The Harmonic Indel Distance

Bob Pepin

Abstract: This short note introduces the harmonic indel distance (HID), a new distance between strings where the cost of an insertion or deletion is inversely proportional to the string length. We present a closed-form formula and show that the HID is a proper distance metric. Then we perform an experimental comparison of HID to normalized and unnormalized versions of the indel distance on benchmark tasks for biomedical sequence data. We finally show planar embeddings of the benchmark datasets to provide some insights into the geometry of the metric spaces associated with the different distance metrics.

Submission Length: Regular submission (no more than 12 pages of main content)

Changes Since Last Submission: Revised to address reviewer comments.

Code: https://github.com/bobpepin/harmonic-indel-distance

Assigned Action Editor: ~Han_Bao2

Submission Number: 3150