A framework for modeling traffic speed in a transportation network analyzes both the spatial and temporal dependencies in probe-based traffic speeds, historical weather data, and forecasted weather data, using multiple machine learning models. A decentralized partial least squares (PLS) regression model predicts short-term speed using localized, historical probe-based traffic data, and a deep learning model applies the predicted short-term speed to further estimate traffic speed at specified times and at specific locations in the transportation network for predicting traffic bottlenecks and other future traffic states.