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https://github.com/aehrc/genomator

Privacy-hardened, hallucination-resistant synthetic data generator.

https://github.com/aehrc/genomator

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 2 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Privacy-hardened, hallucination-resistant synthetic data generator.

Basic Info
  • Host: GitHub
  • Owner: aehrc
  • Language: Python
  • Default Branch: main
  • Size: 20.8 MB
Statistics
  • Stars: 1
  • Watchers: 8
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed 11 months ago
Metadata Files
Readme

README.md

Genomator

This is the repository accompanying the publication of the Genomator paper, in this repository there is the software and experimental procedures that should reproduce the results featured in that paper.

Directories

A breakdown of these directories is given below:

/Genomator

The core software for the Genomator tool itself, which is to be installed in an appropriate python environment for execution on any data source (in VCF) to generate new synthetic data (see included details and documentation) READMEs and documentation for the tool and its install and use are provided therein.

/experiment

Python scripts and tools to reproduce the results of the paper, the tools need to be installed into an appropriate python environment. All data used in the experiments are from the 65K dataset used by Yelman et al. downloaded from URL (https://gitlab.inria.fr/mlgenetics/public/artificialgenomes/-/tree/master/1000Grealgenomes) and all preprocessing is conducted by scripts in /experiment/experiment/source_gen.py and subsequently ingested by experiment code.

/tinicard

A cardinality SAT solver and python wrapper built, which is compatible with Genomator.

Licensing

  • The main codebase (in /genomator) is licensed under the CSIRO Non-Commercial License (based on BSD 3-Clause Clear).
  • The optional module in /tinicard is based on a GPLv2+ codebase and is therefore licensed under the GNU GPLv2+.
  • The optional module is not required for basic functionality.

Also IMPORTANT note: the optional /tinicard module is not required for the main codebase to be operational, as it is a separate SAT solving software with a python wrapper to provide an API for interfacing with various python scripts. The main codebase will only attempt to import and use the API functions associated with this SAT solver if command line parameter --solver_name=tinicard is specified, and if not, will default to using the Minicard SAT solver through the PySAT python library.

Owner

  • Name: The Australian e-Health Research Centre
  • Login: aehrc
  • Kind: organization

The Australian e-Health Research Centre (AEHRC) is CSIRO’s digital health research program.

GitHub Events

Total
  • Push event: 41
  • Create event: 1
Last Year
  • Push event: 41
  • Create event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 57
  • Total Committers: 2
  • Avg Commits per committer: 28.5
  • Development Distribution Score (DDS): 0.018
Past Year
  • Commits: 39
  • Committers: 2
  • Avg Commits per committer: 19.5
  • Development Distribution Score (DDS): 0.026
Top Committers
Name Email Commits
Burgess, Mark (H&B, Black Mountain) M****s@c****u 56
Brendan Hosking b****g@c****u 1
Committer Domains (Top 20 + Academic)
csiro.au: 2

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Dependencies

experiment_tools/requirements.txt pypi
  • Jinja2 ==3.1.3
  • Markdown ==3.5.2
  • MarkupSafe ==2.1.5
  • POT ==0.9.3
  • PyYAML ==6.0.1
  • Pygments ==2.17.2
  • Werkzeug ==3.0.1
  • absl-py ==2.1.0
  • apricot-select ==0.6.1
  • asciitree ==0.3.3
  • astunparse ==1.6.3
  • certifi ==2024.2.2
  • charset-normalizer ==3.3.2
  • click ==8.1.7
  • cloudpickle ==3.0.0
  • coloredlogs ==15.0.1
  • contourpy ==1.2.0
  • cycler ==0.12.1
  • cyvcf2 ==0.30.28
  • dask ==2024.3.0
  • dm-tree ==0.1.8
  • fasteners ==0.19
  • filelock ==3.13.1
  • flatbuffers ==24.3.7
  • fonttools ==4.49.0
  • fsspec ==2024.2.0
  • gast ==0.5.4
  • google-pasta ==0.2.0
  • grpcio ==1.62.1
  • h5py ==3.10.0
  • hmmlearn ==0.3.2
  • humanfriendly ==10.0
  • idna ==3.6
  • importlib_metadata ==7.0.2
  • joblib ==1.3.2
  • keras ==3.0.5
  • kiwisolver ==1.4.5
  • libclang ==16.0.6
  • llvmlite ==0.42.0
  • locket ==1.0.0
  • markdown-it-py ==3.0.0
  • matplotlib ==3.8.3
  • mdurl ==0.1.2
  • ml-dtypes ==0.3.2
  • mpmath ==1.3.0
  • namex ==0.0.7
  • networkx ==3.2.1
  • nose ==1.3.7
  • numba ==0.59.0
  • numcodecs ==0.12.1
  • numexpr ==2.9.0
  • numpy ==1.26.4
  • nvidia-cublas-cu12 ==12.1.3.1
  • nvidia-cuda-cupti-cu12 ==12.1.105
  • nvidia-cuda-nvrtc-cu12 ==12.1.105
  • nvidia-cuda-runtime-cu12 ==12.1.105
  • nvidia-cudnn-cu12 ==8.9.2.26
  • nvidia-cufft-cu12 ==11.0.2.54
  • nvidia-curand-cu12 ==10.3.2.106
  • nvidia-cusolver-cu12 ==11.4.5.107
  • nvidia-cusparse-cu12 ==12.1.0.106
  • nvidia-nccl-cu12 ==2.19.3
  • nvidia-nvjitlink-cu12 ==12.4.99
  • nvidia-nvtx-cu12 ==12.1.105
  • opt-einsum ==3.3.0
  • packaging ==24.0
  • pandas ==2.2.1
  • partd ==1.4.1
  • pillow ==10.2.0
  • pomegranate ==1.0.4
  • protobuf ==4.25.3
  • pyparsing ==3.1.2
  • pysam ==0.22.0
  • python-dateutil ==2.9.0.post0
  • pytz ==2024.1
  • requests ==2.31.0
  • resample ==1.7.1
  • rich ==13.7.1
  • scikit-allel ==1.3.7
  • scikit-learn ==1.4.1.post1
  • scipy ==1.12.0
  • seaborn ==0.13.2
  • six ==1.16.0
  • sympy ==1.12
  • tensorboard ==2.16.2
  • tensorboard-data-server ==0.7.2
  • tensorflow ==2.16.1
  • tensorflow-io-gcs-filesystem ==0.36.0
  • termcolor ==2.4.0
  • threadpoolctl ==3.3.0
  • toolz ==0.12.1
  • torch ==2.2.1
  • tqdm ==4.66.2
  • triton ==2.2.0
  • typing_extensions ==4.10.0
  • tzdata ==2024.1
  • urllib3 ==2.2.1
  • vcfpy ==0.13.8
  • wrapt ==1.16.0
  • zarr ==2.17.1
  • zipp ==3.18.0
experiment_tools/setup.py pypi