Improving on a scientific paper (with source code) - publication of our work possible?
Yes: You can publish work that improves upon earlier results.

Whether changing the architecture of a Deep Learning Network will achieve better results is, of course, an open problem. Whether improvements are sufficient to merit publication is also an open problem. 

In theory, negative results - e.g., we changed the architecture and didn't get better results - are publishable too. But, such results aren't published as often. I think you'd need a surprising-factor, e.g., if better results could be expected from such a change, but aren't achieved, especially if the reason they aren't achieved can be identified.