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Innovation in the physical layer of communication systems has traditionally been achieved by breaking down the transceivers into sets of processing blocks, each optimized independently based on mathematical models. Conversely, deep learning (DL)-based systems are able to handle increasingly complex tasks for which no tractable models are available. This thesis aims at comparing different approaches to unlock the full potential of DL in the physical layer. First, we describe a neural network (NN)-based block strategy, where an NN is optimized to replace a block in a communication system. We apply this strategy to introduce a multi-user multiple-input multiple-output (MU-MIMO) detector that builds on top of an existing DL-based architecture. Second, we detail an end-to-end strategy, in which the transmitter and receiver are modeled as an autoencoder. This approach is illustrated with the design of waveforms that achieve high throughputs while satisfying peak-to-average power ratio (PAPR) and adjacent channel leakage ratio (ACLR) constraints. Lastly, we propose a hybrid strategy, where multiple DL components are inserted into a traditional architecture but are trained to optimize the end-to-end performance. To demonstrate its benefits, we propose a DL-enhanced MU-MIMO receiver that both enable lower bit error rates (BERs) compared to a conventional receiver and remains scalable to any number of users. Each approach has its own strengths and shortcomings. While the first one is the easiest to implement, its individual block optimization does not ensure the overall system optimality. On the other hand, systems designed with the second approach are computationally complex but allow for new opportunities such as pilotless transmissions. Finally, the combined flexibility and end-to-end performance gains of the third approach motivate its use for short-term practical implementations.