Modeling deformable objects is an important preliminary step for performing robotic manipulation tasks with more autonomy and dexterity. Currently, generalization capabilities in unstructured environments using analytical approaches are limited, mainly due to the lack of adaptation to changes in the object shape and properties. Therefore, this paper proposes the design and implementation of a data-driven approach, which combines machine learning techniques on graphs to estimate and predict the state and transition dynamics of deformable objects with initially undefined shape and material characteristics. The learned object model is trained using RGB-D sensor data and evaluated in terms of its ability to estimate the current state of the object shape, in addition to predicting future states with the goal to plan and support the manipulation actions of a robotic hand.