OpenVaccine Machine Learning Workshop Recap – March 9, 2022

This week we hosted a free Kaggle OpenVaccine Machine Learning workshop. The notebook is based on a Kaggle project that leverage’s data science to develop models and design rules for RNA degradation. The model predicts the likely degradation rates at each base of an RNA molecule, trained on a subset of an Eterna dataset comprising over 3000 RNA molecules (which span a panoply of sequences and structures) and their degradation rates at each position. In this blog post we’ll recap some highlights from the workshop. Ok, let’s dig in.

First, thanks for voting for your favorite charity!

With the unprecedented circumstances facing our global community, Arrikto is looking for even more ways to contribute. With this in mind, we thought that in lieu of swag we could give workshop attendees the opportunity to vote for their favorite charity and help guide our monthly donation to charitable causes. The charity that won this workshop’s voting was The Society for Women Engineers. SWE is a not-for-profit educational and service organization that empowers women to succeed and advance in engineering and be recognized for their life-changing contributions as engineers and leaders.s. We are pleased to be making a donation of $100 to them on behalf of the workshop attendees. Again, thanks to all of you who attended and voted!

What topics were covered in the workshop?

  • Kubeflow Overview
  • Notebook Basics
  • Getting the OpenVaccine Notebook Up and Running
  • Exploring the OpenVaccine Notebook 
  • Pipeline Basics
  • Running the OpenVaccine Pipeline
  • Hyperparameter Tuning

What did I miss?

Here’s a short teaser from the 45 minute workshop where I walked folks through how to perform hyperparameter tuning via Kubeflow’s Katib component on the OpenVaccine example.

Want to see more? Here’s the YouTube playlist of all the demos featured in the workshop.

Install MiniKF

In the workshop I showed how MiniKF is the easiest way to get started with Kubeflow on the platform of your choice (AWS or GCP). 

Want to try it for yourself? Here’s the links:

Try the OpenVaccine Example for Yourself

If you’d like to work through the OpenVaccine notebook yourself, check out the guided tutorial on Arrikto Academy.

Need help?

Join the Kubeflow Community on Slack and make sure to add the #minikf channel to your workspace. The #minikf channel is your best resource for immediate technical assistance regarding all things MiniKF!

Missed the March 9 workshop?

If you were unable to join us this week, but would still like to attend a workshop in the future, register for one of these upcoming workshops. 

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