From 15e296db9bd905046ce365ae556f0bfbb1b1c12e Mon Sep 17 00:00:00 2001
From: evelynmitchell <efmphone@gmail.com>
Date: Thu, 25 Jan 2024 12:29:06 -0700
Subject: [PATCH 1/2] example colab notebook

---
 DynamaxSSM.ipynb | 89 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 89 insertions(+)
 create mode 100644 DynamaxSSM.ipynb

diff --git a/DynamaxSSM.ipynb b/DynamaxSSM.ipynb
new file mode 100644
index 00000000..28cc3797
--- /dev/null
+++ b/DynamaxSSM.ipynb
@@ -0,0 +1,89 @@
+{
+  "nbformat": 4,
+  "nbformat_minor": 0,
+  "metadata": {
+    "colab": {
+      "private_outputs": true,
+      "provenance": []
+    },
+    "kernelspec": {
+      "name": "python3",
+      "display_name": "Python 3"
+    },
+    "language_info": {
+      "name": "python"
+    }
+  },
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "Ru6SwSvrCsbl"
+      },
+      "outputs": [],
+      "source": [
+        "!pip install dynamax[notebooks]"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "import jax.numpy as jnp\n",
+        "import jax.random as jr\n",
+        "import matplotlib.pyplot as plt\n",
+        "from dynamax.hidden_markov_model import GaussianHMM\n",
+        "\n",
+        "key1, key2, key3 = jr.split(jr.PRNGKey(0), 3)\n",
+        "num_states = 3\n",
+        "emission_dim = 2\n",
+        "num_timesteps = 1000\n",
+        "\n",
+        "# Make a Gaussian HMM and sample data from it\n",
+        "hmm = GaussianHMM(num_states, emission_dim)\n",
+        "true_params, _ = hmm.initialize(key1)\n",
+        "true_states, emissions = hmm.sample(true_params, key2, num_timesteps)\n",
+        "\n",
+        "# Make a new Gaussian HMM and fit it with EM\n",
+        "params, props = hmm.initialize(key3, method=\"kmeans\", emissions=emissions)\n",
+        "params, lls = hmm.fit_em(params, props, emissions, num_iters=20)\n",
+        "\n",
+        "# Plot the marginal log probs across EM iterations\n",
+        "plt.plot(lls)\n",
+        "plt.xlabel(\"EM iterations\")\n",
+        "plt.ylabel(\"marginal log prob.\")\n",
+        "\n",
+        "# Use fitted model for posterior inference\n",
+        "post = hmm.smoother(params, emissions)\n",
+        "print(post.smoothed_probs.shape) # (1000, 3)"
+      ],
+      "metadata": {
+        "id": "CRtRwx4LD5oe"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "from functools import partial\n",
+        "from jax import vmap\n",
+        "\n",
+        "num_seq = 200\n",
+        "batch_true_states, batch_emissions = \\\n",
+        "    vmap(partial(hmm.sample, true_params, num_timesteps=num_timesteps))(\n",
+        "        jr.split(key2, num_seq))\n",
+        "print(batch_true_states.shape, batch_emissions.shape) # (200,1000) and (200,1000,2)\n",
+        "\n",
+        "# Make a new Gaussian HMM and fit it with EM\n",
+        "params, props = hmm.initialize(key3, method=\"kmeans\", emissions=batch_emissions)\n",
+        "params, lls = hmm.fit_em(params, props, batch_emissions, num_iters=20)"
+      ],
+      "metadata": {
+        "id": "IfgGkfmeFh8R"
+      },
+      "execution_count": null,
+      "outputs": []
+    }
+  ]
+}
\ No newline at end of file

From bfe681af8f6a4be7743159b0fcd37605da0357e0 Mon Sep 17 00:00:00 2001
From: evelynmitchell <efmphone@gmail.com>
Date: Thu, 25 Jan 2024 12:33:10 -0700
Subject: [PATCH 2/2] add link to colab notebook

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index b679bc40..0393ab0c 100644
--- a/README.md
+++ b/README.md
@@ -61,6 +61,10 @@ pytest dynamax/hmm/inference_test.py   # Run a specific test
 pytest -k lgssm                        # Run tests with lgssm in the name
 ```
 
+Run example in Colab: <a target="_blank" href="https://colab.research.google.com/github/evelynmitchell/dynamax/blob/master/DynamaxSSM.ipynb">
+<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
+</a>
+
 ## What are state space models?
 
 A state space model or SSM is a partially observed Markov model, in