Maria Castellanos commited on
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400ef11
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1 Parent(s): 4fc1ec0

Add exp uncertainties

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  1. app.py +26 -3
app.py CHANGED
@@ -137,8 +137,8 @@ with gr.Blocks(title="OpenADMET ADMET Challenge", fill_height=False,
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  Go to the **Leaderboard** to check out how the challenge is going.
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  To participate, head out to the **Submit** tab and upload your results as a `CSV` file.
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- We are releasing an intermediate leaderboard on December 2nd so stay tuned!
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- The submission cutoff for this leaderboard will be **Dec 1st at 11:59PM GMT.**
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  """
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  )
@@ -227,6 +227,28 @@ with gr.Blocks(title="OpenADMET ADMET Challenge", fill_height=False,
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  The training and blinded test set will also be made available on the [CDD Vault](https://www.collaborativedrug.com/). An account to access the CDD Vault can be requested by filling out this [form](https://forms.gle/KiviZ7AaGcuqtrwH8).
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  Note that by joining the Vault, your account will be visible to other participants, so this option is **not recommended for those wishing to remain anonymous.**
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  ## πŸ“ Evaluation
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  The challenge will be judged based on the following criteria:
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  - We welcome submissions of any kind, including machine learning and physics-based approaches. You can also employ pre-training approaches as you see fit,
@@ -247,6 +269,7 @@ with gr.Blocks(title="OpenADMET ADMET Challenge", fill_height=False,
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  - **December 1st:** Intermediate leaderboard release
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  - **January 19, 2026:** Submission closes
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  - **January 26, 2026:** Winners announced
 
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  ## Acknowledgements
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  We gratefully acknowledge Jon Ainsley, Andrew Good, Elyse Bourque, Lakshminarayana Vogeti, Renato Skerlj, Tiansheng Wang, and Mark Ledeboer for generously
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  providing the Expansion Therapeutics dataset used in this challenge as an in-kind contribution.
@@ -262,7 +285,7 @@ with gr.Blocks(title="OpenADMET ADMET Challenge", fill_height=False,
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  </style>
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  <style>
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  #welcome-md table {
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- width: 60%;
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  border-collapse: collapse;
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  font-size: 0.95rem;
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  line-height: 1.2;
 
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  Go to the **Leaderboard** to check out how the challenge is going.
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  To participate, head out to the **Submit** tab and upload your results as a `CSV` file.
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+ We released an intermediate leaderboard on December 2nd, with submissions evaluated against the full blinded test set.
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+ Check it out on the OpenADMET [blog](https://openadmet.ghost.io/openadmet-expansionrx-blind-challenge-2/)!
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  """
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  )
 
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  The training and blinded test set will also be made available on the [CDD Vault](https://www.collaborativedrug.com/). An account to access the CDD Vault can be requested by filling out this [form](https://forms.gle/KiviZ7AaGcuqtrwH8).
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  Note that by joining the Vault, your account will be visible to other participants, so this option is **not recommended for those wishing to remain anonymous.**
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+ ### Experiment uncertainties
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+ For each endpoint, we present the experimental error statistics, measured with different control compounds. Special thanks Jon Ainsley for providing this data!
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+
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+ | Property | Compound | Count | Min | Max | SD | Mean abs. dev. | Median abs. dev. | Mean | Median |
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+ | :---- | :---- | ----- | ----- | ----- | ----- | ----- | ----- | ----- | ----- |
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+ | LogD | Progesterone | 456 | 3.7 | 4.02 | 0.07 | 0.06 | 0.05 | 3.85 | 3.85 |
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+ | KSOL | Progesterone | 336 | 12.33 | 25.69 | 2.28 | 1.79 | 1.48 | 16.88 | 16.8 |
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+ | MLM CLint | Verapamil | 276 | 237.67 | 514.78 | 76.03 | 69.34 | 36.78 | 334.41 | 292.73 |
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+ | HLM CLint | Verapamil | 359 | 104.68 | 304.07 | 61.28 | 57.58 | 61.9 | 197.84 | 210.25 |
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+ | Caco-2 Permeability Efflux | Atenolol | 113 | 0.85 | 1.71 | 0.2 | 0.17 | 0.16 | 1.28 | 1.27 |
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+ | | Digoxin | 383 | 25.08 | 69.71 | 10.8 | 8.77 | 6.17 | 37.76 | 34.22 |
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+ | | Minoxidil | 383 | 0.74 | 1.39 | 0.12 | 0.1 | 0.08 | 1.06 | 1.05 |
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+ | | Propranolol | 270 | 0.66 | 1.29 | 0.13 | 0.11 | 0.09 | 0.96 | 0.94 |
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+ | Caco-2 Permeability Papp A\>B | Atenolol | 113 | 0.23 | 0.96 | 0.17 | 0.14 | 0.13 | 0.57 | 0.56 |
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+ | | Digoxin | 383 | 0.22 | 0.82 | 0.13 | 0.11 | 0.1 | 0.54 | 0.55 |
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+ | | Minoxidil | 383 | 4.99 | 9.98 | 1.17 | 0.98 | 0.87 | 7.8 | 7.81 |
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+ | | Propranolol | 270 | 16.16 | 33.93 | 3.57 | 2.88 | 2.35 | 25.34 | 25.52 |
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+ | MPPB % Unbound | Ketoconazole | 265 | 98.96 | 99.62 | 0.13 | 0.1 | 0.08 | 99.35 | 99.35 |
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+ | MBPB % Unbound | Propranolol | 260 | 96.55 | 97.88 | 0.26 | 0.21 | 0.18 | 97.3 | 97.33 |
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+ | MGPB % Unbound | Propranolol | 95 | 92.28 | 98.53 | 1.06 | 0.76 | 0.54 | 94.18 | 93.94 |
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+
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+
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  ## πŸ“ Evaluation
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  The challenge will be judged based on the following criteria:
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  - We welcome submissions of any kind, including machine learning and physics-based approaches. You can also employ pre-training approaches as you see fit,
 
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  - **December 1st:** Intermediate leaderboard release
270
  - **January 19, 2026:** Submission closes
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  - **January 26, 2026:** Winners announced
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+
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  ## Acknowledgements
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  We gratefully acknowledge Jon Ainsley, Andrew Good, Elyse Bourque, Lakshminarayana Vogeti, Renato Skerlj, Tiansheng Wang, and Mark Ledeboer for generously
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  providing the Expansion Therapeutics dataset used in this challenge as an in-kind contribution.
 
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  </style>
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  <style>
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  #welcome-md table {
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+ width: 80%;
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  border-collapse: collapse;
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  font-size: 0.95rem;
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  line-height: 1.2;