loodvanniekerkginkgo commited on
Commit
9a87acd
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1 Parent(s): 4a37ad2

Added more details on October 13th test set results

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Files changed (2) hide show
  1. about.py +21 -4
  2. app.py +2 -10
about.py CHANGED
@@ -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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@@ -71,7 +83,7 @@ We're working on getting more public models added, so that participants have mor
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  #### How to contribute?
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- We'd like to add some 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)
@@ -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. 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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- We may release private test set results at intermediate points during the competition.
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  ## Cross-validation
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@@ -175,5 +187,10 @@ For the GDPa1 cross-validation predictions, use the `"hierarchical_cluster_IgG_i
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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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+
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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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+
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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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+
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  ABOUT_INTRO = f"""
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  ## About this challenge
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64
 
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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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69
  ---
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83
 
84
  #### How to contribute?
85
 
86
+ We'd like to add more existing developability models to the leaderboard. Some examples of models we'd like to add:
87
  - Absolute folding stability models (for Thermostability)
88
  - PROPERMAB
89
  - AbMelt (requires GROMACS for MD simulations)
 
177
  - **Private Test Set predictions** (final test submission)
178
  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.
 
183
 
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  ## Cross-validation
185
 
 
187
  Submit a CSV file in the same format but also containing the `"hierarchical_cluster_IgG_isotype_stratified_fold"` column.
188
  Check out our tutorial on training an antibody developability prediction model with cross-validation [here]({TUTORIAL_URL}).
189
 
190
+ ## Test set
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+
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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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+
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  Submissions close on **1 November 2025**.
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  """
app.py CHANGED
@@ -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,
@@ -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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- f"""
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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(