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Minor update re: np.arccos #382

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Minor update re: np.arccos #382

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8 changes: 3 additions & 5 deletions tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Tutorial2.ipynb
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Expand Up @@ -298,7 +298,7 @@
"\n",
" rdms_comp = rsatoolbox.rdm.compare(rdms, rdms, method=rdm_comp_method)\n",
" if rdm_comp_method == 'cosine':\n",
" rdms_comp = 1 - rdms_comp\n",
" rdms_comp = np.arccos(rdms_comp)\n",
" rdms_comp = np.nan_to_num(rdms_comp, nan=0.0)\n",
"\n",
" # Symmetrize\n",
Expand Down Expand Up @@ -1244,9 +1244,7 @@
"\n",
"$$\\hat M(\\text{layer i}, \\text{image j x image k})$$\n",
"\n",
"We can then calculate the distances between the different rows of this new matrix. This new measure captures the distances between representational geometries of different layers. So we are now creating an RDM matrix of the RDM matrices!\n",
"\n",
"We compute the similarity between geometries using the cosine dissimilarity. The resulting matrix has the dimensions of `#layers` by `#layers`.\n",
"We can then calculate the cosine similarity between the different rows of this new matrix. By taking the arccos of this measure, we obtain a proper distance between representational geometries of different layers (Williams et al. 2021). So we are now creating an RDM matrix of the RDM matrices! The resulting matrix has the dimensions of `#layers` by `#layers`.\n",
"\n",
"The last step to visualize the path is to embed the distances between the geometries in a lower dimensional space. We use MDS to reduce the dimensions to 2 in order to show each computational step as a point in a 2D space."
]
Expand Down Expand Up @@ -1984,7 +1982,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.19"
"version": "3.8.17"
}
},
"nbformat": 4,
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