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August 7, 2021 22:50
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| { | |
| "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": { | |
| "application/vnd.jupyter.widget-view+json": { | |
| "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" | |
| ] | |
| }, | |
| { | |
| "data": { | |
| "application/vnd.jupyter.widget-view+json": { | |
| "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" | |
| ] | |
| }, | |
| { | |
| "data": { | |
| "application/vnd.jupyter.widget-view+json": { | |
| "model_id": "e6f8ad16f9044f53b839223c562159be", | |
| "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 00:48:14 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" | |
| ] | |
| }, | |
| { | |
| "data": { | |
| "application/vnd.jupyter.widget-view+json": { | |
| "model_id": "ae99717409aa421b9011ec9411d5b6c1", | |
| "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 00:48:20 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" | |
| ] | |
| }, | |
| { | |
| "data": { | |
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| "model_id": "262fa143a41d4310b147854ebbbbbec1", | |
| "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 00:48:25 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" | |
| ] | |
| }, | |
| { | |
| "data": { | |
| "application/vnd.jupyter.widget-view+json": { | |
| "model_id": "d533730d70984a5ca3d486990642a05b", | |
| "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 00:48:31 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]" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| }, | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "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" | |
| ] | |
| }, | |
| { | |
| "data": { | |
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| "model_id": "a8cefa7312974ba183de1e3e8f0a0660", | |
| "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 00:48:42 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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| "data": { | |
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| "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 00:48:47 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" | |
| ] | |
| }, | |
| { | |
| "data": { | |
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| "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 00:48:53 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": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "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);" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "id": "4c3e21f7-c6c1-4a4f-a0a6-e681eb6477b0", | |
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| "display_name": "Python 3 (ipykernel)", | |
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| "name": "ipython", | |
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| "file_extension": ".py", | |
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