Mapping a dataflow-graph of an ML model onto a reconfigurable system is difficult, as different mappings have different throughputs and consume resource constraints differently. To solve this, a model to evaluate the throughput of mappings is necessary as measuring throughput completely is expensive. Many use a hand-designed analytical model, relying on proxy features or intuition, introducing error. We provide a Learned Approach that predicts throughput 31%-52% more accurately over a variety of graphs. In addition, our approach shows no accuracy degradation after removing performance annotations. We show that using this approach results in 5.6% faster compiled graphs.