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96daff0
Added draft support for multi-output prediction and AD estimation
Nov 22, 2024
9c2678f
Merge branch 'main' into AD_calculation.py
Dec 31, 2024
83cde65
Fixed type on Readme
Jan 9, 2025
43088a6
fixed conflict
Feb 3, 2025
7c48055
Added AD domain estimators from MLChemAD, need some work on consisten…
Feb 8, 2025
2f3abfd
Updated README with a reference
Feb 10, 2025
198cfba
Developed a base_class for making AD estimators consistent
Feb 10, 2025
d5d84ad
Made first transition for the kNN implementation. Currently only supp…
Feb 10, 2025
51efb25
Added leverage to our tests.
Feb 10, 2025
f75bc80
Added more AD estimators as children of base_class
Feb 10, 2025
9cafe9f
Moved rest of AD estimators. All test runs.
Feb 10, 2025
c2a9dc4
WIP on the adapter. Not fully there yet as some complications in the …
Feb 12, 2025
f41929e
Merge branch 'main' into AD_calculation.py
Feb 12, 2025
f2ab158
work in progress on adapters
Feb 19, 2025
4273936
It seems to be getting there with the EstimatorUnion. Got feature_nam…
Feb 22, 2025
159432f
predicttotransformwrapper seems to be working now.
Feb 22, 2025
9279008
Also got the fit_transform to work. Seemingly getting there.
Feb 22, 2025
d19322f
Experimental adapters. WIP
Mar 8, 2025
8dfa312
Cleaning up.
Mar 8, 2025
756e6c9
Further fixes in tests and some estimators
Mar 8, 2025
64bc117
Setting numpy random seed automatically for consistent testing behavi…
Mar 8, 2025
c6669b3
Merge branch 'main' into AD_estimators_cleanup
Mar 8, 2025
e8a4c7b
Adding a link for the new notebook
Mar 8, 2025
219c5fd
Merge branch 'main' into AD_estimators_cleanup and update some filena…
Apr 6, 2025
07a25d8
Fixing MD to proper links
Apr 6, 2025
0b804a4
Adding to docs
Apr 6, 2025
6c95acc
Adding baseapplicability to include into docs, and deleing outcomment…
Apr 6, 2025
14758c1
Fixes to mkdocs references
Apr 6, 2025
b7c19d0
Further updates to mkdocs configuration and some cleanup
Apr 6, 2025
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4 changes: 3 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,7 @@ Example notebooks and API documentation are now hosted on [https://scikit-mol.re
- [Testing different fingerprints as part of the hyperparameter optimization](https://scikit-mol.readthedocs.io/en/latest/notebooks/09_Combinatorial_Method_Usage_with_FingerPrint_Transformers/)
- [Using pandas output for easy feature importance analysis and combine pre-existing values with new computations](https://scikit-mol.readthedocs.io/en/latest/notebooks/10_pipeline_pandas_output/)
- [Working with pipelines and estimators in safe inference mode for handling prediction on batches with invalid smiles or molecules](https://scikit-mol.readthedocs.io/en/latest/notebooks/11_safe_inference/)
- [Estimating applicability domain using feature based estimators](https://scikit-mol.readthedocs.io/en/latest/notebooks/11_safe_inference/12_applicability_domain/)

We also put a software note on ChemRxiv. [https://doi.org/10.26434/chemrxiv-2023-fzqwd](https://doi.org/10.26434/chemrxiv-2023-fzqwd)

Expand All @@ -84,6 +85,7 @@ Scikit-Mol has been featured in blog-posts or used in research, some examples wh
- [WAE-DTI: Ensemble-based architecture for drug–target interaction prediction using descriptors and embeddings](https://www.sciencedirect.com/science/article/pii/S2352914824001618)
- [Data Driven Estimation of Molecular Log-Likelihood using Fingerprint Key Counting](https://chemrxiv.org/engage/chemrxiv/article-details/661402ee21291e5d1d646651)
- [AUTONOMOUS DRUG DISCOVERY](https://www.proquest.com/openview/3e830e36bc618f263905a99e787c66c6/1?pq-origsite=gscholar&cbl=18750&diss=y)
- [DrugGym: A testbed for the economics of autonomous drug discovery](https://www.biorxiv.org/content/10.1101/2024.05.28.596296v1.abstract)

## Roadmap and Contributing

Expand All @@ -98,7 +100,7 @@ There are more information about how to contribute to the project in [CONTRIBUTI

Probably still, please check issues at GitHub and report there

## Contributors:
## Contributors

Scikit-Mol has been developed as a community effort with contributions from people from many different companies, consortia, foundations and academic institutions.

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5 changes: 5 additions & 0 deletions docs/api/scikit_mol.applicability.md
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@@ -0,0 +1,5 @@
# `scikit-mol.applicability`

::: scikit_mol.applicability


1 change: 1 addition & 0 deletions docs/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,7 @@ Example notebooks and API documentation are now hosted on [https://scikit-mol.re
- [Using pandas output for easy feature importance analysis and combine pre-existing values with new computations](https://scikit-mol.readthedocs.io/en/latest/notebooks/10_pipeline_pandas_output/)
- [Working with pipelines and estimators in safe inference mode for handling prediction on batches with invalid smiles or molecules](https://scikit-mol.readthedocs.io/en/latest/notebooks/11_safe_inference/)
- [Creating custom fingerprint transformers](https://scikit-mol.readthedocs.io/en/latest/notebooks/12_custom_fingerprint_transformer/)
- [Estimating applicability domain using feature based estimators](https://scikit-mol.readthedocs.io/en/latest/notebooks/11_safe_inference/13_applicability_domain/)

We also put a software note on ChemRxiv. [https://doi.org/10.26434/chemrxiv-2023-fzqwd](https://doi.org/10.26434/chemrxiv-2023-fzqwd)

Expand Down
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