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Abstract Recent technological advances have contributed to the rapid increase in algorithmic complexity of applications, ranging from signal processing to autonomous systems. To control this complexity and endow heterogeneous computing systems with autonomous programming and optimization capabilities, we propose aunified, end-to-end, programmable graph representation learning(PGL) framework that mines the complexity of high-level programs down to low-level virtual machine intermediate representation, extracts specific computational patterns, and predicts which code segments run best on a core in heterogeneous hardware. PGL extracts multifractal features from code graphs and exploits graph representation learning strategies for automatic parallelization and correct assignment to heterogeneous processors. The comprehensive evaluation of PGL on existing and emerging complex software demonstrates a 6.42x and 2.02x speedup compared to thread-based execution and state-of-the-art techniques, respectively. Our PGL framework leads to higher processing efficiency, which is crucial for future AI and high-performance computing applications such as autonomous vehicles and machine vision.