Merge pull request #355 from neuromatch/D3_links

W1D3
neuromatch · Jul 1, 2024 · 5ea14e3 · 5ea14e3
2 parents 1bda1fc + 25eec7c
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diff --git a/tutorials/README.md b/tutorials/README.md
@@ -50,7 +50,7 @@ Slides: [Intro](https://mfr.ca-1.osf.io/render?url=https://osf.io/gsuhq/?direct%
 
 [YouTube Playlist](https://www.youtube.com/playlist?list=PLkBQOLLbi18O2wSDMRLrZNyKBuRwvoE6K)
 
-Slides: [Intro](https://mfr.ca-1.osf.io/render?url=https://osf.io/g8jzu/?direct%26mode=render%26action=download%26mode=render) | [Tutorials](https://mfr.ca-1.osf.io/render?url=https://osf.io/uwn2g/?direct%26mode=render%26action=download%26mode=render)
+Slides: [Intro](https://mfr.ca-1.osf.io/render?url=https://osf.io/g8jzu/?direct%26mode=render%26action=download%26mode=render) | [Tutorials](https://mfr.ca-1.osf.io/render?url=https://osf.io/uwn2g/?direct%26mode=render%26action=download%26mode=render) | [Bonus](https://mfr.ca-1.osf.io/render?url=https://osf.io/8fx23/?direct%26mode=render%26action=download%26mode=render)
 
 |   | Run | Run | View |
 | - | --- | --- | ---- |
@@ -59,6 +59,7 @@ Slides: [Intro](https://mfr.ca-1.osf.io/render?url=https://osf.io/g8jzu/?direct%
 | Tutorial 2 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb?flush_cache=true) |
 | Tutorial 3 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb?flush_cache=true) |
 | Tutorial 4 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb?flush_cache=true) |
+| Tutorial 5 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb?flush_cache=true) |
 | Outro | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb?flush_cache=true) |
 
 

diff --git a/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/README.md b/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/README.md
@@ -9,6 +9,7 @@
 | Tutorial 2 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial2.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial2.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial2.ipynb?flush_cache=true) |
 | Tutorial 3 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial3.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial3.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial3.ipynb?flush_cache=true) |
 | Tutorial 4 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial4.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial4.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial4.ipynb?flush_cache=true) |
+| Tutorial 5 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial5.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial5.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial5.ipynb?flush_cache=true) |
 | Outro | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb?flush_cache=true) |
 
 
@@ -21,5 +22,6 @@
 | Tutorial 2 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb?flush_cache=true) |
 | Tutorial 3 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb?flush_cache=true) |
 | Tutorial 4 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb?flush_cache=true) |
+| Tutorial 5 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb?flush_cache=true) |
 | Outro | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb?flush_cache=true) |
 
diff --git a/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Tutorial1.ipynb b/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Tutorial1.ipynb
@@ -110,7 +110,6 @@
    "outputs": [],
    "source": [
     "# @title Install dependencies\n",
-    "# @markdown Notice that you need to uncomment some of the lines below\n",
     "\n",
     "!pip install -q ipympl ipywidgets mpl_interactions[\"jupyter\"] rsatoolbox torchlens\n",
     "!pip install -q graphviz\n",
@@ -1196,17 +1195,8 @@
     "# @title Extract model features with torchlens\n",
     "\n",
     "return_layers = ['input_1', 'conv1', 'conv2', 'fc1', 'fc2']\n",
-    "features_model_imgs = extract_features(model, imgs, return_layers, plot = 'rolled') #comment this line if Graphviz installation was unsuccessful for you"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "execution": {}
-   },
-   "outputs": [],
-   "source": [
+    "features_model_imgs = extract_features(model, imgs, return_layers, plot = 'rolled') #comment this line if Graphviz installation was unsuccessful for you\n",
+    "\n",
     "features_model_advimgs = extract_features(model, adv_imgs, return_layers)\n",
     "features_advmodel_imgs = extract_features(model_robust, imgs, return_layers)\n",
     "features_advmodel_advimgs = extract_features(model_robust, adv_imgs_advmodel, return_layers)"

diff --git a/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Tutorial2.ipynb b/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Tutorial2.ipynb
@@ -90,7 +90,7 @@
    "source": [
     "# @title Install and import feedback gadget\n",
     "\n",
-    "!pip install torch torchvision matplotlib numpy scikit-learn rsatoolbox scipy --quiet\n",
+    "!pip install torch torchvision matplotlib numpy scikit-learn rsatoolbox scipy vibecheck --quiet\n",
     "\n",
     "from vibecheck import DatatopsContentReviewContainer\n",
     "def content_review(notebook_section: str):\n",
@@ -117,6 +117,8 @@
    },
    "outputs": [],
    "source": [
+    "# @title Import dependencies\n",
+    "\n",
     "# Standard library imports\n",
     "from collections import OrderedDict\n",
     "import logging\n",

diff --git a/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Tutorial3.ipynb b/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Tutorial3.ipynb
@@ -102,7 +102,7 @@
    "source": [
     "# @title Install and import feedback gadget\n",
     "\n",
-    "!pip install numpy pandas torch torchvision matplotlib ipython Pillow rsatoolbox plotly networkx requests --quiet\n",
+    "!pip install numpy pandas torch torchvision matplotlib ipython Pillow rsatoolbox plotly networkx requests vibecheck --quiet\n",
     "\n",
     "from vibecheck import DatatopsContentReviewContainer\n",
     "def content_review(notebook_section: str):\n",
@@ -1674,7 +1674,7 @@
     "execution": {}
    },
    "source": [
-    "## Coding Exercise 1: RDMS of AlexNet\n",
+    "## Coding Exercise 1: RDMs of AlexNet\n",
     "\n",
     "Use the RSA toolbox to compute the RDMs for the layers of AlexNet."
    ]

diff --git a/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Tutorial4.ipynb b/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Tutorial4.ipynb
@@ -582,7 +582,7 @@
     "            ax[i].set_xlabel(\"dimensionality\", fontsize=7)\n",
     "            ax[i].tick_params(axis='both', which='major', labelsize=5)\n",
     "            ax[i].axhline(y=true_dist[n_neurons], linestyle=\"dashed\", color=\"gray\")\n",
-    "            ax[i].text(n_dims_list[-1], true_dist[n_neurons], 'true euclidean distance', color='gray', ha='right', va='top', fontsize=8)\n",
+    "            ax[i].text(n_dims_list[-1], true_dist[n_neurons], 'true euclidean distance', color='gray', ha='right', va='top', fontsize=4)\n",
     "            title = \"two neurons\" if n_neurons == 2 else \"100 neurons\"\n",
     "            ax[i].set_title(title, fontsize=7)\n",
     "        plt.tight_layout()"