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Created August 7, 2021 22:50
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umap_progress_bar.ipynb
{
"cells": [
{
"cell_type": "markdown",
"id": "00194853-8c88-4fc0-8aaf-fccda642fa29",
"metadata": {},
"source": [
"## Demonstrating usage of tqdm progress bar within UMAP package"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "9f16986e-8863-4551-a0bc-c3329074a3ea",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"UMAP version: 0.5.1\n",
"time: 1.69 s (started: 2021-08-08 00:47:36 +02:00)\n"
]
}
],
"source": [
"%load_ext autotime\n",
"\n",
"from sklearn.datasets import load_digits\n",
"import umap\n",
"\n",
"print (\"UMAP version: \", umap.__version__)"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "b9aa52b2-4653-41f3-8362-3534f5f57d22",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"time: 78 ms (started: 2021-08-08 00:47:37 +02:00)\n"
]
}
],
"source": [
"digits = load_digits()"
]
},
{
"cell_type": "markdown",
"id": "ce59cf11-a0e6-47c8-8f10-6aa7b36e0efe",
"metadata": {},
"source": [
"### Instantiating UMAP class and running the fit method. Here the default value of `verbose` (False) will be used and hence no log or progress bar is printed"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "56061f1f-d607-4dda-98f3-039c647f4e7f",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"time: 10 s (started: 2021-08-08 00:47:37 +02:00)\n"
]
}
],
"source": [
"umap.UMAP(random_state=42).fit(digits.data);"
]
},
{
"cell_type": "markdown",
"id": "ac36083d-1c45-46d5-aefa-b6a9be54e548",
"metadata": {},
"source": [
"### Now we set `verbose=True`. Notice that now we see the log and tqdm progress bar with the default settings"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "69bca6b0-7eec-4988-8ac1-c2a02c5615c0",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"UMAP(random_state=42, verbose=True)\n",
"Sun Aug 8 00:47:47 2021 Construct fuzzy simplicial set\n",
"Sun Aug 8 00:47:49 2021 Finding Nearest Neighbors\n",
"Sun Aug 8 00:47:49 2021 Finished Nearest Neighbor Search\n",
"Sun Aug 8 00:47:49 2021 Construct embedding\n"
]
},
{
"data": {
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"model_id": "c93f06f834da4326b5ce55992dd23783",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Epochs completed: 0%| 0/500 [00:00]"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Sun Aug 8 00:47:53 2021 Finished embedding\n",
"time: 5.19 s (started: 2021-08-08 00:47:47 +02:00)\n"
]
}
],
"source": [
"umap.UMAP(random_state=42, verbose=True).fit(digits.data);"
]
},
{
"cell_type": "markdown",
"id": "070df82d-e17e-495b-a9e2-a68b4613c96c",
"metadata": {},
"source": [
"### By setting `verbose=False` explicitly, the log as well as the progress bar can be disabled"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "98eb63db-e2a6-4552-9818-2b73dc1fa85f",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"time: 5.27 s (started: 2021-08-08 00:47:53 +02:00)\n"
]
}
],
"source": [
"umap.UMAP(random_state=42, verbose=False).fit(digits.data);"
]
},
{
"cell_type": "markdown",
"id": "3b53d0fb-d45c-4378-b934-0c595e6b52b4",
"metadata": {},
"source": [
"### The `tqdm_kwds` parameter can be used to pass arguments to `tqdm`. Here, the width and color of the progress bar were changed."
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "fd879503-3b45-4916-b253-b9c644cce1c8",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"UMAP(random_state=42, verbose=True)\n",
"Sun Aug 8 00:47:58 2021 Construct fuzzy simplicial set\n",
"Sun Aug 8 00:48:00 2021 Finding Nearest Neighbors\n",
"Sun Aug 8 00:48:00 2021 Finished Nearest Neighbor Search\n",
"Sun Aug 8 00:48:00 2021 Construct embedding\n"
]
},
{
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"model_id": "c62649d08d3d49c1882dbdda6df52182",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Epochs completed: 0%| …"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Sun Aug 8 00:48:03 2021 Finished embedding\n",
"time: 5.58 s (started: 2021-08-08 00:47:58 +02:00)\n"
]
}
],
"source": [
"tqdm_kwds = {\n",
" \"ncols\": 400,\n",
" \"colour\": \"#FFC0CB\",\n",
"}\n",
"umap.UMAP(random_state=42, verbose=True, tqdm_kwds=tqdm_kwds).fit(digits.data);"
]
},
{
"cell_type": "markdown",
"id": "8794f295-cd24-437d-9a7c-f1e9fe266e17",
"metadata": {},
"source": [
"### Sometimes, it can be useful have the UMAP logs but not the progress bar itself. A common use case is when running UMAP in some batch script. In such cases, `verbose` is set to `True` and `disable=True` is used in the `tqdm_kwds` argument"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "8d2c2606-286c-4ad3-9200-99ae4a271571",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"UMAP(random_state=42, verbose=True)\n",
"Sun Aug 8 00:48:03 2021 Construct fuzzy simplicial set\n",
"Sun Aug 8 00:48:05 2021 Finding Nearest Neighbors\n",
"Sun Aug 8 00:48:05 2021 Finished Nearest Neighbor Search\n",
"Sun Aug 8 00:48:05 2021 Construct embedding\n",
"Sun Aug 8 00:48:09 2021 Finished embedding\n",
"time: 5.59 s (started: 2021-08-08 00:48:03 +02:00)\n"
]
}
],
"source": [
"tqdm_kwds = {\"disable\": True}\n",
"umap.UMAP(random_state=42, verbose=True, tqdm_kwds=tqdm_kwds).fit(digits.data);"
]
},
{
"cell_type": "markdown",
"id": "227ce17a-dbd7-4fc9-81bb-b6bece41965a",
"metadata": {},
"source": [
"### Benchmarking runtime in scenarios where the progress bar is either enabled or disabled"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "19240422-336c-44d9-8d4e-ab1524d3a08e",
"metadata": {
"scrolled": true,
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"UMAP(random_state=42, verbose=True)\n",
"Sun Aug 8 00:48:09 2021 Construct fuzzy simplicial set\n",
"Sun Aug 8 00:48:11 2021 Finding Nearest Neighbors\n",
"Sun Aug 8 00:48:11 2021 Finished Nearest Neighbor Search\n",
"Sun Aug 8 00:48:11 2021 Construct embedding\n"
]
},
{
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"model_id": "e6f8ad16f9044f53b839223c562159be",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Epochs completed: 0%| 0/500 [00:00]"
]
},
"metadata": {},
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},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Sun Aug 8 00:48:14 2021 Finished embedding\n",
"UMAP(random_state=42, verbose=True)\n",
"Sun Aug 8 00:48:14 2021 Construct fuzzy simplicial set\n",
"Sun Aug 8 00:48:16 2021 Finding Nearest Neighbors\n",
"Sun Aug 8 00:48:16 2021 Finished Nearest Neighbor Search\n",
"Sun Aug 8 00:48:16 2021 Construct embedding\n"
]
},
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"Epochs completed: 0%| 0/500 [00:00]"
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"text": [
"Sun Aug 8 00:48:20 2021 Finished embedding\n",
"UMAP(random_state=42, verbose=True)\n",
"Sun Aug 8 00:48:20 2021 Construct fuzzy simplicial set\n",
"Sun Aug 8 00:48:22 2021 Finding Nearest Neighbors\n",
"Sun Aug 8 00:48:22 2021 Finished Nearest Neighbor Search\n",
"Sun Aug 8 00:48:22 2021 Construct embedding\n"
]
},
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"text": [
"Sun Aug 8 00:48:25 2021 Finished embedding\n",
"UMAP(random_state=42, verbose=True)\n",
"Sun Aug 8 00:48:25 2021 Construct fuzzy simplicial set\n",
"Sun Aug 8 00:48:27 2021 Finding Nearest Neighbors\n",
"Sun Aug 8 00:48:27 2021 Finished Nearest Neighbor Search\n",
"Sun Aug 8 00:48:27 2021 Construct embedding\n"
]
},
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"Epochs completed: 0%| 0/500 [00:00]"
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"text": [
"Sun Aug 8 00:48:31 2021 Finished embedding\n",
"UMAP(random_state=42, verbose=True)\n",
"Sun Aug 8 00:48:31 2021 Construct fuzzy simplicial set\n",
"Sun Aug 8 00:48:32 2021 Finding Nearest Neighbors\n",
"Sun Aug 8 00:48:33 2021 Finished Nearest Neighbor Search\n",
"Sun Aug 8 00:48:33 2021 Construct embedding\n"
]
},
{
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"Epochs completed: 0%| 0/500 [00:00]"
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"text": [
"Sun Aug 8 00:48:36 2021 Finished embedding\n",
"UMAP(random_state=42, verbose=True)\n",
"Sun Aug 8 00:48:36 2021 Construct fuzzy simplicial set\n",
"Sun Aug 8 00:48:38 2021 Finding Nearest Neighbors\n",
"Sun Aug 8 00:48:38 2021 Finished Nearest Neighbor Search\n",
"Sun Aug 8 00:48:38 2021 Construct embedding\n"
]
},
{
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"Epochs completed: 0%| 0/500 [00:00]"
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"text": [
"Sun Aug 8 00:48:42 2021 Finished embedding\n",
"UMAP(random_state=42, verbose=True)\n",
"Sun Aug 8 00:48:42 2021 Construct fuzzy simplicial set\n",
"Sun Aug 8 00:48:43 2021 Finding Nearest Neighbors\n",
"Sun Aug 8 00:48:43 2021 Finished Nearest Neighbor Search\n",
"Sun Aug 8 00:48:43 2021 Construct embedding\n"
]
},
{
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"Epochs completed: 0%| 0/500 [00:00]"
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"text": [
"Sun Aug 8 00:48:47 2021 Finished embedding\n",
"UMAP(random_state=42, verbose=True)\n",
"Sun Aug 8 00:48:47 2021 Construct fuzzy simplicial set\n",
"Sun Aug 8 00:48:49 2021 Finding Nearest Neighbors\n",
"Sun Aug 8 00:48:49 2021 Finished Nearest Neighbor Search\n",
"Sun Aug 8 00:48:49 2021 Construct embedding\n"
]
},
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"text": [
"Sun Aug 8 00:48:53 2021 Finished embedding\n",
"5.47 s ± 95.5 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n",
"time: 43.8 s (started: 2021-08-08 00:48:09 +02:00)\n"
]
}
],
"source": [
"%%timeit\n",
"umap.UMAP(random_state=42, verbose=True).fit(digits.data);"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "ef05b8d2-e62e-4f93-acfe-615442c55570",
"metadata": {},
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"5.24 s ± 78.9 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n",
"time: 42.2 s (started: 2021-08-08 00:48:53 +02:00)\n"
]
}
],
"source": [
"%%timeit\n",
"umap.UMAP(random_state=42, verbose=False).fit(digits.data);"
]
},
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"cell_type": "code",
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