlation between their positions, the submarine often wanders off from the ship, so while it's often near it, it can also be on the other side of the world occasionally. You want to predict the path of the submarine, but unfortunately it is hidden from you.
But one month in April you notice the submarine forgets to hide itself, so you have a series of coordinates for both the submarine and the ship throughout 1,000 trips. Using this data, you'd like to build a model to predict the hidden submarine's path given just the ship's movements. The naive baseline would be to say "submarine position guess = "ship's current position" but from the April data where the submarine was visible, you notice there is a tendency for the submarine to be ahead of the ship a bit, so "submarine position guess = ship's position in 1 minute" is an even better estimate. Furthermore, the April data shows that when the ship pauses in the water for an extended period, the submarine is likely to be far away patrolling the coastal waters. There are other patterns of course.
How would you build this model, given the April data as training data, to predict the submarine's path? My current solution is an ad-hoc linear regression where the factors are "trip time", "ship's x coordinate", "was ship idle for 1 day", etc. and then having R figure out the weights and doing a cross-validation. But I would really love a way to generate these factors automatically from the April data. Also, a model that uses sequence or time would be nice, since the linear regression doesn't and I think it's relevant.
Thanks for reading through all this and I would be happy to clarify anything.