Isomap is one of the “oldest” tools for dimensionality reduction. It aims at reproducing geodesic distances (geodesic distances are a property of Riemanian manifolds) on the manifold in an Euclidiean space.

To compute the approximated geodesic distances, a graph is created, an edge linking two close points (K-neighboors or Parzen windows can be used to choose the closest points) with its weight being the Euclidean distance between them. Then, a square matrix is computed with the shortest path between two points with a Dijkstra or Floyd-Warshall algorithm. This follows some distance and Riemanian manifolds properties. The number of points is generally chosen based on the estimated distance on the manifold.

Finally, an classical MDS procedure is performed to get a set of coordinates.

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