https://github.com/kundajelab/locusselect
extraction of data embeddings from deep learning model layers; computation of embedding distance and visualization with umap/tsne
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
3 of 6 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (1.6%) to scientific vocabulary
Keywords from Contributors
deeplift
guided-backpropagation
integrated-gradients
interpretability
interpretable-deep-learning
saliency-map
sensitivity-analysis
Last synced: 6 months ago
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Repository
extraction of data embeddings from deep learning model layers; computation of embedding distance and visualization with umap/tsne
Basic Info
- Host: GitHub
- Owner: kundajelab
- Language: Jupyter Notebook
- Default Branch: master
- Size: 48.8 MB
Statistics
- Stars: 2
- Watchers: 5
- Forks: 1
- Open Issues: 0
- Releases: 0
Created almost 7 years ago
· Last pushed over 5 years ago
https://github.com/kundajelab/locusselect/blob/master/
# locusselect
* extraction of data embeddings from deep learning model layers;
* computation of embedding distance for inputs;
* clustering and visualization of embeddings with umap/tsne
See examples/example.sh for usage examples.
```
compute_embeddings \
--input_bed_file optimal_peak.narrowPeak.gz \
--weights 13kb_context_3b_prediction_dnase.hdf5 \
--json k562_dnase_profile_arch.json \
--ref_fasta /mnt/data/annotations/by_release/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta \
--center_on_summit \
--flank 6500 \
--output_npz_file k562_dnase_profile_embeddings_layer_-2.npz \
--embedding_layer -2 \
--threads 40
```
Owner
- Name: Kundaje Lab
- Login: kundajelab
- Kind: organization
- Location: Stanford University
- Website: http://anshul.kundaje.net
- Repositories: 117
- Profile: https://github.com/kundajelab
Compbio and machine learning code repositories from the Kundaje Lab at Stanford Genetics and Computer Science Depts.
GitHub Events
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Last Year
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| anna shcherbina | a****a@g****m | 42 |
| Av Shrikumar | a****r@g****m | 22 |
| mhfzsharmin | m****n@u****u | 5 |
| soumyakundu | s****u@s****u | 3 |
| annashcherbina | a****h@s****u | 1 |
| mhfzsharmin | m****n@g****m | 1 |
Committer Domains (Top 20 + Academic)
stanford.edu: 2
umiacs.umd.edu: 1
Packages
- Total packages: 1
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Total downloads:
- pypi 11 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 3
- Total maintainers: 1
pypi.org: locusselect
Compute deep learning embeddings for narrowPeak files; compute pairwise distance between embeddings and cluster with tSNE
- Documentation: https://locusselect.readthedocs.io/
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Latest release: 0.3
published almost 7 years ago
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Average: 31.6%
Downloads: 63.1%
Maintainers (1)
Last synced:
7 months ago