Pixel antenna is a promising antenna technology that enables flexible adjustment of radiation characteristics and enhancement of wireless systems through antenna coding. This work proposes a novel deep learning-based antenna coding optimization algorithm. Specifically, the proposed algorithm is supported by a heterogeneous multi-head selection mechanism, whose main idea is to train multiple neural networks based on various coding schemes and select the one that leads to the best system performance. Unlike traditional heuristic searching-based algorithms that require high computational complexity to achieve satisfactory performance, the proposed data-driven deep learning approach can achieve 98\% of the performance achieved by the searching-based algorithms with significantly reduced computational complexity. Results demonstrate that in pixel antenna empowered single-input single-output systems, the proposed algorithm achieves a computational speed 81 times faster than the searching-based algorithm. For more complex pixel antenna empowered multiple-input multiple-output systems, the computational speed is 297 times faster than the existing searching-based algorithm. Benefiting from the high performance and low computational complexity, this algorithm demonstrates the significant potential of pixel antennas as a novel and practical technology to enhance wireless systems.