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spencerldixon · Mar 9, 2018 · 4583749 · 4583749
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diff --git a/.gitignore b/.gitignore
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+data/*
diff --git a/.ipynb_checkpoints/1. Classifying Partial Permits-checkpoint.ipynb b/.ipynb_checkpoints/1. Classifying Partial Permits-checkpoint.ipynb
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+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/1. Classifying Partial Permits.ipynb b/1. Classifying Partial Permits.ipynb
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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Goal 1\n",
+    "## Given a partial permit, can we predict what classification it belongs to?\n",
+    "\n",
+    "### Getting Started\n",
+    "- Open up the CITES trade database at https://trade.cites.org/\n",
+    "- Select a year range and click *Search*\n",
+    "- Download a Comparative Tabulation report and place it in `data/`\n",
+    "- Install requirements with `pip install -r requirements.txt`\n",
+    "- Run this notebook"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Using TensorFlow backend.\n"
+     ]
+    },
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'tensorflow'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-3-5f38681609db>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mnumpy\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpandas\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mkeras\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodels\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mSequential\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      4\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mkeras\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlayers\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mDense\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mkeras\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwrappers\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mscikit_learn\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mKerasClassifier\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m/usr/local/lib/python3.6/site-packages/keras/__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0m__future__\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mabsolute_import\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mutils\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      4\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mactivations\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mapplications\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m/usr/local/lib/python3.6/site-packages/keras/utils/__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mdata_utils\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mio_utils\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mconv_utils\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      7\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      8\u001b[0m \u001b[0;31m# Globally-importable utils.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m/usr/local/lib/python3.6/site-packages/keras/utils/conv_utils.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0msix\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmoves\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      8\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mnumpy\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 9\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mbackend\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mK\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     10\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     11\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m/usr/local/lib/python3.6/site-packages/keras/backend/__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     82\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0m_BACKEND\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'tensorflow'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     83\u001b[0m     \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstderr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwrite\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Using TensorFlow backend.\\n'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 84\u001b[0;31m     \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0mtensorflow_backend\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     85\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     86\u001b[0m     \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Unknown backend: '\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_BACKEND\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m/usr/local/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0m__future__\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mprint_function\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 5\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mtensorflow\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mtf\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      6\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mtensorflow\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpython\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mmoving_averages\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mtensorflow\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpython\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mops\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mtensor_array_ops\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'tensorflow'"
+     ]
+    }
+   ],
+   "source": [
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "from keras.models import Sequential\n",
+    "from keras.layers import Dense\n",
+    "from keras.wrappers.scikit_learn import KerasClassifier\n",
+    "from keras.utils import np_utils\n",
+    "from sklearn.model_selection import cross_val_score\n",
+    "from sklearn.model_selection import KFold\n",
+    "from sklearn.preprocessing import LabelEncoder\n",
+    "from sklearn.pipeline import Pipeline"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "np.random.seed(1)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/README.md b/README.md
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+# CITES ML
+## Machine Learning with the CITES Trade Database
+
+### Installation
+
+Install Python 3.6, jupyter notebook, and run `pip install -r requirements.txt`
+
+### Aims
+
+This repo is an exploratory effort to see how Machine Learning can be applied to the CITES Trade Database, with three main objectives and experiments, each represented in a jupyter notebook:
+
+1. Given a partial permit, can we figure out what category it belongs to?
+2. Given some trade data over time, can we predict future trade numbers, per country and per species?
+3. Given valid and invalid permits (raw data before validation steps), can we learn the sanity checks and validation processes to spot invalid permits automatically?
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,66 @@
+absl-py==0.1.11
+appnope==0.1.0
+astor==0.6.2
+bleach==1.5.0
+certifi==2018.1.18
+chardet==3.0.4
+decorator==4.2.1
+docopt==0.6.2
+entrypoints==0.2.3
+gast==0.2.0
+grpcio==1.10.0
+html5lib==0.9999999
+idna==2.6
+ipykernel==4.8.2
+ipython==6.2.1
+ipython-genutils==0.2.0
+ipywidgets==7.1.2
+jedi==0.11.1
+Jinja2==2.10
+jsonschema==2.6.0
+jupyter==1.0.0
+jupyter-client==5.2.2
+jupyter-console==5.2.0
+jupyter-core==4.4.0
+Keras==2.1.5
+Markdown==2.6.11
+MarkupSafe==1.0
+mistune==0.8.3
+nbconvert==5.3.1
+nbformat==4.4.0
+notebook==5.4.0
+numpy==1.14.1
+pandas==0.22.0
+pandocfilters==1.4.2
+parso==0.1.1
+pexpect==4.4.0
+pickleshare==0.7.4
+prompt-toolkit==1.0.15
+protobuf==3.5.2
+ptyprocess==0.5.2
+Pygments==2.2.0
+python-dateutil==2.6.1
+pytz==2018.3
+PyYAML==3.12
+pyzmq==17.0.0
+qtconsole==4.3.1
+requests==2.18.4
+scikit-learn==0.19.1
+scipy==1.0.0
+Send2Trash==1.5.0
+simplegeneric==0.8.1
+six==1.11.0
+sklearn==0.0
+tensorboard==1.6.0
+tensorflow==1.6.0
+termcolor==1.1.0
+terminado==0.8.1
+testpath==0.3.1
+tornado==5.0
+traitlets==4.3.2
+urllib3==1.22
+wcwidth==0.1.7
+webencodings==0.5.1
+Werkzeug==0.14.1
+widgetsnbextension==3.1.4
+yarg==0.1.9