DITTO using Neural Networks and SHAP #21

tkmamidi · 2024-01-06T07:44:34Z

This PR includes enhancements to the repo for interpreting genetic variants from using traditional ML models to explainable Neural Networks. This branch includes the setup for local usage with installation details and the web application version of DITTO.

Here are the tasks you need to review:

Usage:

Review the readME:
- Assess the resource requirements (CPU, storage, RAM) for typical use cases.
Webapp:
- Confirm the webapp is accessible and functional at the provided link.
Local Setup:
- Assess the resource requirements (CPU, storage, RAM) for typical use cases.
OpenCravat Setup:
- Review the install_openCravat.md document for clarity and completeness.
Reproducibility:
- Review the build_DITTO.md document for clarity and completeness.

This PR should close #8 #10 #20 .

…iles

.gz files

…into training

README.md

docs/build_DITTO.md

README.md

.test_data/file_list_partaa

README.md

ManavalanG

Good job, Tarun! Back at your court.

CHANGELOG.md

README.md

docs/build_DITTO.md

src/analysis/filter.sh

README.md

docs/build_DITTO.md

adding whitespace Co-authored-by: Manavalan Gajapathy <[email protected]>

tkmamidi added 30 commits April 26, 2023 16:33

first pass

b858e1b

until dbnsp

822e9f0

training config ready

dcbca0b

fixing clinvar config to get ID

b83a2c4

update col_config and python notebook for generating train and test f…

3039724

…iles

training models

0abd693

fixing wierd instance with fatHMM values in parsing

658279e

changing NN script to use argparse instead of hardcoded file paths

937f1fa

adding DExTR to parsing stuff

442a3ab

adding DExTR file

9f34f68

parser can read and write

698dfe8

.gz files

fixing duplicate columns in config

b7955a1

adjusting clinvar review column values

a2f9cd4

removing mitomap as there were no scores for training data

db66be8

Merge branch 'training' of https://github.com/uab-cgds-worthey/DITTO …

cb30221

…into training

adding class weight to NN

f78fc1a

working DITTO NN

4dfbc59

concat training is working. need to test shap

794656b

DeepExplainer works but can't get shap_values. need to debug

7afa53b

DExTR scaled

b1cd211

NN on GPU and benchmarking for so

07d0435

added try:except to skip errors like sample size errors

a77063e

updated config file adding varity predictions

ad68913

adding more columns for clinvar parsing

7920c1b

new clinvar filtering with the actual clinvar column

74304ab

trying out GPU but it didn't work

2dadb5b

roc_auc and shap scores

6936244

split train and test by variants and retraining

1462faf

adds benchmark output as an excel sheet for all tools

fe3233f

fixing roc scores

453ed83

adding benchmark details to readme

2afb006

tkmamidi requested review from wilkb777 and ManavalanG January 6, 2024 07:45

tkmamidi self-assigned this Jan 6, 2024

removing all benchmarking plots

d79232f

ManavalanG requested changes Jan 9, 2024

View reviewed changes

tkmamidi added 10 commits January 24, 2024 22:37

rewording readme

f889b75

fixes links

cecda38

adds linting workflow

7e5e303

formatting document

a150750

linting json

23bee66

line length fix

0383375

skipping some links

24e19ab

python notebook link check

dc8d4c1

ignores python notebook links for linting

c5d370c

PR change request from mana - 1

cba0db1

tkmamidi removed the request for review from wilkb777 January 31, 2024 23:02

This was linked to issues Jan 31, 2024

package version differences for training and testing #10

Closed

Feedback on the pipeline #20

Closed

ManavalanG reviewed Feb 1, 2024

View reviewed changes

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ManavalanG requested changes Feb 1, 2024

View reviewed changes

tkmamidi and others added 6 commits February 1, 2024 16:29

contact info and mypackage info update

9910642

Update docs/build_DITTO.md

9e0dc66

adding whitespace Co-authored-by: Manavalan Gajapathy <[email protected]>

PR requests part-2

e324714

removes link check disabler

2424301

link fix

87bfa1f

disable broken links

db07a13

ManavalanG approved these changes Feb 2, 2024

View reviewed changes

tkmamidi merged commit 5c08367 into main Feb 2, 2024
3 checks passed

tkmamidi deleted the dev branch February 2, 2024 16:55

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DITTO using Neural Networks and SHAP #21

DITTO using Neural Networks and SHAP #21

tkmamidi commented Jan 6, 2024 •

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DITTO using Neural Networks and SHAP #21

DITTO using Neural Networks and SHAP #21

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