DeepAutism-ChiSquare.ipynb is the cloned notebook from Wang et al.
DeepAutism-ChiSquare_final.ipynb is the notebook provided by email from Wang and said to be the actual final version of the code used in the paper, as opposed to DeepAutism-ChiSquare.ipynb that is in his github. The only difference between the two is the commenting out (i.e. '#') of the shuffle line that makes DeepAutism-ChiSquare.ipynb incorrect. However, there are discrepancies between the code and outputs in this notebook.
SFARI_paper_CNN.ipynb is a replication of key parts of this notebook as well as figure generation for the letter to editor.
Wang_Avillach_Code_Reproduce.ipynb produces histograms of accuracy results both with and without the shuffle function.