A method for modeling data affinities and data structures. In one implementation, a contextual distance may be calculated between a selected data point in a data sample and a data point in a contextual set of the selected data point. The contextual set may include the selected data point and one or more data points in the neighborhood of the selected data point. The contextual distance may be the difference between the selected data point's contribution to the integrity of the geometric structure of the contextual set and the data point's contribution to the integrity of the geometric structure of the contextual set. The process may be repeated for each data point in the contextual set of the selected data point. The process may be repeated for each selected data point in the data sample. A digraph may be created using a plurality of contextual distances generated by the process.