Reproduce example

Hello, I tried to reproduce the example of the first figure (3 inputs, 3 outputs and 2 dense layers of 4 neurons) and the mask is not the same (result: https://imgur.com/5P5C2fn).

```
output 0 depends on inputs: [] : OK
output 1 depends on inputs: [] : OK
output 2 depends on inputs: [0, 1] : OK
```

So two outputs remain without dependence. What could be the problem? Thank you.

Start by reproducing the first-figure example with 3 inputs, 3 outputs, and two dense layers of 4 neurons, then compare the generated mask with the linked image. Investigate why outputs 0 and 1 have no input dependencies while output 2 depends on inputs 0 and 1. Done means the reproduction matches the example or clearly documents the cause of the discrepancy.

Written by the indexing model from the issue text.