Survboard Demo Video

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Introduction

Welcome to Survboard's demo guide! In this article, we'll walk you through the process of preparing your results for a successful submission to our leaderboard. Follow these steps to ensure your submission is organized, your folder is properly compressed, and your results are uploaded and evaluated efficiently.

Organizing Your Results

In the root folder of your submission, it’s crucial to organize all your results by cohort. For instance, when working with The Cancer Genome Atlas (TCGA), you will find various cancer datasets. If we take a closer look at bladder cancer specifically, there will be 25 distinct files, one for each split, since we implement five-fold cross-validation repeated five times.

  • Split Number One contains all the time steps as columns, with the predicted survival probability for each patient listed accordingly.

Compressing Your Folder

Next, ensure that you compress your folder using either command line instructions or a user interface tool available on your operating system. Be sure to remove any unnecessary artifacts, such as the .DS_Store file commonly found on Mac operating systems.

Submission Process

To submit your results, visit the landing page of the Survboard website, where detailed instructions for submissions are provided. Here, you can also access the public leaderboard, which displays various models, modalities they are testing, specific settings, and scores associated with different datasets.

Filtering the Leaderboard

On the leaderboard, you can filter views for specific datasets like TCGA, or switch to ICGC, TARGET, or METABRIK. Additionally, filtering by setting and metric is available. For instance, you can examine the integrated BR score associated with the TCGA project under the missing and pan-cancer settings, and also explore the concordance metrics.

Account Creation and Login

Before making a submission, you need to log in. If you do not already have an account, please sign up using your email address, create a strong password, and provide the name of your organization.

Once you are signed in, you'll see a "Your Submissions" tab where you can review all your previous submissions.

Uploading Results

To upload your results, click on the upload button, select your zip file, and enter model details such as:

  • Model name
  • GitHub repository link (where the code to reproduce your model is hosted)
  • The setting your model is testing
  • A model description
  • The modality used in your experiments

When you’re ready to submit, simply click on the submit button. Please note that results might take a few minutes to appear in your "Your Submissions" tab. During this time, evaluators will compute scores for your submitted results, and an admin will review your submission to ensure the GitHub repository is public and reproducible. Once all internal criteria are met, your submission will become public.

In the interim, you can view scores related to your results on your private leaderboard, including metrics such as integrated BR score, concordance, and decoupling.

Thank you for watching, and we hope you find benefit from using our web service!

Keywords

  • Survboard
  • Submission
  • TCGA
  • Cancer datasets
  • Cross-validation
  • Compressing folder
  • Public leaderboard
  • Model details
  • Evaluation metrics

FAQ

Q1: How do I organize my submission results?
A1: Organize your results by cohort in the root folder. For TCGA, ensure each cancer dataset is neatly categorized and split files are included as required.

Q2: What should I do before compressing my folder?
A2: Make sure to remove any artifacts, such as the .DS_Store file on Mac systems, before compressing your folder.

Q3: How do I access the public leaderboard?
A3: You can access the public leaderboard from the landing page of the Survboard website, where you can filter views based on datasets, metrics, and settings.

Q4: What information do I need to provide when uploading results?
A4: You need to upload your zip file and provide details like the model name, GitHub repository link, the setting your model is testing, a description, and the modality used.

Q5: What happens after I submit my results?
A5: After submission, your results will be evaluated, and it might take a few minutes for scores to appear on your private leaderboard. An admin will review your model's repository for reproducibility.