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We study the problem of learning the preferences of drivers and planners in the context of last mile delivery. Given a data set containing historical decisions and delivery locations, the goal is to capture the implicit preferences of the decision-makers. We consider two ways to use the historical data: one is through a probability estimation method that learns transition probabilities between stops (or zones). This is a fast and accurate method, recently studied in a VRP setting. Furthermore, we explore the use of machine learning to infer how to best balance multiple objectives such as distance, probability and penalties. Specifically, we cast the learning problem as a structured output prediction problem, where training is done by repeatedly calling the TSP solver. Another important aspect we consider is that for last-mile delivery, every address is a potential client and hence the data is very sparse. Hence, we propose a two-stage approach that first learns preferences at the zone level in order to compute a zone routing; after which a penalty-based TSP computes the stop routing. Results show that the zone transition probability estimation performs well, and that the structured output prediction learning can improve the results further. We hence showcase a successful combination of both probability estimation and machine learning, all the while using standard TSP solvers, both during learning and to compute the final solution; this means the methodology is applicable to other, real-life, TSP variants, or proprietary solvers.