GPU-based HPC clusters are attracting more scientific application developers due to their extensive parallelism and energy efficiency. In order to achieve portability among a variety of multi/many core architectures, a popular choice for an application developer is to utilize directive-based parallel programming models, such as OpenMP. However, even with OpenMP, the developer must choose from among many strategies for exploiting a GPU or a CPU. Recently, Machine Learning (ML) approaches have brought significant advances in the optimizations of HPC applications. To this end, several ways have been proposed to represent application characteristics for ML models. However, the available techniques fail to capture features that are crucial for exposing parallelism. In this paper, we introduce a new graph-based program representation for parallel applications that extends the Abstract Syntax Tree to represent control and data flow information. The originality of this work lies in the addition of new edges exploiting the implicit ordering and parent-child relationships in ASTs, as well as the introduction of edge weights to account for loop and condition information. We evaluate our proposed representation by training a Graph Neural Network (GNN) to predict the runtime of an OpenMP code region across CPUs and GPUs. Various transformations utilizing collapse and data transfer between the CPU and GPU are used to construct the dataset. The predicted runtime of the model is used to determine which transformation provides the best performance. Results show that our approach is indeed effective and has normalized RMSE as low as 0.004 to at most 0.01 in its runtime predictions.