Static analysis plays a key role in finding bugs, including security issues. A critical step in static analysis is building accurate call graphs that model function calls in a program. However, due to hard-to-analyze language features, existing call graph construction algorithms for JavaScript are neither sound nor complete. Prior work shows that even advanced solutions produce false edges and miss valid ones. In this work, we assist these tools by identifying missed call edges. Our main idea is to frame the problem as link prediction on full program graphs, using a rich representation with multiple edge types. Our approach, GRAPHIA, leverages recent advances in graph neural networks to model non-local relationships between code elements. Concretely, we propose representing JavaScript programs using a combination of syntactic- and semantic-based edges. GRAPHIA can learn from imperfect labels, including static call edges from existing tools and dynamic edges from tests, either from the same or different projects. Because call graphs are sparse, standard machine learning metrics like ROC are not suitable. Instead, we evaluate GRAPHIA by ranking function definitions for each unresolved call site. We conduct a large-scale evaluation on 50 popular JavaScript libraries with 163K call edges (150K static and 13K dynamic). GRAPHIA builds program graphs with 6.6M structural and 386K semantic edges. It ranks the correct target as the top candidate in over 42% of unresolved cases and within the top 5 in 72% of cases, reducing the manual effort needed for analysis. Our results show that learning-based methods can improve the recall of JavaScript call graph construction. To our knowledge, this is the first work to apply GNN-based link prediction to full multi-file program graphs for interprocedural analysis.