multi-animal-alignment
2021-2023 project on similarity of neural dynamics across monkeys and mice
Science Score: 54.0%
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○Scientific vocabulary similarity
Low similarity (12.7%) to scientific vocabulary
Repository
2021-2023 project on similarity of neural dynamics across monkeys and mice
Basic Info
- Host: GitHub
- Owner: AtMostafa
- License: mit
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://www.nature.com/articles/s41586-023-06714-0
- Size: 417 MB
Statistics
- Stars: 2
- Watchers: 2
- Forks: 7
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
Preserved neural dynamics across animals performing similar behaviour
By: Mostafa Safaie*, Joanna C. Chang*, Junchol Park, Lee E. Miller, Joshua T. Dudman, Matthew G. Perich and Juan A. Gallego.
This repository includes code to reproduce the figures in Safaie & Chang et. al., Nature, 2023.
Getting Started
Create a conda environment with conda env create -f env.yml and activate the environment with conda activate cca.
Note that a version of MATLAB is needed for matlabengine, which is used for Fig S2. Comment out the matlabengine line if you do not have MATLAB installed. Otherwise, change the version of matlabengine according to the MATLAB version you have installed.
Reproducing Figures
Each figure in the paper has an associated Jupyter notebook under /paper. Running the cells reproduces all of the panels.
For the RNN simulations associated with Figure 5 and Figure S10, first run the simulations:
bash
cd rnn && bash rnn.sh
System Requirements
The code has been tested on Linux (Ubuntu >18.04).
Data Availability
After the publication of the paper, all the monkey datasets used in this work (and more) were deposited in this DANDI repository, in the NWB format. Following an easy format conversion (e.g., see here), it will be easy to reproduce the analyses on the monkey datasets. Furthermore, the datasets of the example sessions used throughout the manuscript are deposited here and can be used to reproduce some panels and to provide a template for the format conversion. The mouse datasets will be made available on reasonable request.
License
MIT.
Code Credit
Code from the following sources have been copied and used here under /packages or /tools with slight modifications:
- config_manager from Sebastian Lee
- pyaldata from Neural Analysis
- dPCA from machenslab
- TME from Gamaleldin Elsayed
Associated publications are referenced in the paper.
Questions
Questions can be directed to the corresponding authors, as issues on this repository, or to Mostafa or Joanna.
Funders
This work was supported in part by: - grant number H2020-MSCA-IF-2020-101025630 from the Commission of the European Union (M.S.) - grant number 108908/Z/15/Z from the Wellcome Trust (J.C.C.) - grant numbers NS053603 and NS074044 from the NIH National Institute of Neurological Disorders and Stroke (L.E.M.) - grant chercheurs-boursiers en intelligence artificielle from the Fonds de recherche du Quebec Santé (M.G.P.) - grant number EP/T020970/1 from the UKRI Engineering and Physical Sciences Research Council (J.A.G.) - grant number ERC-2020-StG-949660 from the European Research Council (J.A.G.).
Owner
- Name: Mostafa Safaie
- Login: AtMostafa
- Kind: user
- Location: London, UK
- Company: Imperial College London
- Twitter: TweetAtMostafa
- Repositories: 6
- Profile: https://github.com/AtMostafa
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit !
cff-version: 1.2.0
title: >-
Preserved neural dynamics across animals performing similar behaviour
message: >-
If you use this software, please cite the paper.
authors:
- given-names: Mostafa
family-names: Safaie
email: mostafa.safaie@gmail.com
affiliation: Imperial College London
orcid: 'https://orcid.org/0000-0002-6384-8629'
- given-names: Joanna
name-particle: C
family-names: Chang
email: joanna.changc@gmail.com
affiliation: Imperial College London
identifiers:
- type: doi
value: 10.1038/s41586-023-06714-0
- type: url
value: 'https://www.nature.com/articles/s41586-023-06714-0'
repository-code: 'https://github.com/BeNeuroLab/2022-preserved-dynamics'
repository: 'https://github.com/AtMostafa/multi-animal-alignment'
abstract: >-
Animals of the same species exhibit similar behaviours
that are advantageously adapted to their body and
environment. These behaviours are shaped at the species
level by selection pressures over evolutionary timescales.
Yet, it remains unclear how these common behavioural
adaptations emerge from the idiosyncratic neural circuitry
of each individual. The overall organization of neural
circuits is preserved across individuals because of their
common evolutionarily specified developmental programme.
Such organization at the circuit level may constrain
neural activity, leading to low-dimensional latent
dynamics across the neural population. Accordingly, here
we suggested that the shared circuit-level constraints
within a species would lead to suitably preserved latent
dynamics across individuals. We analysed recordings of
neural populations from monkey and mouse motor cortex to
demonstrate that neural dynamics in individuals from the
same species are surprisingly preserved when they perform
similar behaviour. Neural population dynamics were also
preserved when animals consciously planned future
movements without overt behaviour and enabled the decoding
of planned and ongoing movement across different
individuals. Furthermore, we found that preserved neural
dynamics extend beyond cortical regions to the dorsal
striatum, an evolutionarily older structure. Finally, we
used neural network models to demonstrate that behavioural
similarity is necessary but not sufficient for this
preservation. We posit that these emergent dynamics result
from evolutionary constraints on brain development and
thus reflect fundamental properties of the neural basis of
behaviour.
license: MIT
preferred-citation:
type: article
authors:
- given-names: Mostafa
family-names: Safaie
email: mostafa.safaie@gmail.com
affiliation: Imperial College London
orcid: 'https://orcid.org/0000-0002-6384-8629'
- given-names: Joanna
family-names: Chang
- given-names: Junchol
family-names: Park
- given-names: Lee
family-names: Miller
- given-names: Joshua
family-names: Dudman
- given-names: Matthew
family-names: Perich
- given-names: Juan
family-names: Gallego
doi: "10.1038/s41586-023-06714-0"
journal: "Nature"
month: 11
start: 765 # First page number
end: 771 # Last page number
title: "Preserved neural dynamics across animals performing similar behaviour"
issue: 623
year: 2023
GitHub Events
Total
- Delete event: 2
- Push event: 9
- Pull request event: 2
- Fork event: 1
- Create event: 1
Last Year
- Delete event: 2
- Push event: 9
- Pull request event: 2
- Fork event: 1
- Create event: 1
Dependencies
- pyyaml *
- numpy *
- pandas >=1.2.0
- scikit-learn *
- scipy >=1.5