Quantifying Pathogen Surveillance Using Temporal Genomic Data

Chan, Joseph M.; Rabadan, Raul

Persistence homology as a measurement of surveillance. Another possible surveillance measure can be derived by using persistence homology techniques like bar coding (40), a method of identifying topological invariants in cloud data. First, sequenced isolates can be transformed in high-dimensional space by using distance measures, such as pairwise genetic distance. From these cloud data, points can be linked together on the basis of certain criteria to form a simplicial complex, i.e., a network of points, line segments, triangles, and even n-dimensional counterparts. When this criterion is a distance less than some , a filtered simplicial complex or Vietoris-Rips stream is created.