  We consider knot invariants in the context of large $N$ transitions of
topological strings. In particular we consider aspects of Lagrangian cycles
associated to knots in the conifold geometry. We show how these can be
explicity constructed in the case of algebraic knots. We use this explicit
construction to explain a recent conjecture relating study of stable pairs on
algebraic curves with HOMFLY polynomials. Furthermore, for torus knots, using
the explicit construction of the Lagrangian cycle, we also give a direct
A-model computation and recover the HOMFLY polynomial for this case.
