*2.5. Combined Models*

To combine the features from two data sources, we constructed 1 or 2 hidden layers (Figure 3 and Table S2). We saved high-level features extracted from the previous CNNs for sequence and epigenomic data, then combined them together as input to the first hidden layer in the combined model. We also tested more complex combination schemes but found no performance improvement; for example, we trained and combined the individual models simultaneously, instead of doing the two steps sequentially.

**Figure 3.** Combined model structure with the sequence and epigenomic models.
