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First, we formulate sum rate (SR) and energy efficiency (EE) maximization problems in a unified framework, subject to constraints on the movable region of PAs, total power budget, and tunable phase of RIS elements. Then, by leveraging a graph-structured topology of the RIS-assisted PASS, a novel three-stage graph neural network (GNN) is proposed, which learns PA positions based on user locations, and RIS phase shifts according to composite channel conditions at the first two stages, respectively, and finally determines beamforming vectors. 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