ValueError: probabilities contain NaN

Trying run node2vec on my dataset using the example code from the ReadMe. During the walk generation, I am receiving the following error:

File "mtrand.pyx", line 920, in numpy.random.mtrand.RandomState.choice
ValueError: probabilities contain NaN

Any idea where this is coming from? My dataset is ~ 120 MB, but I can provide it if helpful

[eliorc]

@davidfstein I figured out the problem - the problem is that most of your weights are zero. In the algorithm node2vec, weights cannot be zero - because weights (after normalization) are treated as walk probabilities, so essentially using the weights you can control how strongly two nodes are connected.

Zero edge weight is essentially no edge, so you cannot use zero weights. So before applying node2vec, depending on your use case decide what to do with the zero weights, you can either train without weights, or decide anything else that serves your problem - as long as you avoid assigning zero weights.

Thanks for this issue, I will make sure in the next version to give a better error message for zero weights

[davidfstein]

That makes sense. Thanks @eliorc!