3.0.0-mmvec.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/biom/table.py:4068: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return constructor(mat, index=index, columns=columns)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/sparse/frame.py:257: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n",
      "Use a Series with sparse values instead.\n",
      "\n",
      "    >>> series = pd.Series(pd.SparseArray(...))\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  sparse_index=BlockIndex(N, blocs, blens),\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/generic.py:4583: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n",
      "Use a Series with sparse values instead.\n",
      "\n",
      "    >>> series = pd.Series(pd.SparseArray(...))\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return self._constructor(new_data).__finalize__(self)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/sparse/frame.py:854: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  default_kind=self._default_kind,\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/frame.py:3471: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n",
      "Use a Series with sparse values instead.\n",
      "\n",
      "    >>> series = pd.Series(pd.SparseArray(...))\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return klass(values, index=self.index, name=items, fastpath=True)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/sparse/frame.py:785: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return self._constructor(new_arrays, index=index, columns=columns).__finalize__(\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/ops/__init__.py:1641: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n",
      "Use a Series with sparse values instead.\n",
      "\n",
      "    >>> series = pd.Series(pd.SparseArray(...))\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return self._constructor(new_values, index=self.index, name=self.name)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/sparse/frame.py:339: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  default_fill_value=self.default_fill_value,\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/generic.py:6289: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return self._constructor(new_data).__finalize__(self)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/generic.py:5884: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n",
      "Use a Series with sparse values instead.\n",
      "\n",
      "    >>> series = pd.Series(pd.SparseArray(...))\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return self._constructor(new_data).__finalize__(self)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/generic.py:3606: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  result = self._constructor(new_data).__finalize__(self)\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/bin/mmvec:160: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/bin/mmvec:161: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.\n",
      "\n",
      "2021-06-14 13:27:52.031622: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA\n",
      "2021-06-14 13:27:52.052960: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7fdb01051400 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n",
      "2021-06-14 13:27:52.052983: I tensorflow/compiler/xla/service/service.cc:176]   StreamExecutor device (0): Host, Default Version\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:90: The name tf.log is deprecated. Please use tf.math.log instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:91: multinomial (from tensorflow.python.ops.random_ops) is deprecated and will be removed in a future version.\n",
      "Instructions for updating:\n",
      "Use `tf.random.categorical` instead.\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:102: The name tf.random_normal is deprecated. Please use tf.random.normal instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:118: Normal.__init__ (from tensorflow.python.ops.distributions.normal) is deprecated and will be removed after 2019-01-01.\n",
      "Instructions for updating:\n",
      "The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use `tfp.distributions` instead of `tf.distributions`.\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/tensorflow_core/python/ops/distributions/normal.py:160: Distribution.__init__ (from tensorflow.python.ops.distributions.distribution) is deprecated and will be removed after 2019-01-01.\n",
      "Instructions for updating:\n",
      "The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use `tfp.distributions` instead of `tf.distributions`.\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:135: Multinomial.__init__ (from tensorflow.python.ops.distributions.multinomial) is deprecated and will be removed after 2019-01-01.\n",
      "Instructions for updating:\n",
      "The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use `tfp.distributions` instead of `tf.distributions`.\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:183: The name tf.summary.scalar is deprecated. Please use tf.compat.v1.summary.scalar instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:185: The name tf.summary.histogram is deprecated. Please use tf.compat.v1.summary.histogram instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:189: The name tf.summary.merge_all is deprecated. Please use tf.compat.v1.summary.merge_all instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:191: The name tf.summary.FileWriter is deprecated. Please use tf.compat.v1.summary.FileWriter instead.\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:196: The name tf.train.AdamOptimizer is deprecated. Please use tf.compat.v1.train.AdamOptimizer instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/tensorflow_core/python/ops/clip_ops.py:301: where (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version.\n",
      "Instructions for updating:\n",
      "Use tf.where in 2.0, which has the same broadcast rule as np.where\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:206: The name tf.global_variables_initializer is deprecated. Please use tf.compat.v1.global_variables_initializer instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:243: The name tf.train.Saver is deprecated. Please use tf.compat.v1.train.Saver instead.\n",
      "\n",
      "100%|█████████████████████████████████████████| 477/477 [05:25<00:00,  1.46it/s]\n"
     ]
    }
   ],
   "source": [
    "!mmvec paired-omics\\\n",
    "    --microbe-file ../data/matched-mmvec/micro.biom\\\n",
    "    --metabolite-file ../data/matched-mmvec/met.biom\\\n",
    "    --training-column 'stratified_test_labels'\\\n",
    "    --epochs 500\\\n",
    "    --batch-size 4000\\\n",
    "    --latent-dim 3\\\n",
    "    --summary-interval 20\\\n",
    "    --summary-dir ../results/mmvec/run-stats\\\n",
    "    --embeddings-file ../results/mmvec/embeddings.txt\\\n",
    "    --ranks-file ../results/mmvec/ranks.tsv\\\n",
    "    --ordination-file ../results/mmvec/ordination.txt\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/biom/table.py:4068: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return constructor(mat, index=index, columns=columns)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/sparse/frame.py:257: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n",
      "Use a Series with sparse values instead.\n",
      "\n",
      "    >>> series = pd.Series(pd.SparseArray(...))\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  sparse_index=BlockIndex(N, blocs, blens),\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/generic.py:4583: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n",
      "Use a Series with sparse values instead.\n",
      "\n",
      "    >>> series = pd.Series(pd.SparseArray(...))\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return self._constructor(new_data).__finalize__(self)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/sparse/frame.py:854: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  default_kind=self._default_kind,\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/frame.py:3471: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n",
      "Use a Series with sparse values instead.\n",
      "\n",
      "    >>> series = pd.Series(pd.SparseArray(...))\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return klass(values, index=self.index, name=items, fastpath=True)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/sparse/frame.py:785: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return self._constructor(new_arrays, index=index, columns=columns).__finalize__(\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/ops/__init__.py:1641: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n",
      "Use a Series with sparse values instead.\n",
      "\n",
      "    >>> series = pd.Series(pd.SparseArray(...))\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return self._constructor(new_values, index=self.index, name=self.name)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/sparse/frame.py:339: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  default_fill_value=self.default_fill_value,\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/generic.py:6289: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return self._constructor(new_data).__finalize__(self)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/generic.py:5884: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n",
      "Use a Series with sparse values instead.\n",
      "\n",
      "    >>> series = pd.Series(pd.SparseArray(...))\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  return self._constructor(new_data).__finalize__(self)\n",
      "/Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/pandas/core/generic.py:3606: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n",
      "Use a regular DataFrame whose columns are SparseArrays instead.\n",
      "\n",
      "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n",
      "\n",
      "  result = self._constructor(new_data).__finalize__(self)\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/bin/mmvec:160: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/bin/mmvec:161: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.\n",
      "\n",
      "2021-05-24 07:54:00.909259: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA\n",
      "2021-05-24 07:54:00.962996: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7ff3d0f3d130 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n",
      "2021-05-24 07:54:00.963087: I tensorflow/compiler/xla/service/service.cc:176]   StreamExecutor device (0): Host, Default Version\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:90: The name tf.log is deprecated. Please use tf.math.log instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:91: multinomial (from tensorflow.python.ops.random_ops) is deprecated and will be removed in a future version.\n",
      "Instructions for updating:\n",
      "Use `tf.random.categorical` instead.\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:102: The name tf.random_normal is deprecated. Please use tf.random.normal instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:118: Normal.__init__ (from tensorflow.python.ops.distributions.normal) is deprecated and will be removed after 2019-01-01.\n",
      "Instructions for updating:\n",
      "The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use `tfp.distributions` instead of `tf.distributions`.\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/tensorflow_core/python/ops/distributions/normal.py:160: Distribution.__init__ (from tensorflow.python.ops.distributions.distribution) is deprecated and will be removed after 2019-01-01.\n",
      "Instructions for updating:\n",
      "The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use `tfp.distributions` instead of `tf.distributions`.\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:135: Multinomial.__init__ (from tensorflow.python.ops.distributions.multinomial) is deprecated and will be removed after 2019-01-01.\n",
      "Instructions for updating:\n",
      "The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use `tfp.distributions` instead of `tf.distributions`.\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:183: The name tf.summary.scalar is deprecated. Please use tf.compat.v1.summary.scalar instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:185: The name tf.summary.histogram is deprecated. Please use tf.compat.v1.summary.histogram instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:189: The name tf.summary.merge_all is deprecated. Please use tf.compat.v1.summary.merge_all instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:191: The name tf.summary.FileWriter is deprecated. Please use tf.compat.v1.summary.FileWriter instead.\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:196: The name tf.train.AdamOptimizer is deprecated. Please use tf.compat.v1.train.AdamOptimizer instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/tensorflow_core/python/ops/clip_ops.py:301: where (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version.\n",
      "Instructions for updating:\n",
      "Use tf.where in 2.0, which has the same broadcast rule as np.where\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:206: The name tf.global_variables_initializer is deprecated. Please use tf.compat.v1.global_variables_initializer instead.\n",
      "\n",
      "WARNING:tensorflow:From /Users/cmartino/miniconda3/envs/qiime2-2021.2.songbird.mmvec/lib/python3.6/site-packages/mmvec/multimodal.py:243: The name tf.train.Saver is deprecated. Please use tf.compat.v1.train.Saver instead.\n",
      "\n",
      "100%|███████████████████████████████████████| 1319/1319 [10:03<00:00,  2.19it/s]\n"
     ]
    }
   ],
   "source": [
    "!mmvec paired-omics\\\n",
    "    --microbe-file ../data/matched-mmvec/met.biom\\\n",
    "    --metabolite-file ../data/matched-mmvec/micro.biom\\\n",
    "    --training-column 'stratified_test_labels'\\\n",
    "    --epochs 50\\\n",
    "    --batch-size 4000\\\n",
    "    --latent-dim 3\\\n",
    "    --summary-interval 20\\\n",
    "    --min-feature-count 10\\\n",
    "    --summary-dir ../results/mmvec-microbe/run-stats\\\n",
    "    --embeddings-file ../results/mmvec-microbe/embeddings\\\n",
    "    --ranks-file ../results/mmvec-microbe/ranks\\\n",
    "    --ordination-file ../results/mmvec-microbe/ordination\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "    --num-testing-examples 16\\\n",
    "    --input-prior 1.0\\\n",
    "    --output-prior 1.0\\\n",
    "    --learning-rate 1e-5\\\n",
    "    --beta1 0.9\\\n",
    "    --beta2 0.95\\\n",
    "    --clipnorm 10.0\\"
   ]
  }
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