.. image:: https://circleci.com/gh/AllenInstitute/deepinterpolation.svg?style=svg :target: https://circleci.com/gh/AllenInstitute/deepinterpolation
deepinterpolation is a Python library to denoise data by removing independent noise. Importantly training does NOT require ground truth. This repository is currently meant to support the publication : https://www.nature.com/articles/s41592-021-01285-2
.. image:: /docs/principle.png :alt: principle of deep interpolation :width: 700 px
Figure 1 - Schematic introducing the principles of deep interpolation. A. An interpolation model is trained to predict a noisy block from other blocks with independent noise. The loss is the difference between the predicted data and a new noisy block. B. The interpolation model is used to create a noiseless version of the input data.
For more information, consult the associated publication : https://www.nature.com/articles/s41592-021-01285-2
For bug and issues, please submit issue tickets on this repository. For installation and running support, we are trying to move to using the more public discussion forum on this repository (https://github.com/AllenInstitute/deepinterpolation/discussions). Alternatively you can join the slack channel where the past support history was saved (if invitation has expired: email to Jerome): https://join.slack.com/t/deepinterpolation/shared_invite/zt-rkmcw7h1-v8y0Grwe3fZg4m~DiAQVMg
In all cases, unless you only want to work from CPU, you will have to consider installing tensorflow GPU dependencies (ie. cuda drivers). To that end, you might have to consult tensorflow documentation to enable your GPU.
To install the package, you have 2 options.
Create new conda environment called 'local_env'
conda create -n local_env python=3.7Our integration tests on the CI server are currently running with python 3.7. While it is likely working with other versions, we cannot guarantee it.
pip install deepinterpolationThis will install the latest deployed stable version and only the core components of the library. You will NOT have access to sample datasets present on this repository.
This will give you access to the latest developments as well as the provided sample data. Our step by step example assume this installation mode as it depends on the sample datasets.
The small training examples below works on both CPU and GPU architecture (ie. even a small macbook). If you are not familiar with using deep learning, we recommend to play with smaller datasets first, such as the example Neuropixel data provided.
Clone the repository locally on a directory 'local_dir'
git clone https://github.com/AllenInstitute/deepinterpolation.git
Go to that directory
cd 'local_dir'
Create new conda environment called 'local_env'
conda create -n local_env python=3.7
Our integration tests on the CI server are currently running with python 3.7. While it is likely working with other versions, we cannot guarantee it.
activate environment
conda activate local_env
install necessary packages
make init
install deepinterpolation package
python setup.py install
The files in the deepinterpolation folder contain the core classes for training, inference, loss calculation and network generations. Those are called 'Collection'. Each collection is essentially a local list of functions that are used to create different type of objects and can be extended on one another. For instance, the network_collection.py contains a list of networks that can be generated for training. This allows for quick iteration and modification of an architecture while keeping the code organized.
See here : https://github.com/AllenInstitute/deepinterpolation/tree/master/faq
To try out training your own DeepInterpolation network, we recommend to start with this file: https://github.com/AllenInstitute/deepinterpolation/blob/master/examples/example_tiny_ephys_training.py
In this file, you will need to edit the paths to a local folder appropriate to save your models.
Then, activate your conda env called 'local_env'
conda activate local_envthen run
python example_tiny_ephys_training.pyIf everything runs correctly, you should see the following in just a few minutes :
2020-10-19 18:01:03.735098: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN)to use the following CPU instructions in performance-critical operations: AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
sh: sysctl: command not found
2020-10-19 18:01:03.749184: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7f9b1f115860 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2020-10-19 18:01:03.749202: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
WARNING:tensorflow:`period` argument is deprecated. Please use `save_freq` to specify the frequency in number of batches seen.
Epoch 1/5
10/10 [==============================] - 19s 2s/step - loss: 0.4597 - val_loss: 0.3987
Epoch 2/5
10/10 [==============================] - 20s 2s/step - loss: 0.3796 - val_loss: 0.3785
Epoch 3/5
10/10 [==============================] - 22s 2s/step - loss: 0.3646 - val_loss: 0.3709
Epoch 4/5
10/10 [==============================] - 21s 2s/step - loss: 0.3797 - val_loss: 0.3698
Epoch 5/5
10/10 [==============================] - 21s 2s/step - loss: 0.3835 - val_loss: 0.3675
Saved model to diskThis is a toy example but you can increase the number of training frames to increase the quality of the model. All parameters are commented in the file. To adjust to a larger dataset, change the path parameters, the start_frame and end_frame parameters. Please consult the annotated example for more details of each parameter.
Raw pre-trained models are available as separate h5 file to download.
The following models are currently available :
Two-photon Ai93 excitatory line DeepInterpolation network:
Key recording parameters:
Key recording parameters:
Neuropixel DeepInterpolation network:
Key recording parameters:
fMRI DeepInterpolation network:
Key recording parameters:
To start inference, we recommend to start with this file: https://github.com/AllenInstitute/deepinterpolation/blob/master/examples/example_tiny_ephys_inference.py
In this file, you will need to edit the paths strings to fit your local paths.
Then, activate your conda env called 'local_env'
conda activate local_envthen run:
python example_tiny_ephys_inference.pyIf everything runs correctly, you should see the following in just a few minutes:
2020-10-20 14:10:37.549061: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN)to use the following CPU instructions in performance-critical operations: AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
sh: sysctl: command not found
2020-10-20 14:10:37.564133: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7f82ada8a520 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2020-10-20 14:10:37.564156: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default VersionThis is a toy example but you can increase the start_frame and end_frame variable for larger data.
It is important to keep in mind that this process is easily parallelizable. In practice, we wrapped this code with additional routines to leverage 20 to 100 cluster CPU nodes to accelerate this process. You could also use GPU nodes as well, we just had access to a much larger number of CPU machines quickly.
To adapt DeepInterpolation to a new dataset, you will need to use or recreate a generator in 'generator_collection.py'. Those are all constructed from core classes called DeepGenerator and SequentialGenerator.
The CollectorGenerator class allows to group generators if your dataset is distributed across many files/folder/sources. This system was designed to allow to train very large DeepInterpolation models from TB of data distributed on a network infrastructure.
Allen Institute Software License – This software license is the 2-clause BSD license plus clause a third clause that prohibits redistribution and use for commercial purposes without further permission.
Copyright © 2019. Allen Institute. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
Redistributions and use for commercial purposes are not permitted without the Allen Institute’s written permission. For purposes of this license, commercial purposes are the incorporation of the Allen Institute's software into anything for which you will charge fees or other compensation or use of the software to perform a commercial service for a third party. Contact terms@alleninstitute.org for commercial licensing opportunities.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.