It is widely believed that tens of thousands of physical qubits are needed to build a practically useful quantum computer. Atom arrays formed by optical tweezers are among the most promising platforms for achieving this goal, owing to the excellent scalability and mobility of atomic qubits. However, assembling a defect-free atom array with ~ 10^4 qubits remains algorithmically challenging, alongside other hardware limitations. This is due to the computationally hard path-planning problems and the time-consuming generation of suffciently smooth trajectories for optical tweezer potentials by spatial light modulators (SLM). Here, we present a unified framework comprising two innovative components to fully address these algorithmic challenges: (1) a path-planning module that employs a supervised learning approach using a graph neural network combined with a modified auction decoder, and (2) a potential-generation module called the phase and profile-aware Weighted Gerchberg-Saxton algorithm. The inference time for the first module is nearly a size-independent constant overhead of ~ 5 ms, and the second module generates a potential frame with about 0.5 ms, a timescale shorter than the current commercial SLM refresh time. Altogether, our algorithm enables the assembly of an atom array with 10^4 qubits on a timescale much shorter than the typical vacuum lifetime of the trapped atoms.