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morganjwilliams committed Jun 23, 2020
2 parents 8e35070 + 2763087 commit 062eff7
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398 changes: 204 additions & 194 deletions 011_classification.ipynb
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46 changes: 29 additions & 17 deletions 012_datavis.ipynb
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@@ -1,5 +1,15 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import matplotlib.pyplot as plt\n",
"from util import render_audio_sample"
]
},
{
"cell_type": "markdown",
"metadata": {},
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},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"metadata": {
"slideshow": {
"slide_type": "subslide"
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},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 3,
"metadata": {
"slideshow": {
"slide_type": "fragment"
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},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<style>div.sk-top-container {color: black;background-color: white;}div.sk-toggleable {background-color: white;}label.sk-toggleable__label {cursor: pointer;display: block;width: 100%;margin-bottom: 0;padding: 0.2em 0.3em;box-sizing: border-box;text-align: center;}div.sk-toggleable__content {max-height: 0;max-width: 0;overflow: hidden;text-align: left;background-color: #f0f8ff;}div.sk-toggleable__content pre {margin: 0.2em;color: black;border-radius: 0.25em;background-color: #f0f8ff;}input.sk-toggleable__control:checked~div.sk-toggleable__content {max-height: 200px;max-width: 100%;overflow: auto;}div.sk-estimator input.sk-toggleable__control:checked~label.sk-toggleable__label {background-color: #d4ebff;}div.sk-label input.sk-toggleable__control:checked~label.sk-toggleable__label {background-color: #d4ebff;}input.sk-hidden--visually {border: 0;clip: rect(1px 1px 1px 1px);clip: rect(1px, 1px, 1px, 1px);height: 1px;margin: -1px;overflow: hidden;padding: 0;position: absolute;width: 1px;}div.sk-estimator {font-family: monospace;background-color: #f0f8ff;margin: 0.25em 0.25em;border: 1px dotted black;border-radius: 0.25em;box-sizing: border-box;}div.sk-estimator:hover {background-color: #d4ebff;}div.sk-parallel-item::after {content: \"\";width: 100%;border-bottom: 1px solid gray;flex-grow: 1;}div.sk-label:hover label.sk-toggleable__label {background-color: #d4ebff;}div.sk-serial::before {content: \"\";position: absolute;border-left: 1px solid gray;box-sizing: border-box;top: 2em;bottom: 0;left: 50%;}div.sk-serial {display: flex;flex-direction: column;align-items: center;background-color: white;}div.sk-item {z-index: 1;}div.sk-parallel {display: flex;align-items: stretch;justify-content: center;background-color: white;}div.sk-parallel-item {display: flex;flex-direction: column;position: relative;background-color: white;}div.sk-parallel-item:first-child::after {align-self: flex-end;width: 50%;}div.sk-parallel-item:last-child::after {align-self: flex-start;width: 50%;}div.sk-parallel-item:only-child::after {width: 0;}div.sk-dashed-wrapped {border: 1px dashed gray;margin: 0.2em;box-sizing: border-box;padding-bottom: 0.1em;background-color: white;position: relative;}div.sk-label label {font-family: monospace;font-weight: bold;background-color: white;display: inline-block;line-height: 1.2em;}div.sk-label-container {position: relative;z-index: 2;text-align: center;}div.sk-container {display: inline-block;position: relative;}</style><div class=\"sk-top-container\"><div class=\"sk-container\"><div class=\"sk-item sk-dashed-wrapped\"><div class=\"sk-label-container\"><div class=\"sk-label sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"72e908e0-8d92-4507-b52e-bc9b0addc59b\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"72e908e0-8d92-4507-b52e-bc9b0addc59b\">GridSearchCV</label><div class=\"sk-toggleable__content\"><pre>GridSearchCV(cv=5,\n",
"<style>div.sk-top-container {color: black;background-color: white;}div.sk-toggleable {background-color: white;}label.sk-toggleable__label {cursor: pointer;display: block;width: 100%;margin-bottom: 0;padding: 0.2em 0.3em;box-sizing: border-box;text-align: center;}div.sk-toggleable__content {max-height: 0;max-width: 0;overflow: hidden;text-align: left;background-color: #f0f8ff;}div.sk-toggleable__content pre {margin: 0.2em;color: black;border-radius: 0.25em;background-color: #f0f8ff;}input.sk-toggleable__control:checked~div.sk-toggleable__content {max-height: 200px;max-width: 100%;overflow: auto;}div.sk-estimator input.sk-toggleable__control:checked~label.sk-toggleable__label {background-color: #d4ebff;}div.sk-label input.sk-toggleable__control:checked~label.sk-toggleable__label {background-color: #d4ebff;}input.sk-hidden--visually {border: 0;clip: rect(1px 1px 1px 1px);clip: rect(1px, 1px, 1px, 1px);height: 1px;margin: -1px;overflow: hidden;padding: 0;position: absolute;width: 1px;}div.sk-estimator {font-family: monospace;background-color: #f0f8ff;margin: 0.25em 0.25em;border: 1px dotted black;border-radius: 0.25em;box-sizing: border-box;}div.sk-estimator:hover {background-color: #d4ebff;}div.sk-parallel-item::after {content: \"\";width: 100%;border-bottom: 1px solid gray;flex-grow: 1;}div.sk-label:hover label.sk-toggleable__label {background-color: #d4ebff;}div.sk-serial::before {content: \"\";position: absolute;border-left: 1px solid gray;box-sizing: border-box;top: 2em;bottom: 0;left: 50%;}div.sk-serial {display: flex;flex-direction: column;align-items: center;background-color: white;}div.sk-item {z-index: 1;}div.sk-parallel {display: flex;align-items: stretch;justify-content: center;background-color: white;}div.sk-parallel-item {display: flex;flex-direction: column;position: relative;background-color: white;}div.sk-parallel-item:first-child::after {align-self: flex-end;width: 50%;}div.sk-parallel-item:last-child::after {align-self: flex-start;width: 50%;}div.sk-parallel-item:only-child::after {width: 0;}div.sk-dashed-wrapped {border: 1px dashed gray;margin: 0.2em;box-sizing: border-box;padding-bottom: 0.1em;background-color: white;position: relative;}div.sk-label label {font-family: monospace;font-weight: bold;background-color: white;display: inline-block;line-height: 1.2em;}div.sk-label-container {position: relative;z-index: 2;text-align: center;}div.sk-container {display: inline-block;position: relative;}</style><div class=\"sk-top-container\"><div class=\"sk-container\"><div class=\"sk-item sk-dashed-wrapped\"><div class=\"sk-label-container\"><div class=\"sk-label sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"48843435-f3a7-4804-908b-d890bed840ad\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"48843435-f3a7-4804-908b-d890bed840ad\">GridSearchCV</label><div class=\"sk-toggleable__content\"><pre>GridSearchCV(cv=5,\n",
" estimator=Pipeline(steps=[('featureunion',\n",
" FeatureUnion(transformer_list=[('abundances '\n",
" '--> '\n",
Expand All @@ -206,7 +216,7 @@
" n_jobs=1,\n",
" param_grid={'svc__C': array([ 0.31622777, 1.33352143, 5.62341325, 23.71373706,\n",
" 100. ]),\n",
" 'svc__gamma': array([0.00501187, 0.01154782, 0.02660725, 0.06130558, 0.14125375])})</pre></div></div></div><div class=\"sk-parallel\"><div class=\"sk-parallel-item\"><div class=\"sk-item\"><div class=\"sk-serial\"><div class=\"sk-item\"><div class=\"sk-serial\"><div class=\"sk-item sk-dashed-wrapped\"><div class=\"sk-label-container\"><div class=\"sk-label sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"67ad9ded-9665-4ef7-b545-493514242a66\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"67ad9ded-9665-4ef7-b545-493514242a66\">featureunion: FeatureUnion</label><div class=\"sk-toggleable__content\"><pre>FeatureUnion(transformer_list=[('abundances --> CLR',\n",
" 'svc__gamma': array([0.00501187, 0.01154782, 0.02660725, 0.06130558, 0.14125375])})</pre></div></div></div><div class=\"sk-parallel\"><div class=\"sk-parallel-item\"><div class=\"sk-item\"><div class=\"sk-serial\"><div class=\"sk-item\"><div class=\"sk-serial\"><div class=\"sk-item sk-dashed-wrapped\"><div class=\"sk-label-container\"><div class=\"sk-label sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"2dffa3c7-a13b-4976-b3bf-c54d2f20be16\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"2dffa3c7-a13b-4976-b3bf-c54d2f20be16\">featureunion: FeatureUnion</label><div class=\"sk-toggleable__content\"><pre>FeatureUnion(transformer_list=[('abundances --> CLR',\n",
" Pipeline(steps=[('compositionalselector',\n",
" CompositionalSelector()),\n",
" ('clrtransform',\n",
Expand All @@ -215,7 +225,7 @@
" Pipeline(steps=[('compositionalselector',\n",
" CompositionalSelector(inverse=True)),\n",
" ('logtransform',\n",
" LogTransform())]))])</pre></div></div></div><div class=\"sk-parallel\"><div class=\"sk-parallel-item\"><div class=\"sk-item\"><div class=\"sk-label-container\"><div class=\"sk-label sk-toggleable\"><label>abundances --&gt; CLR</label></div></div><div class=\"sk-serial\"><div class=\"sk-item\"><div class=\"sk-serial\"><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"ffd00259-4668-4265-880c-4ce8d934619b\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"ffd00259-4668-4265-880c-4ce8d934619b\">CompositionalSelector</label><div class=\"sk-toggleable__content\"><pre>CompositionalSelector()</pre></div></div></div><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"3f5460e3-3682-4b3f-b62b-689204732e7a\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"3f5460e3-3682-4b3f-b62b-689204732e7a\">CLRTransform</label><div class=\"sk-toggleable__content\"><pre>CLRTransform()</pre></div></div></div></div></div></div></div></div><div class=\"sk-parallel-item\"><div class=\"sk-item\"><div class=\"sk-label-container\"><div class=\"sk-label sk-toggleable\"><label>isotopes</label></div></div><div class=\"sk-serial\"><div class=\"sk-item\"><div class=\"sk-serial\"><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"3b841a04-46b8-4a00-b178-ace83f638568\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"3b841a04-46b8-4a00-b178-ace83f638568\">CompositionalSelector</label><div class=\"sk-toggleable__content\"><pre>CompositionalSelector(inverse=True)</pre></div></div></div><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"17e46a71-8cae-4e6b-967a-fd079f3253d2\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"17e46a71-8cae-4e6b-967a-fd079f3253d2\">LogTransform</label><div class=\"sk-toggleable__content\"><pre>LogTransform()</pre></div></div></div></div></div></div></div></div></div></div><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"43f84399-cb84-4d7c-abe1-119a18367874\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"43f84399-cb84-4d7c-abe1-119a18367874\">StandardScaler</label><div class=\"sk-toggleable__content\"><pre>StandardScaler()</pre></div></div></div><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"73c9a664-20d3-4d4e-9aee-82e241015a61\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"73c9a664-20d3-4d4e-9aee-82e241015a61\">SVC</label><div class=\"sk-toggleable__content\"><pre>SVC(cache_size=500, class_weight='balanced', decision_function_shape='ovo',\n",
" LogTransform())]))])</pre></div></div></div><div class=\"sk-parallel\"><div class=\"sk-parallel-item\"><div class=\"sk-item\"><div class=\"sk-label-container\"><div class=\"sk-label sk-toggleable\"><label>abundances --&gt; CLR</label></div></div><div class=\"sk-serial\"><div class=\"sk-item\"><div class=\"sk-serial\"><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"4f98a060-8473-44b4-a611-5d4a567d59d9\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"4f98a060-8473-44b4-a611-5d4a567d59d9\">CompositionalSelector</label><div class=\"sk-toggleable__content\"><pre>CompositionalSelector()</pre></div></div></div><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"781aa290-5d49-411d-9371-727e93080936\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"781aa290-5d49-411d-9371-727e93080936\">CLRTransform</label><div class=\"sk-toggleable__content\"><pre>CLRTransform()</pre></div></div></div></div></div></div></div></div><div class=\"sk-parallel-item\"><div class=\"sk-item\"><div class=\"sk-label-container\"><div class=\"sk-label sk-toggleable\"><label>isotopes</label></div></div><div class=\"sk-serial\"><div class=\"sk-item\"><div class=\"sk-serial\"><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"d3e47e2b-4f00-4f62-ba19-0b23767d469d\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"d3e47e2b-4f00-4f62-ba19-0b23767d469d\">CompositionalSelector</label><div class=\"sk-toggleable__content\"><pre>CompositionalSelector(inverse=True)</pre></div></div></div><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"d1243a4d-cb35-49bf-95cd-0c38694b43fc\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"d1243a4d-cb35-49bf-95cd-0c38694b43fc\">LogTransform</label><div class=\"sk-toggleable__content\"><pre>LogTransform()</pre></div></div></div></div></div></div></div></div></div></div><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"8cf95014-572e-4ab3-a14f-20c9cd37911e\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"8cf95014-572e-4ab3-a14f-20c9cd37911e\">StandardScaler</label><div class=\"sk-toggleable__content\"><pre>StandardScaler()</pre></div></div></div><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"2c6b8e75-e473-4f7c-9a13-7d55ccc7202a\" type=\"checkbox\" ><label class=\"sk-toggleable__label\" for=\"2c6b8e75-e473-4f7c-9a13-7d55ccc7202a\">SVC</label><div class=\"sk-toggleable__content\"><pre>SVC(cache_size=500, class_weight='balanced', decision_function_shape='ovo',\n",
" probability=True)</pre></div></div></div></div></div></div></div></div></div></div></div></div>"
],
"text/plain": [
Expand Down Expand Up @@ -245,7 +255,7 @@
" 'svc__gamma': array([0.00501187, 0.01154782, 0.02660725, 0.06130558, 0.14125375])})"
]
},
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -309,7 +319,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -344,7 +354,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 6,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -372,7 +382,8 @@
"ax.legend([proxy_line(c=coll.get_facecolors()[0], marker='o', ls='none') for coll in ax.collections],\n",
" df.Class.unique(),\n",
" frameon=False,\n",
" facecolor=None);"
" facecolor=None)\n",
"plt.show()"
]
},
{
Expand All @@ -392,7 +403,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -407,7 +418,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 8,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -449,7 +460,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -466,7 +477,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 10,
"metadata": {},
"outputs": [
{
Expand All @@ -481,6 +492,7 @@
}
],
"source": [
"%matplotlib inline\n",
"fig, ax = plt.subplots(1, figsize=(5,5))\n",
"ax.scatter(*embedding.T, \n",
" c=csample,\n",
Expand Down Expand Up @@ -510,7 +522,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -525,13 +537,13 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "0ca32b1bb8404d16a9aeaae7c123d40b",
"model_id": "f2ec0358b9ba4b5ebcb2a26d4e24fc53",
"version_major": 2,
"version_minor": 0
},
Expand Down
1 change: 1 addition & 0 deletions binder/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ dependencies:
- widgetsnbextension
- imagemagick
- nodejs # if using ipyvolume and lab
- jupyterlab
- pip:
- jupyter_contrib_nbextensions
- -e git+git://github.com/morganjwilliams/pyrolite.git@develop#egg=pyrolite[skl]

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