Commit
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9a87acd
1
Parent(s):
4a37ad2
Added more details on October 13th test set results
Browse files
about.py
CHANGED
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@@ -8,6 +8,18 @@ from constants import (
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TUTORIAL_URL,
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)
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ABOUT_INTRO = f"""
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## About this challenge
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@@ -52,7 +64,7 @@ ABOUT_TEXT = f"""
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Check out our introductory tutorial on training an antibody developability prediction model with cross-validation [here]({TUTORIAL_URL}).
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⏰ Submissions close on **1 November 2025
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---
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#### How to contribute?
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We'd like to add
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- Absolute folding stability models (for Thermostability)
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- PROPERMAB
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- AbMelt (requires GROMACS for MD simulations)
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@@ -165,9 +177,9 @@ You do **not** need to predict all 5 properties — each property has its own le
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- **Private Test Set predictions** (final test submission)
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2. Each CSV should contain `antibody_name` + one column per property you are predicting (e.g. `"antibody_name,Titer,PR_CHO"` if your model predicts Titer and Polyreactivity).
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- List of valid property names: `{', '.join(ASSAY_LIST)}`.
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The GDPa1 results should appear on the leaderboard within a minute, and can also be calculated manually using Spearman rank correlation
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We may release private test set results at intermediate points during the competition.
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## Cross-validation
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Submit a CSV file in the same format but also containing the `"hierarchical_cluster_IgG_isotype_stratified_fold"` column.
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Check out our tutorial on training an antibody developability prediction model with cross-validation [here]({TUTORIAL_URL}).
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Submissions close on **1 November 2025**.
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"""
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TUTORIAL_URL,
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)
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WEBSITE_HEADER = f"""
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## Welcome to the Ginkgo Antibody Developability Benchmark!
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Participants can submit their model to the leaderboards by simply uploading a CSV file (see the "✉️ Submit" tab).
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You can **predict any or all of the 5 properties**, and you can filter the main leaderboard by property.
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See more details in the "{ABOUT_TAB_NAME}" tab.
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🗓️ There will be a test set scoring on **October 13th** (which will score all the latest test set submissions at that point).
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Use this to refine your models before the final submission deadline on **1 November 2025**.
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"""
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ABOUT_INTRO = f"""
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## About this challenge
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Check out our introductory tutorial on training an antibody developability prediction model with cross-validation [here]({TUTORIAL_URL}).
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⏰ Submissions close on **1 November 2025**, but there will be an early test set scoring on **October 13th** (which will score all the latest test set submissions at that point, and then you can refine your model and resubmit).
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---
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#### How to contribute?
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We'd like to add more existing developability models to the leaderboard. Some examples of models we'd like to add:
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- Absolute folding stability models (for Thermostability)
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- PROPERMAB
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- AbMelt (requires GROMACS for MD simulations)
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- **Private Test Set predictions** (final test submission)
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2. Each CSV should contain `antibody_name` + one column per property you are predicting (e.g. `"antibody_name,Titer,PR_CHO"` if your model predicts Titer and Polyreactivity).
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- List of valid property names: `{', '.join(ASSAY_LIST)}`.
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3. Submit as many times as you like, and the latest submission will be used for the leaderboard (and test set scoring at the end of the competition).
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The GDPa1 results should appear on the leaderboard within a minute, and can also be calculated manually using average Spearman rank correlation across the 5 folds.
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## Cross-validation
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Submit a CSV file in the same format but also containing the `"hierarchical_cluster_IgG_isotype_stratified_fold"` column.
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Check out our tutorial on training an antibody developability prediction model with cross-validation [here]({TUTORIAL_URL}).
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## Test set
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The **private test set results will not appear on the leaderboards at first**, and will be used to determine the winners at the close of the competition.
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🗓️ There will be a test set scoring on **October 13th** (which will score all the latest test set submissions at that point).
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Submissions close on **1 November 2025**.
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"""
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app.py
CHANGED
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@@ -8,7 +8,7 @@ from dotenv import load_dotenv
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load_dotenv() # Load environment variables from .env file (before imports)
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from about import ABOUT_INTRO, ABOUT_TEXT, FAQS, SUBMIT_INSTRUCTIONS
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from constants import (
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ASSAY_RENAME, # noqa: F401
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SEQUENCES_FILE_DICT,
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@@ -88,15 +88,7 @@ with gr.Blocks(theme=gr.themes.Default(text_size=sizes.text_lg)) as demo:
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with gr.Row():
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with gr.Column(scale=6): # bigger text area
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gr.Markdown(
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-
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## Welcome to the Ginkgo Antibody Developability Benchmark!
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-
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Participants can submit their model to the leaderboards by simply uploading a CSV file (see the "✉️ Submit" tab).
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-
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You can **predict any or all of the 5 properties**, and you can filter the main leaderboard by property.
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See more details in the "{ABOUT_TAB_NAME}" tab.
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Submissions close on 1 November 2025.
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"""
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)
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with gr.Column(scale=2): # smaller side column for logo
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gr.Image(
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load_dotenv() # Load environment variables from .env file (before imports)
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from about import ABOUT_INTRO, ABOUT_TEXT, FAQS, SUBMIT_INSTRUCTIONS, WEBSITE_HEADER
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from constants import (
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ASSAY_RENAME, # noqa: F401
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SEQUENCES_FILE_DICT,
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with gr.Row():
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with gr.Column(scale=6): # bigger text area
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gr.Markdown(
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WEBSITE_HEADER
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)
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with gr.Column(scale=2): # smaller side column for logo
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gr.Image(
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