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README.md

AstroNet: A Neural Network for Identifying Exoplanets in Light Curves

Transit Animation

Code Author

Chris Shallue: @cshallue

Background

This directory contains TensorFlow models and data processing code for identifying exoplanets in astrophysical light curves. For complete background, see our paper in The Astronomical Journal.

For shorter summaries, see:

Citation

If you find this code useful, please cite our paper:

Shallue, C. J., & Vanderburg, A. (2018). Identifying Exoplanets with Deep Learning: A Five-planet Resonant Chain around Kepler-80 and an Eighth Planet around Kepler-90. The Astronomical Journal, 155(2), 94.

Full text available at The Astronomical Journal.

Walkthrough

Setup

First, ensure that you have installed the required packages and that the unit tests pass.

Next, use Bazel to create exectuable Python scripts. (Alternatively, since all code is pure Python and does not need to be compiled, we could instead add the exoplanet-ml directory to PYTHONPATH.)

cd exoplanet-ml  # Bazel must run from a directory with a WORKSPACE file
bazel build astronet/...

Kepler Data and TCEs

A light curve is a plot of the brightness of a star over time. We will be focusing on light curves produced by the Kepler space telescope, which monitored the brightness of 200,000 stars in our milky way galaxy for 4 years. One of the light curves produced by Kepler is shown below.

Kepler-934

To train a model to identify planets in Kepler light curves, we will need a training set of labeled Threshold Crossing Events (TCEs). A TCE is a periodic signal that has been detected in a Kepler light curve, and is associated with a period (the number of days between each occurrence of the detected signal), a duration (the time elapsed by each occurrence of the signal), an epoch (the time of the first observed occurrence of the signal), and possibly additional metadata like the signal-to-noise ratio. A TCE that was detected in our example light curve is shown with red arrows in the image below.

Kepler-934 Transits

We will train our model to classify whether a given TCE is an actual planet signal or whether it was caused by some other phenomenon (e.g. a binary star). We will train and evaluate our model using the TCEs from the DR24 TCE table that have been assigned ground truth labels by humans.

Shortcut: Download a Pre-Computed Training Set

A pre-computed training set (along with held-out evaluation and test sets) is available for download at the following URL: https://drive.google.com/drive/folders/1Gw-o7sgWC1Y_mlaehN85qH5XC161EHSE?usp=sharing

If you like, you can read through the following sections to understand how the training set was created. Otherwise, you can jump directly to Train an AstroNet Model.

Download the Kepler Data

To create our training set, the first step is to download the list of labeled TCEs that will comprise the training set. You can download the DR24 TCE Table in CSV format from the NASA Exoplanet Archive. Ensure the following columns are selected:

  • rowid: Integer ID of the row in the TCE table.
  • kepid: Kepler ID of the target star.
  • tce_plnt_num: TCE number within the target star.
  • tce_period: Period of the detected event, in days.
  • tce_time0bk: The time corresponding to the center of the first detected event in Barycentric Julian Day (BJD) minus a constant offset of 2,454,833.0 days.
  • tce_duration: Duration of the detected event, in hours.
  • av_training_set: Autovetter training set label; one of PC (planet candidate), AFP (astrophysical false positive), NTP (non-transiting phenomenon), UNK (unknown).

Next, you will need to download the light curves of the stars corresponding to the TCEs in the training set. These are available at the Mikulski Archive for Space Telescopes. However, you almost certainly don't want all of the Kepler data, which consists of almost 3 million files, takes up over a terabyte of space, and may take several weeks to download! To train our model, we only need to download the subset of light curves that are associated with TCEs in the DR24 file. To download just those light curves, follow these steps:

NOTE: Even though we are only downloading a subset of the entire Kepler dataset, the files downloaded by the following script take up about 90 GB.

# Filename containing the CSV file of TCEs in the training set.
TCE_CSV_FILE="${HOME}/astronet/dr24_tce.csv"

# Directory to download Kepler light curves into.
KEPLER_DATA_DIR="${HOME}/astronet/kepler/"

# Generate a bash script that downloads the Kepler light curves in the training set.
python astronet/data/generate_download_script.py \
  --kepler_csv_file=${TCE_CSV_FILE} \
  --download_dir=${KEPLER_DATA_DIR}

# Run the download script to download Kepler light curves.
./get_kepler.sh

The final line should read: Finished downloading 12669 Kepler targets to ${KEPLER_DATA_DIR}

Let's explore the downloaded light curve of the Kepler-90 star! Note that Kepler light curves are divided into four quarters each year, which are separated by the quarterly rolls that the spacecraft made to reorient its solar panels. In the downloaded light curves, each .fits file corresponds to a specific Kepler quarter, but some quarters are divided into multiple .fits files.

# Launch iPython (or Python) from the exoplanet-ml directory.
ipython

In[1]:
from light_curve import kepler_io
import matplotlib.pyplot as plt
import numpy as np

In[2]:
KEPLER_DATA_DIR = "/path/to/kepler/"
KEPLER_ID = 11442793  # Kepler-90.

In[3]:
# Read the light curve.
file_names = kepler_io.kepler_filenames(KEPLER_DATA_DIR, KEPLER_ID)
assert file_names, "Failed to find .fits files in {}".format(KEPLER_DATA_DIR)
all_time, all_flux = kepler_io.read_kepler_light_curve(file_names)
print("Read light curve with {} segments".format(len(all_time)))

In[4]:
# Plot the fourth segment.
plt.plot(all_time[3], all_flux[3], ".")
plt.show()

In[5]:
# Plot all light curve segments. We first divide by the median flux in each
# segment, because the segments are on different scales.
for f in all_flux:
  f /= np.median(f)
plt.plot(np.concatenate(all_time), np.concatenate(all_flux), ".")
plt.show()

The output plots should look something like this:

Kepler 90 Q4

Kepler 90 All

The first plot is a single segment of approximately 20 days. You can see a planet transit --- that's Kepler-90 g! Also, notice that the brightness of the star is not flat over time --- there is natural variation in the brightness, even away from the planet transit.

The second plot is the full light curve over the entire Kepler mission (aproximately 4 years). You can easily see two transiting planets by eye --- they are Kepler-90 h (the biggest known planet in the system with the deepest transits) and Kepler-90 g (the second biggest known planet in the system with the second deepest transits).

Process Kepler Data

To train a model to identify exoplanets, we will need to provide TensorFlow with training data in TFRecord format. The TFRecord format consists of a set of sharded files containing serialized tf.Example protocol buffers.

The command below will generate a set of sharded TFRecord files for the TCEs in the training set. Each tf.Example proto will contain the following light curve representations:

  • global_view: Vector of length 2001: a "global view" of the TCE.
  • local_view: Vector of length 201: a "local view" of the TCE.

In addition, each tf.Example will contain the value of each column in the input TCE CSV file. The columns include:

  • rowid: Integer ID of the row in the TCE table.
  • kepid: Kepler ID of the target star.
  • tce_plnt_num: TCE number within the target star.
  • av_training_set: Autovetter training set label.
  • tce_period: Period of the detected event, in days.
# Directory to save output TFRecord files into.
TFRECORD_DIR="${HOME}/astronet/tfrecord"

# Preprocess light curves into sharded TFRecord files using 5 worker processes.
bazel-bin/astronet/data/generate_input_records \
  --input_tce_csv_file=${TCE_CSV_FILE} \
  --kepler_data_dir=${KEPLER_DATA_DIR} \
  --output_dir=${TFRECORD_DIR} \
  --num_worker_processes=5

When the script finishes you will find 8 training files, 1 validation file and 1 test file in TFRECORD_DIR. The files will match the patterns train-0000?-of-00008, val-00000-of-00001 and test-00000-of-00001 respectively.

Here's a quick description of what the script does. For a full description, see Section 3 of our paper.

For each light curve, we first fit a normalization spline to remove any low-frequency variability (that is, the natural variability in light from star) without removing any deviations caused by planets or other objects. For example, the following image shows the normalization spline for the segment of Kepler-90 that we considered above:

Kepler 90 Q4 Spline

Next, we divide by the spline to make the star's baseline brightness approximately flat. Notice that after normalization the transit of Kepler-90 g is still preserved:

Kepler 90 Q4 Normalized

Finally, for each TCE in the input CSV table, we generate two representations of the light curve of that star. Both representations are phase-folded, which means that we combine all periods of the detected TCE into a single curve, with the detected event centered.

Let's explore the generated representations of Kepler-90 g in the output.

# Launch iPython (or Python) from the exoplanet-ml directory.
ipython

In[1]:
import matplotlib.pyplot as plt
import numpy as np
import os.path
import tensorflow as tf

In[2]:
KEPLER_ID = 11442793  # Kepler-90
TFRECORD_DIR = "/path/to/tfrecords/dir"

In[3]:
# Helper function to find the tf.Example corresponding to a particular TCE.
def find_tce(kepid, tce_plnt_num, filenames):
  for filename in filenames:
    for record in tf.python_io.tf_record_iterator(filename):
      ex = tf.train.Example.FromString(record)
      if (ex.features.feature["kepid"].int64_list.value[0] == kepid and
          ex.features.feature["tce_plnt_num"].int64_list.value[0] == tce_plnt_num):
        print("Found {}_{} in file {}".format(kepid, tce_plnt_num, filename))
        return ex
  raise ValueError("{}_{} not found in files: {}".format(kepid, tce_plnt_num, filenames))

In[4]:
# Find Kepler-90 g.
filenames = tf.gfile.Glob(os.path.join(TFRECORD_DIR, "*"))
assert filenames, "No files found in {}".format(TFRECORD_DIR)
ex = find_tce(KEPLER_ID, 1, filenames)

In[5]:
# Plot the global and local views.
global_view = np.array(ex.features.feature["global_view"].float_list.value)
local_view = np.array(ex.features.feature["local_view"].float_list.value)
fig, axes = plt.subplots(1, 2, figsize=(20, 6))
axes[0].plot(global_view, ".")
axes[1].plot(local_view, ".")
plt.show()

The output should look something like this:

Kepler 90 g Processed

Train an AstroNet Model

This repository contains several choices of neural network architecture and various configuration options. To train a convolutional neural network to classify Kepler TCEs as either "planet" or "not planet", using the best configuration from our paper, run the following training script:

# Directory to save model checkpoints into.
MODEL_DIR="${HOME}/astronet/model/"

# Run the training script.
bazel-bin/astronet/train \
  --model=AstroCNNModel \
  --config_name=local_global \
  --train_files=${TFRECORD_DIR}/train* \
  --eval_files=${TFRECORD_DIR}/val* \
  --model_dir=${MODEL_DIR}

Optionally, you can also run a TensorBoard server in a separate process for real-time monitoring of training progress and evaluation metrics.

# Launch TensorBoard server.
tensorboard --logdir ${MODEL_DIR}

The TensorBoard server will show a page like this:

TensorBoard

Evaluate an AstroNet Model

Run the following command to evaluate a model on the test set. The result will be printed on the screen, and a summary file will also be written to the model directory, which will be visible in TensorBoard.

# Run the evaluation script.
bazel-bin/astronet/evaluate \
  --model=AstroCNNModel \
  --config_name=local_global \
  --eval_files=${TFRECORD_DIR}/test* \
  --model_dir=${MODEL_DIR}

The output should look something like this:

INFO:tensorflow:Saving dict for global step 10000: accuracy/accuracy = 0.9625159, accuracy/num_correct = 1515.0, auc = 0.988882, confusion_matrix/false_negatives = 10.0, confusion_matrix/false_positives = 49.0, confusion_matrix/true_negatives = 1165.0, confusion_matrix/true_positives = 350.0, global_step = 10000, loss = 0.112445444, losses/weighted_cross_entropy = 0.11295206, num_examples = 1574.

Make Predictions

Suppose you detect a weak TCE in the light curve of the Kepler-90 star, with period 14.44912 days, duration 2.70408 hours (0.11267 days) beginning 2.2 days after 12:00 on 1/1/2009 (the year the Kepler telescope launched). To run this TCE though your trained model, execute the following command:

# If you skipped the step of downloading the Kepler data, you will first need
# to download the light curve for Kepler-90 (~5.7MB):
KEPLER_DATA_DIR="${HOME}/astronet/kepler/"
wget -nH --cut-dirs=6 -r -l0 -c -N -np -erobots=off -R 'index*' -A _llc.fits \
  -P ${KEPLER_DATA_DIR}/0114/011442793 \
  http://archive.stsci.edu/pub/kepler/lightcurves/0114/011442793/

# Generate a prediction for a new TCE.
bazel-bin/astronet/predict \
  --model=AstroCNNModel \
  --config_name=local_global \
  --model_dir=${MODEL_DIR} \
  --kepler_data_dir=${KEPLER_DATA_DIR} \
  --kepler_id=11442793 \
  --period=14.44912 \
  --t0=2.2 \
  --duration=0.11267 \
  --output_image_file="${HOME}/astronet/kepler-90i.png"

The output should look like this:

Prediction: 0.9480018

This means the model is about 95% confident that the input TCE is a planet. Of course, this is only a small step in the overall process of discovering and validating an exoplanet: the model’s prediction is not proof one way or the other. The process of validating this signal as a real exoplanet requires significant follow-up work by an expert astronomer --- see Sections 6.3 and 6.4 of our paper for the full details. In this particular case, our follow-up analysis validated this signal as a bona fide exoplanet: it’s now called Kepler-90 i, and is the record-breaking eighth planet discovered around the Kepler-90 star!

In addition to the output prediction, the script will also produce a plot of the input representations. For Kepler-90 i, the plot should look something like this:

Kepler 90 h Processed