Fix bugs in latest version of NumPy

[will945945945]

Fix bugs in using latest version of NumPy for tree-based model.

1. np.full(..., 0) returns an np.array with int64, but we need float64.
2. np.matrix ** 2 will be represented as the square of a ``square matrix'' in the latest NumPy version.
   For the element-wise square of an np.matrix, we should use np.square( np.matrix ).

Test CLI & API (bash tests/autotest.sh)

Test APIs used by main.py.

• Test Pass
  • (Copy and paste the last outputted line here.)
• Not Applicable (i.e., the PR does not include API changes.)

Check API Document

If any new APIs are added, please check if the description of the APIs is added to API document.

• API document is updated (linear, nn)
• Not Applicable (i.e., the PR does not include API changes.)

Test quickstart & API (bash tests/docs/test_changed_document.sh)

If any APIs in quickstarts or tutorials are modified, please run this test to check if the current examples can run correctly after the modified APIs are released.