Initial commit

README.md

@@ -1,2 +1,68 @@
-# tox24challenge
-Dataset used in Tox24 challenge
+Tox24 Challenge Dataset
+===========
+
+This repository contains molecular structures and descriptors for the Tox24 challenge prepared by me (team name: **filipsPL**). The goal of the challenge was to predict the in vitro activity of compounds' activity against [Transthyretin (TTR)](https://en.wikipedia.org/wiki/Transthyretin) using chemical structure data.
+
+- [Tox24 Challenge Dataset](#tox24-challenge-dataset)
+  - [Dataset](#dataset)
+  - [Descriptors](#descriptors)
+  - [Importance of features](#importance-of-features)
+  - [The Challenge Results](#the-challenge-results)
+  - [References](#references)
+
+
+## Dataset
+
+This repository includes:
+
+- The [chemical structures](data/smiles_org+fixed.csv) provided by the organizers and curated by me using my RDKit pipeline.
+- **Training set** - a diversified set of 1000 compounds, used for training models [data/train.csv.xz](data/train.csv.xz)
+- **Validation set**: a diversified set of 100 compounds, used for final validation of models [data/validation.csv.xz](data/validation.csv.xz)
+- **Test set**: 500 compounds used to make predictions. It contains a leaderboard set (200 compounds) and a blind set (300 compounds) [data/test.csv.xz](data/test.csv.xz)
+
+## Descriptors
+
+The csv files contain 2D descriptors of molecules, including:
+
+- DRKitDescriptors (2D)
+- molecular fingerprints:
+  - CDK:
+    - CDKECFP4
+    - CDKEState
+    - CDKFCFP4
+    - CDKmolprop
+    - CDKpubchem
+    - CDKstandard
+  - Indigo fingerprints:
+    - IndigoResonanceSubstructure
+    - IndigoSimilarity
+  - RDKit fingerprints:
+    - RDkitFP-AtomPair
+    - RDkitFP-Avalon
+    - RDkitFP-FeatMorgan4
+    - RDkitFP-Layered
+    - RDkitFP-MACCS
+    - RDkitFP-Morgan2
+    - RDkitFP-Morgan3
+    - RDkitFP-Morgan4
+    - RDkitFP-Pattern
+    - RDkitFP-RDKit
+    - RDkitFP-Torsion
+
+## Importance of features
+
+Feature importances according to the final catboost model
+
+![bar plot](feature_importance.png)
+
+
+## The Challenge Results
+
+Bar plot showing RMSE of submitted predictions (by me, based on the official results). Congratulations to the winning team Amidoff 🎉!
+
+![rank](ranking.png)
+
+## References
+
+1. [OCHEM Platform for Tox24](https://ochem.eu/static/challenge.do)
+2. [Chem. Res. Toxicol. 2024, 37, 6, 825–826](https://pubs.acs.org/doi/10.1021/acs.chemrestox.4c00192)

data/smiles_org+fixed.csv

@@ -0,0 +1,201 @@
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