From 8b778c127c652552d895e6e2b0d1bd669b69b87a Mon Sep 17 00:00:00 2001 From: dkobak Date: Tue, 10 Mar 2020 13:20:48 +0100 Subject: [PATCH 01/10] Changing default parameters in the Python wrapper --- examples/test.ipynb | 1305 +++++++------------------------------------ fast_tsne.py | 86 ++- 2 files changed, 262 insertions(+), 1129 deletions(-) diff --git a/examples/test.ipynb b/examples/test.ipynb index 535d69b..56a715a 100644 --- a/examples/test.ipynb +++ b/examples/test.ipynb @@ -33,903 +33,44 @@ "metadata": {}, "outputs": [ { - "name": "stderr", - "output_type": "stream", - "text": [ - "Using TensorFlow backend.\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "(70000, 784)\n" - ] - } - ], - "source": [ - "# Load MNIST data\n", - "from keras.datasets import mnist\n", - "(x_train, y_train), (x_test, y_test) = mnist.load_data()\n", - "x_train = x_train.reshape(60000, 784).astype('float') / 255\n", - "x_test = x_test.reshape(10000, 784).astype('float') / 255\n", - "X = np.concatenate((x_train, x_test))\n", - "y = np.concatenate((y_train, y_test))\n", - "print(X.shape)\n", - "\n", - "# Do PCA and keep 50 dimensions\n", - "X = X - X.mean(axis=0)\n", - "U, s, V = np.linalg.svd(X, full_matrices=False)\n", - "X50 = np.dot(U, np.diag(s))[:,:50]\n", - "\n", - "# 10 nice colors\n", - "col = np.array(['#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99',\n", - " '#e31a1c','#fdbf6f','#ff7f00','#cab2d6','#6a3d9a'])" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CPU times: user 706 ms, sys: 60.3 ms, total: 766 ms\n", - "Wall time: 52.4 s\n" - ] - } - ], - "source": [ - "# Running t-SNE on the full MNIST in the default way (this uses perplexity=30)\n", - "\n", - "%time Z = fast_tsne(X50, seed=42)" - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "metadata": {}, - "outputs": [ - { - "data": { - "application/javascript": [ - "/* Put everything inside the global mpl namespace */\n", - "window.mpl = {};\n", - "\n", - "\n", - "mpl.get_websocket_type = function() {\n", - " if (typeof(WebSocket) !== 'undefined') {\n", - " return WebSocket;\n", - " } else if (typeof(MozWebSocket) !== 'undefined') {\n", - " return MozWebSocket;\n", - " } else {\n", - " alert('Your browser does not have WebSocket support. ' +\n", - " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", - " 'Firefox 4 and 5 are also supported but you ' +\n", - " 'have to enable WebSockets in about:config.');\n", - " };\n", - "}\n", - "\n", - "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", - " this.id = figure_id;\n", - "\n", - " this.ws = websocket;\n", - "\n", - " this.supports_binary = (this.ws.binaryType != undefined);\n", - "\n", - " if (!this.supports_binary) {\n", - " var warnings = document.getElementById(\"mpl-warnings\");\n", - " if (warnings) {\n", - " warnings.style.display = 'block';\n", - " warnings.textContent = (\n", - " \"This browser does not support binary websocket messages. \" +\n", - " \"Performance may be slow.\");\n", - " }\n", - " }\n", - "\n", - " this.imageObj = new Image();\n", - "\n", - " this.context = undefined;\n", - " this.message = undefined;\n", - " this.canvas = undefined;\n", - " this.rubberband_canvas = undefined;\n", - " this.rubberband_context = undefined;\n", - " this.format_dropdown = undefined;\n", - "\n", - " this.image_mode = 'full';\n", - "\n", - " this.root = $('
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