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Molecule-electrode interfaces in molecular electronic junctions are prone to chemical reactions, structural changes, and localized heating effects caused by electric current. These can be exploited for device functionality or may be degrading processes that limit performance and device lifetime. We develop a nonequilibrium Green's function based transport theory in which the central region atoms and, more importantly, atoms on molecule-electrode interfaces are allowed to move. The separation of time-scales of slow nuclear motion and fast electronic dynamics enables the algebraic solution of the Kadanoff-Baym equations in the Wigner space. As a result, analytical expressions for dynamical corrections to the adiabatically computed Green's functions are produced. These dynamical corrections depend not only on the instantaneous molecular geometry but also on the nuclear velocities. To make the theoretical approach fully self-consistent, the same time-separation approach is used to develop expressions for the adiabatic, dissipative, and stochastic components of current-induced forces in terms of adiabatic Green's functions. Using these current induced forces, the equation of motion for the nuclear degrees of freedom is cast in the form of a Langevin equation. The theory is applied to model molecular electronic junctions. We observe that the interplay between the value of the spring constant for the molecule-electrode chemical bond and electronic coupling strength to the corresponding electrode is critical for the appearance of structural instabilities and, consequently, telegraphic switching in the electric current. The range of model parameters is identified to observe structurally stable molecular junctions as well as various different kinds of current-induced telegraphic switching. The interfacial structural instabilities are also quantified based on current noise calculations.