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How do I train a transformer for pointwise inference of time series data?

My dataset is composed of different particle trajectories over time [x(t), y(t)]. Each trajectory has a different length from another and my goal is to perform pointwise regression, i.e. estimate a continuous value a(t) for each time step. Thus if my input is of dimension [batch_size, sequence_length, trajectory_coordinates] I expect my output to be something like [batch_size, sequence_length, 1].