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nMOR
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README.md

README.md

nMOR: neural Model Order Reduction

Deep learning framework for model reduction of dynamial systems

Authors: Francisco J. Gonzalez

This code was primarily developed for the paper Deep convolutional recurrent autoencoders for learning low-dimensional feature dynamics of fluid systems.


Figure 1. Learning low-dimensional dynamics - this animation depicts the process of learning the dynamics of two vortices governed by the Navier-Stokes equations using nMOR.

Introduction

nMOR (neural Model Order Reduction) is a deep convolutional recurrent autoencoder architecture for completely data-driven model reduction of high-dimensional dynamical systems. At the heart of this approach is a modular architecture consisting of a convolutional autoencoder (or encoder-decoder network) and a evolver RNN (constructed using a modified version of an LSTM), depicted in Figures 2 and 3.

Convolutional Autoencoder


Figure 2. Convolutional Autoencoder - this architecture is used to learn an efficient low-dimensional representation of the physical data.

The main idea behind using a convolutional autoencoder method is that it exploits local, location-invariant correlations present in physical data through the use of convolutional neural networks. That is, rather than of applying a fully-connected autoencoder to the high-dimensional input data we instead apply it to a vectorized feature map produced by a convolutional encoder, and similarly the reverse is done for reconstruction. The result is the identification of an expressive low-dimensional manifold obtained at a much lower cost while offering specific advantages over both traditional POD-based ROMs and fully-connected autoencoders

Evolver RNN


Figure 3. Modified LSTM network - this RNN architecture is used to learn the dynamics of low-dimensional representation on its underlying nonlinear manifold.

We propose a modified LSTM network to model the evolution of low-dimensional data representations on this manifold that avoids costly state reconstructions at every step. In doing this, we ensure that the evaluation of new steps scales only with the size of the low-dimensional representation and not with the size of the full dimensional data, which may be large for some problems.

Installing nMOR

To install this code first make sure you have TensorFlow (>= v1.3) installed on your system. To install TensorFlow visit the installation instructions here.

Once you have TensorFlow installed, you can download the source code by running:

git clone https://github.com/franjgonzalez/nMOR

Training - How to build an nMOR model

Dataset Construction

By default, this code assumes that the data is in some specific format. Since this approach is targeting computational modeling applications having structured data on which to train the nMOR model requires only some light preprocessing.

Ultimately, you should have a dataset $\mathcal{X}$ which has the following form

$$ \mathcal{X} = { \mathbf{X}^1, \mathbf{X}^2, ..., \mathbf{X}^{N_s} }\in[0,1]^{N_x\times N_y\times N_t\times N_s} $$

where each $\mathbf{X}^i=[\mathbf{x}_i^1,...,\mathbf{x}_i^{N_t}]$ is a training sample consisting of a $N_t$ solution snapshots $\mathbf{x}_i^n\in[0,1]^{N_x\times N_y}$. In this case $N_s$ represents the number of training samples. It is recommended that the each solution snapshot is defiend on a uniform grid as this allows each convolutional filter to act equally over the entire domain. By default, this code reads datasets saved using the h5py library under the dataset name dataset. It is then read by

with h5py.File("datafile.h5", "r") as hf:
    dataset = hf["dataset"][:]

Typically, a dataset is split into a training set which is used to make parameter updates, and a validation set which does not make parameter updates. The performance of the model on the validation set can be used to tune hyper-parameters or prevent overfitting. In addition this code assumes the existance of a inference set: a dataset consisting of a training sample and a validation sample. This can be used for futher analysis on the training progress.

Offline Training

For each model you will need to pre-define some environment variables

# nMOR package directory and base directory
nMOR_DIR=${HOME}/nMOR
BASE_DIR=`pwd`

# Model and data directories from args
OUTPUT_DIR=${BASE_DIR}
DATA_DIR=${HOME}/path/to/the/data
NUM_UNITS=16
NUM_STEPS=100000

# Train and test datasets to use
TRAIN_DATA_DIR=${DATA_DIR}/trainset.h5
TEST_DATA_DIR=${DATA_DIR}/testset.h5
INFER_DATA_DIR=${DATA_DIR}/inferset.h5

To start training run the following command:

python3 -m nMOR.nMOR \
    --num_units=${NUM_UNITS} \
    --time_major=True \
    --optimizer=adam \
    --learning_rate=0.0005 \
    --num_steps=${NUM_STEPS} \
    --out_dir=${OUTPUT_DIR} \
    --data_file=${TRAIN_DATA_DIR} \
    --dev_data_file=${TEST_DATA_DIR} \
    --sample_infer_data_file=${INFER_DATA_DIR} \
    --data_size 64 64 \
    --batch_size=32 \
    --dropout=0.01 \
    --init_weight=0.5 \
    --steps_per_stats=10 \
    --num_gpus=1 \
    --steps_per_eval=800

If the setup was done correctly you should eventually see an output that looks like this

# First eval, global_step 0 dev loss 5.02981
# Start step 0, lr 0.0005, Sat May 26 09:48:39 2018
# Init train iterator.
# Training for 600000 steps
  step 10 lr 0.0005 step-time 0.44s loss 5.00348 gN 8.99 , Sat May 26 09:48:46 2018
  step 20 lr 0.0005 step-time 0.28s loss 4.90889 gN 8.87 , Sat May 26 09:48:48 2018
  step 30 lr 0.0005 step-time 0.28s loss 4.84085 gN 8.80 , Sat May 26 09:48:51 2018
  step 40 lr 0.0005 step-time 0.28s loss 4.77679 gN 8.74 , Sat May 26 09:48:54 2018
  step 50 lr 0.0005 step-time 0.28s loss 4.70085 gN 8.65 , Sat May 26 09:48:57 2018
  step 60 lr 0.0005 step-time 0.28s loss 4.62944 gN 8.57 , Sat May 26 09:49:00 2018

Online Evaluation

To evaluate a trained model, first define the following environment variables:

# Number of time steps to run evaluation
NUM_INFER_STEPS=2500

# Desired checkpoint on which to evaluate model
CKPT=100000

# Checkpoint directory
CKPT_DIR=/path/to/checkpoint/directory/ckpt/nMOR_model.ckpt-${CKPT}

# Dataset to perform inference on and output directory
INFER_DATA_DIR=${DATA_DIR}/infer_ic.h5
INFER_OUTPUT=${CASE_DIR}/infer_h-${NUM_UNITS}_ckpt-${CKPT}_s_${NUM_INFER_STEPS}.h5

To evaluate run the following command:

python3 -m nMOR.nMOR \
    --num_units=${NUM_UNITS} \
    --num_infer_steps=${NUM_INFER_STEPS} \
    --time_major=True \
    --optimizer=adam \
    --out_dir=${OUTPUT_DIR} \
    --infer_data_file=${INFER_DATA_DIR} \
    --infer_output_file=${INFER_OUTPUT} \
    --data_size 64 64 \
    --batch_size=1 \
    --num_gpus=0 \
    --ckpt=${CKPT_DIR}

BibTex

@article{gonzalez18,
  author = {Francisco J. Gonzalez and Maciej Balajewicz},
  title = {Deep convolutional recurrent autoencoders for learning low-dimensional feature dynamics of fluid systems},
  archivePrefix = {arXiv},
  arxivId = {1808.01346}
}