Linking numbers and non-holomorphic Siegel modular forms

We study generating series encoding linking numbers between geodesics in arithmetic hyperbolic $3$-folds. We show that the series converge to functions on genus $2$ Siegel space and that certain explicit modifications have the transformation properties of genus $2$ Siegel modular forms of weight $2$. This is done by carefully analyzing the integral of the Kudla–Millson theta series over a Seifert surface with geodesic boundary. As a corollary, we deduce a polynomial bound on the linking numbers.