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In this paper, we examine the properties of the Jones polynomial using dimensionality reduction learning techniques combined with ideas from topological data analysis. Our data set consists of more than 10 million knots up to 17 crossings and two other special families up to 2001 crossings. We introduce and describe a method for using filtrations to analyze infinite data sets where representative sampling is impossible or impractical, an essential requirement for working with knots and the data from knot invariants. In particular, this method provides a new approach for analyzing knot invariants using Principal Component Analysis. Using this approach on the Jones polynomial data, we find that it can be viewed as an approximately three-dimensional subspace, that this description is surprisingly stable with respect to the filtration by the crossing number, and that the results suggest further structures to be examined and understood.