Somehow some people meet this ValueError numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject. This issue also happens in other python packages such hdbscan, top2vec.

There are some ongoing discussions on this issue in hdbscan repository scikit-learn-contrib/hdbscan#457. It seems that the problem is related to python, numpy, scipy and cython version. It seems that this problem is triggered by the latest version of numpy

One workable solution is upgrading numpy to 1.20.0

This issue is a reminder if sparse_dot_topn users meet the same question