Machine Learning Method For Creating Chemical Formula
When picking an ML method, a great place to start is the sklearn algorithm cheat sheet:

You are predicting quantities, so regression class of variables is what you're looking for. Specifically you have multiple continuous inputs and multiple continuous outputs, which is a multivariate (linear) regression family.
As highlighted in the comments, start with a simple baseline model and build up in complexity to attempt to improve performance, towards CNNs or other.