Duplicate from openadmet/openadmet-expansionrx-challenge-train-data

Co-authored-by: Maria A Castellaos <mariacm12@users.noreply.huggingface.co>

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LICENSE.md

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+(Revise this)
+This Dataset is licensed under CC BY 4.0 for commercial use not involving the sale, transfer, or licensing of the Dataset (or any data or information contained therein) itself.

README.md

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+---
+license: cc-by-4.0
+license_link: LICENSE.md
+tags:
+  - admet
+  - drug discovery
+pretty_name: openadmet-challenge-train-data
+size_categories:
+  - n<1K
+configs:
+  - config_name: default
+    data_files:
+      - split: train
+        path: expansion_data_train.csv
+  - config_name: raw
+    data_files:
+      - split: train
+        path: expansion_data_train_raw.csv
+extra_gated_fields:
+  First name: text
+  Last name: text
+  Company: text
+  Work email: text
+  I want to use this dataset for: text
+---
+
+# OpenADMET-ExpansionRx Challenge training dataset
+
+This dataset contains real-work ADMET data from a recently prosecuted series of drug discovery campaigns by Expansion Therapeutics on RNA mediated diseases. While optimising candidate molecules for their preclinical programs Expansion collected a variety of ADMET data for off-targets and properties of interest in the traditional game of “whack-a-mole” familiar to all drug hunters. Now, they’ve made the bold and generous decision to open-source their high-quality ADMET dataset for public use and benefit. In their words:
+
+*"We have decided to release all of our ADME datasets from our programs to the public, and we’re asking the scientific community to put them to work. We do this because we believe open science is the fastest and most reliable path to new and better computational tools that will help patients. To translate this principle into progress, we are collaborating with OpenADMET to launch a blind challenge.*
+
+*Scientific progress is built layer by layer, with each discovery resting on the work that came before. As Newton put it, “If I have seen further, it is only because I was standing on the shoulders of giants.” We hope this dataset and challenge can be part of that shared foundation, a resource grounded in the messy reality of drug discovery, and a step toward a future where ADME can be reliably predicted without the need to iteratively synthesize and test individual molecules.*
+
+*Although these particular molecules did not become medicines, the data they generated still holds value. If sharing it helps one team build better predictive models, avoid a toxic compound, shorten a development timeline, or design a safer trial, then the patients we set out to help will have benefited. Let this also be a call to others with similar troves of knowledge: publish what you can, and give the community better problems to solve. Together, we can make drug discovery more predictable, leading to better medicines, faster, to help the patients who need this most.”* - **ExpansionRx team**
+
+
+
+## Endpoints 
+
+Participants will be tasked with solving real-world ADMET prediction problems ExpansionRx faced during lead optimization. Specifically, you will be asked to predict the ADMET properties of late-stage molecules based on earlier-stage data from the same campaigns. For this challenge we selected nine (9) crucial endpoints for the community to predict:
+
+* LogD
+* Kinetic Solubility KSOL: uM
+* Mouse Liver Microsomal (MLM) CLint: mL/min/kg
+* Human Liver Microsomal (HLM) Clint: mL/min/kg
+* Caco-2 Efflux Ratio
+* Caco-2 Papp A>B (10^-6 cm/s)
+* Mouse Plasma Protein Binding (MPPB): % Unbound
+* Mouse Brain Protein Binding (MBPB): % Unbound
+* Mouse Gastrocnemius Muscle Binding (MGMB): % Unbound
+
+We provide two training sets. One is the dataset in "ML-ready" format where only in-range measurements are included. The "raw" dataset is also available that includes measurements with out of range modifiers e.g ">" or ">"
+## Example usage
+
+Using Hugging Face datasets:
+
+```
+from datasets import load_dataset
+
+ds = load_dataset("openadmet/openadmet-expansionrx-challenge-train-data")
+```
+
+Using Pandas:
+
+```
+import pandas as pd
+
+df = pd.read_csv("hf://datasets/openadmet/openadmet-expansionrx-challenge-train-data/expansion_data_train.csv")
+```
+
+Or for the raw dataset 
+
+```
+import pandas as pd
+
+df = pd.read_csv("hf://datasets/openadmet/openadmet-expansionrx-challenge-train-data/expansion_data_train_raw.csv")
+```