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For turbulent bubbly flows, multi-phase simulations resolving both the liquid and bubbles are prohibitively expensive in the context of different natural phenomena. One example is breaking waves, where bubbles strongly influence wave impact loads, acoustic emissions, and atmospheric-ocean transfer, but detailed simulations in all but the simplest settings are infeasible. An alternative approach is to resolve only large scales, and model small scale bubbles adopting sub-resolution closures. Here we introduce a large eddy simulation (LES) Smoothed Particle Hydrodynamics (SPH) scheme for simulations of bubbly flows. The continuous liquid phase is resolved with a semi-implicit isothermally compressible SPH framework. This is coupled with a discrete Lagrangian bubble model. Bubbles and liquid interact via exchanges of volume and momentum, through turbulent closures, bubble breakup and entrainment, and free-surface interaction models. By representing bubbles as individual particles, they can be tracked over their lifetimes, allowing closure models for sub-resolution fluctuations, bubble deformation, breakup and free-surface interaction in integral form, accounting for the finite timescales over which these events occur. We investigate two flows: bubble plumes, and breaking waves, and find close quantitative agreement with published experimental and numerical data. In particular, for plunging breaking waves, our framework accurately predicts the Hinze scale, bubble size distribution, and growth rate of the entrained bubble population. This is the first coupling of an SPH framework with a discrete bubble model, with potential for cost effective simulations of wave-structure interactions and more accurate predictions of wave impact loads.