Merge pull request #422 from neuromatch/W1D1-superset

W1D1 Post-Course Feedback (Superset)
neuromatch · Aug 26, 2024 · 78158f7 · 78158f7
2 parents 29332f5 + 91fea35
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diff --git a/tutorials/W1D1_Generalization/W1D1_Tutorial1.ipynb b/tutorials/W1D1_Generalization/W1D1_Tutorial1.ipynb
@@ -606,7 +606,7 @@
     "execution": {}
    },
    "source": [
-    "We build a simple interface in `gradio` to try out the model interactively. Go ahead and try some example text to see how it works. You can use images from the internet, or scan your own handwriting. Just make sure that the text fits on one line."
+    "We build a simple interface in `gradio` to try out the model interactively. Go ahead and try some example text to see how it works. You can use images from the internet, or scan your own handwriting. Just make sure that the text fits on one line. Observe the result of the recognized text."
    ]
   },
   {
@@ -1034,7 +1034,7 @@
     "    ############################################################\n",
     "    # Fill in this code to calculate character error rate and word error rate.\n",
     "    # Hint: have a look at the torchmetrics documentation for the proper\n",
-    "    # metrics.\n",
+    "    # metrics (type the proper metric name in the search bar).\n",
     "    #\n",
     "    # https://lightning.ai/docs/torchmetrics/stable/\n",
     "    raise NotImplementedError(\"Student has to fill in these lines\")\n",
@@ -1675,7 +1675,7 @@
     "execution": {}
    },
    "source": [
-    "### Code exercise 3.1: Understanding the inputs and outputs of the decoder\n",
+    "### Code exercise 3.1: Understanding the inputs and outputs of the encoder\n",
     "\n",
     "Let's make sure we understand how the encoder operates by giving it a sample input and checking that its output matches the expected shape."
    ]
@@ -1689,9 +1689,9 @@
    },
    "outputs": [],
    "source": [
-    "def inspect_decoder(model):\n",
+    "def inspect_encoder(model):\n",
     "    \"\"\"\n",
-    "    Inspect decoder to verify that it processes inputs in the expected way.\n",
+    "    Inspect encoder to verify that it processes inputs in the expected way.\n",
     "\n",
     "    Args:\n",
     "        model: the TrOCR model\n",
@@ -1730,9 +1730,9 @@
    "source": [
     "# to_remove solution\n",
     "\n",
-    "def inspect_decoder(model):\n",
+    "def inspect_encoder(model):\n",
     "    \"\"\"\n",
-    "    Inspect decoder to verify that it processes inputs in the expected way.\n",
+    "    Inspect encoder to verify that it processes inputs in the expected way.\n",
     "\n",
     "    Args:\n",
     "        model: the TrOCR model\n",
@@ -1763,7 +1763,7 @@
    },
    "outputs": [],
    "source": [
-    "inspect_decoder(model)"
+    "inspect_encoder(model)"
    ]
   },
   {

diff --git a/tutorials/W1D1_Generalization/W1D1_Tutorial2.ipynb b/tutorials/W1D1_Generalization/W1D1_Tutorial2.ipynb
@@ -1054,6 +1054,8 @@
     "\n",
     "$$z = \\mathbf{W}\\mathbf{r} + c$$\n",
     "\n",
+    "In this notation, we can interpret $\\mathbf{r}$ as the firing rates of the neurons. Take a look at the equation above: the hidden state, $\\mathbf{x}$ (representation of stimuli in the brain), is evolving over time and is driven by current stimuli input $\\mathbf{u}$ and firing rates of neurons in the previous time step, $\\mathbf{r}$. EMG activity, $z$, is a direct linear projection from firing rates. \n",
+    "\n",
     "Let's code up this unregularized neural network."
    ]
   },
@@ -1250,7 +1252,7 @@
     "    #################################################\n",
     "    inputs = inputs.to(device)\n",
     "    batch_size = inputs.size(0)\n",
-    "    h = ...\n",
+    "    h = ... #note that `UnregularizedRNN` has a specific method for that\n",
     "\n",
     "    loss = 0\n",
     "    outputs = []\n",
@@ -1281,7 +1283,7 @@
     "def generate_trajectory(model, inputs, device):\n",
     "    inputs = inputs.to(device)\n",
     "    batch_size = inputs.size(0)\n",
-    "    h = model.init_hidden(batch_size).to(device)\n",
+    "    h = model.init_hidden(batch_size).to(device) #note that `UnregularizedRNN` has a specific method for that\n",
     "\n",
     "    loss = 0\n",
     "    outputs = []\n",
@@ -1658,7 +1660,7 @@
     "        # Project the firing rate linearly to form the output\n",
     "        output = self.output_linear(firing_rate)\n",
     "\n",
-    "        # Regularization terms\n",
+    "        # Regularization terms (used for R1 calculation)\n",
     "        firing_rate_reg = firing_rate.pow(2).sum()\n",
     "\n",
     "        return output, hidden, firing_rate_reg\n",
@@ -1800,7 +1802,7 @@
    "source": [
     "## Activity 3.2: Comparing trained RNN with real data\n",
     "\n",
-    "Let's see if this regularized network's activity is aligned with the brain."
+    "Let's see if this regularized network's activity is aligned with the brain. PSTH (peristimulus time histogram) is the type of plot that shows the firing rates of neurons over time (or their actual firings, depending on the granularity level)."
    ]
   },
   {

diff --git a/tutorials/W1D1_Generalization/instructor/W1D1_Tutorial1.ipynb b/tutorials/W1D1_Generalization/instructor/W1D1_Tutorial1.ipynb
@@ -606,7 +606,7 @@
     "execution": {}
    },
    "source": [
-    "We build a simple interface in `gradio` to try out the model interactively. Go ahead and try some example text to see how it works. You can use images from the internet, or scan your own handwriting. Just make sure that the text fits on one line."
+    "We build a simple interface in `gradio` to try out the model interactively. Go ahead and try some example text to see how it works. You can use images from the internet, or scan your own handwriting. Just make sure that the text fits on one line. Observe the result of the recognized text."
    ]
   },
   {
@@ -1034,7 +1034,7 @@
     "    ############################################################\n",
     "    # Fill in this code to calculate character error rate and word error rate.\n",
     "    # Hint: have a look at the torchmetrics documentation for the proper\n",
-    "    # metrics.\n",
+    "    # metrics (type the proper metric name in the search bar).\n",
     "    #\n",
     "    # https://lightning.ai/docs/torchmetrics/stable/\n",
     "    raise NotImplementedError(\"Student has to fill in these lines\")\n",
@@ -1681,7 +1681,7 @@
     "execution": {}
    },
    "source": [
-    "### Code exercise 3.1: Understanding the inputs and outputs of the decoder\n",
+    "### Code exercise 3.1: Understanding the inputs and outputs of the encoder\n",
     "\n",
     "Let's make sure we understand how the encoder operates by giving it a sample input and checking that its output matches the expected shape."
    ]
@@ -1695,9 +1695,9 @@
    },
    "source": [
     "```python\n",
-    "def inspect_decoder(model):\n",
+    "def inspect_encoder(model):\n",
     "    \"\"\"\n",
-    "    Inspect decoder to verify that it processes inputs in the expected way.\n",
+    "    Inspect encoder to verify that it processes inputs in the expected way.\n",
     "\n",
     "    Args:\n",
     "        model: the TrOCR model\n",
@@ -1738,9 +1738,9 @@
    "source": [
     "# to_remove solution\n",
     "\n",
-    "def inspect_decoder(model):\n",
+    "def inspect_encoder(model):\n",
     "    \"\"\"\n",
-    "    Inspect decoder to verify that it processes inputs in the expected way.\n",
+    "    Inspect encoder to verify that it processes inputs in the expected way.\n",
     "\n",
     "    Args:\n",
     "        model: the TrOCR model\n",
@@ -1771,7 +1771,7 @@
    },
    "outputs": [],
    "source": [
-    "inspect_decoder(model)"
+    "inspect_encoder(model)"
    ]
   },
   {

diff --git a/tutorials/W1D1_Generalization/instructor/W1D1_Tutorial2.ipynb b/tutorials/W1D1_Generalization/instructor/W1D1_Tutorial2.ipynb
@@ -1054,6 +1054,8 @@
     "\n",
     "$$z = \\mathbf{W}\\mathbf{r} + c$$\n",
     "\n",
+    "In this notation, we can interpret $\\mathbf{r}$ as the firing rates of the neurons. Take a look at the equation above: the hidden state, $\\mathbf{x}$ (representation of stimuli in the brain), is evolving over time and is driven by current stimuli input $\\mathbf{u}$ and firing rates of neurons in the previous time step, $\\mathbf{r}$. EMG activity, $z$, is a direct linear projection from firing rates. \n",
+    "\n",
     "Let's code up this unregularized neural network."
    ]
   },
@@ -1252,7 +1254,7 @@
     "    #################################################\n",
     "    inputs = inputs.to(device)\n",
     "    batch_size = inputs.size(0)\n",
-    "    h = ...\n",
+    "    h = ... #note that `UnregularizedRNN` has a specific method for that\n",
     "\n",
     "    loss = 0\n",
     "    outputs = []\n",
@@ -1285,7 +1287,7 @@
     "def generate_trajectory(model, inputs, device):\n",
     "    inputs = inputs.to(device)\n",
     "    batch_size = inputs.size(0)\n",
-    "    h = model.init_hidden(batch_size).to(device)\n",
+    "    h = model.init_hidden(batch_size).to(device) #note that `UnregularizedRNN` has a specific method for that\n",
     "\n",
     "    loss = 0\n",
     "    outputs = []\n",
@@ -1662,7 +1664,7 @@
     "        # Project the firing rate linearly to form the output\n",
     "        output = self.output_linear(firing_rate)\n",
     "\n",
-    "        # Regularization terms\n",
+    "        # Regularization terms (used for R1 calculation)\n",
     "        firing_rate_reg = firing_rate.pow(2).sum()\n",
     "\n",
     "        return output, hidden, firing_rate_reg\n",
@@ -1804,7 +1806,7 @@
    "source": [
     "## Activity 3.2: Comparing trained RNN with real data\n",
     "\n",
-    "Let's see if this regularized network's activity is aligned with the brain."
+    "Let's see if this regularized network's activity is aligned with the brain. PSTH (peristimulus time histogram) is the type of plot that shows the firing rates of neurons over time (or their actual firings, depending on the granularity level)."
    ]
   },
   {

diff --git a/...tions/W1D1_Tutorial1_Solution_fe1c0573.py → ...tions/W1D1_Tutorial1_Solution_22613224.py b/...tions/W1D1_Tutorial1_Solution_fe1c0573.py → ...tions/W1D1_Tutorial1_Solution_22613224.py
@@ -1,7 +1,7 @@
 
-def inspect_decoder(model):
+def inspect_encoder(model):
     """
-    Inspect decoder to verify that it processes inputs in the expected way.
+    Inspect encoder to verify that it processes inputs in the expected way.
 
     Args:
         model: the TrOCR model

diff --git a/...tions/W1D1_Tutorial2_Solution_dc6b3d2e.py → ...tions/W1D1_Tutorial2_Solution_c14a4735.py b/...tions/W1D1_Tutorial2_Solution_dc6b3d2e.py → ...tions/W1D1_Tutorial2_Solution_c14a4735.py
@@ -1,7 +1,7 @@
 def generate_trajectory(model, inputs, device):
     inputs = inputs.to(device)
     batch_size = inputs.size(0)
-    h = model.init_hidden(batch_size).to(device)
+    h = model.init_hidden(batch_size).to(device) #note that `UnregularizedRNN` has a specific method for that
 
     loss = 0
     outputs = []

diff --git a/tutorials/W1D1_Generalization/student/W1D1_Tutorial1.ipynb b/tutorials/W1D1_Generalization/student/W1D1_Tutorial1.ipynb
@@ -606,7 +606,7 @@
     "execution": {}
    },
    "source": [
-    "We build a simple interface in `gradio` to try out the model interactively. Go ahead and try some example text to see how it works. You can use images from the internet, or scan your own handwriting. Just make sure that the text fits on one line."
+    "We build a simple interface in `gradio` to try out the model interactively. Go ahead and try some example text to see how it works. You can use images from the internet, or scan your own handwriting. Just make sure that the text fits on one line. Observe the result of the recognized text."
    ]
   },
   {
@@ -1025,7 +1025,7 @@
     "    ############################################################\n",
     "    # Fill in this code to calculate character error rate and word error rate.\n",
     "    # Hint: have a look at the torchmetrics documentation for the proper\n",
-    "    # metrics.\n",
+    "    # metrics (type the proper metric name in the search bar).\n",
     "    #\n",
     "    # https://lightning.ai/docs/torchmetrics/stable/\n",
     "    raise NotImplementedError(\"Student has to fill in these lines\")\n",
@@ -1572,7 +1572,7 @@
     "execution": {}
    },
    "source": [
-    "### Code exercise 3.1: Understanding the inputs and outputs of the decoder\n",
+    "### Code exercise 3.1: Understanding the inputs and outputs of the encoder\n",
     "\n",
     "Let's make sure we understand how the encoder operates by giving it a sample input and checking that its output matches the expected shape."
    ]
@@ -1586,9 +1586,9 @@
    },
    "outputs": [],
    "source": [
-    "def inspect_decoder(model):\n",
+    "def inspect_encoder(model):\n",
     "    \"\"\"\n",
-    "    Inspect decoder to verify that it processes inputs in the expected way.\n",
+    "    Inspect encoder to verify that it processes inputs in the expected way.\n",
     "\n",
     "    Args:\n",
     "        model: the TrOCR model\n",
@@ -1624,7 +1624,7 @@
     "execution": {}
    },
    "source": [
-    "[*Click for solution*](https://github.com/neuromatch/NeuroAI_Course/tree/main/tutorials/W1D1_Generalization/solutions/W1D1_Tutorial1_Solution_fe1c0573.py)\n",
+    "[*Click for solution*](https://github.com/neuromatch/NeuroAI_Course/tree/main/tutorials/W1D1_Generalization/solutions/W1D1_Tutorial1_Solution_22613224.py)\n",
     "\n"
    ]
   },
@@ -1637,7 +1637,7 @@
    },
    "outputs": [],
    "source": [
-    "inspect_decoder(model)"
+    "inspect_encoder(model)"
    ]
   },
   {

diff --git a/tutorials/W1D1_Generalization/student/W1D1_Tutorial2.ipynb b/tutorials/W1D1_Generalization/student/W1D1_Tutorial2.ipynb
@@ -1054,6 +1054,8 @@
     "\n",
     "$$z = \\mathbf{W}\\mathbf{r} + c$$\n",
     "\n",
+    "In this notation, we can interpret $\\mathbf{r}$ as the firing rates of the neurons. Take a look at the equation above: the hidden state, $\\mathbf{x}$ (representation of stimuli in the brain), is evolving over time and is driven by current stimuli input $\\mathbf{u}$ and firing rates of neurons in the previous time step, $\\mathbf{r}$. EMG activity, $z$, is a direct linear projection from firing rates. \n",
+    "\n",
     "Let's code up this unregularized neural network."
    ]
   },
@@ -1211,7 +1213,7 @@
     "    #################################################\n",
     "    inputs = inputs.to(device)\n",
     "    batch_size = inputs.size(0)\n",
-    "    h = ...\n",
+    "    h = ... #note that `UnregularizedRNN` has a specific method for that\n",
     "\n",
     "    loss = 0\n",
     "    outputs = []\n",
@@ -1237,7 +1239,7 @@
     "execution": {}
    },
    "source": [
-    "[*Click for solution*](https://github.com/neuromatch/NeuroAI_Course/tree/main/tutorials/W1D1_Generalization/solutions/W1D1_Tutorial2_Solution_dc6b3d2e.py)\n",
+    "[*Click for solution*](https://github.com/neuromatch/NeuroAI_Course/tree/main/tutorials/W1D1_Generalization/solutions/W1D1_Tutorial2_Solution_c14a4735.py)\n",
     "\n"
    ]
   },
@@ -1600,7 +1602,7 @@
     "        # Project the firing rate linearly to form the output\n",
     "        output = self.output_linear(firing_rate)\n",
     "\n",
-    "        # Regularization terms\n",
+    "        # Regularization terms (used for R1 calculation)\n",
     "        firing_rate_reg = firing_rate.pow(2).sum()\n",
     "\n",
     "        return output, hidden, firing_rate_reg\n",
@@ -1742,7 +1744,7 @@
    "source": [
     "## Activity 3.2: Comparing trained RNN with real data\n",
     "\n",
-    "Let's see if this regularized network's activity is aligned with the brain."
+    "Let's see if this regularized network's activity is aligned with the brain. PSTH (peristimulus time histogram) is the type of plot that shows the firing rates of neurons over time (or their actual firings, depending on the granularity level)."
    ]
   },
   {