NF2 Tumor Genomics Hackathon

INTRODUCTION

On June 23rd,  Accel.ai + SVAI + NF2 Project, are kicking off our first AI Genomics hackathon at Google Launchpad in San Francisco! We're also happy to announce the NCBI as a community partner. This event will focus on analyzing Genomic data and research publications using AI and other computational methods. We have a special opportunity to work with patient data from an ongoing medical case, provided by Onno Faber, a serial entrepreneur and NF2 Patient. This event kicks off our first open source medical AI community project and we're super excited for it!

 

PURPOSE

  • Contribute to a real, ongoing patient case.
  • Try to advance our understanding of NF2 mutations.
  • Encourage more AI researchers to pursue healthcare and biology problems.
  • Explore this unique, high definition NF2 Tumor Genomics dataset.
  • Establish an open source community for future Medical AI collaborative hacking.

 

PROBLEM TRACKS

The main issue with NF2 is that patients develop tumors in the central nervous system, slowly knocking out senses and body functions (hearing for most, facial paralysis and sight/muscles/sensory functions for some). All the ‘tracks’ below are ways to find out why these tumors are there, what makes them grow and most importantly how to stop them.

*We encourage you to analyze the NF2 dataset based on your interests and expertise* 

  1. Drug treatment pathways for existing medications.
  2. Ranking dataset mutations.
  3. Use NLP to mine NF2 research and present novel treatment options.
  4. Create a novel drug intervention with DeepChem

Advanced: NF2 Expanded Problem Tracks and Vision for Ongoing Investigation.

 

THE DATASET

Whole Genome sequence data set for NF2: a genetic condition that causes tumors to grow from Schwann cells. The dataset has a tumor/normal pair and a sibling. All three Whole Genome Sequences were done at 60-90X and available as .bam-files. The dataset was acquired in the context of finding the driver mutations for a particular NF2 patient. For registered participants, we will release the dataset 1-week prior to the start of the hackathon. Get the NF2 Dataset.

 

WHY YOU SHOULD COME:

  • Learn how to work with Genomic Data.
  • Awesome mentoring sessions on AI and Genomics.
  • Make new friends.
  • Connect with us and our event partners.

 

All of our In-person event invitation have been sent! You may still apply to participate remotely.

 

 

Neurofibromatosis Type II Intro by Marco Giovannini M.D Ph. D - www.houseearclinic.com

 

MENTORING SESSIONS

Our mentors will float around during the event and check in with teams to help with problems and answer questions. Please feel free to seek them out at the event and say hi! Some of our mentors will also be participating on teams, so we may post specific hours they are available to help. Also: Don't hesitate to ask others at the event for help - everyone participating in this event has extraordinary skill.

 

COMPUTATIONAL POWER

We will be administering $150,000 in Google Cloud credits to teams over the weekend. Yay! If you have a pre-formed team and plan to do especially rigorous  computation, feel free to get in touch with us ahead of the event and we'll help you get set up. 

 

SUBMISSIONS

We'd like to see submissions follow the same format as an (abbreviated) academic poster. Submissions are not restricted to this format and we encourage you to be as creative as you want. Submission link coming.

  1. Introduction
  2. Purpose
  3. Approach
  4. Methods / Algorithms / Models
  5. Results and Discussion 

 

FINAL PRESENTATIONS

Each team or individual will have 5 Minutes to present what they worked on. Presentations will be fast! But don't worry, we will link submissions here afterwards so you can get a closer look at what everyone worked on.

 

JUDGING CRITERIA

Each presentation will be judged on the following criteria weighted in this order:

  1. How well does the solution lead to positive outcomes for NF2 Cancer patient treatment?
  2. How novel is the approach to finding a solution?
  3. Quality and depth of the problem analysis.
  4. Team dynamics, diversity, and intersectionality including cross discipline and specialization collaboration.

 

PRIZES

We’re giving away three Titan X Pascal boards valued at ~$1,500 a piece, compliments of NVIDIA. Great for local TensorFlow and access with the NVIDIA Deep Learning tool chain etc.  Thanks NVIDIA!

 


 

EVENT COMMUNICATIONS

We created a few slack channels for easy communication during the event Join: #hackathon or #hackathon-remote. 

SVAI Slack Channel

 

TWITTER

The official NF2 AI Genomics Hackathon Hashtag is: #NF2Hack

We will use Twitter for live announcements and updates from the event. Follow us at @AccelerateAI & @SVAIresearch.

 

FACEBOOK

Join our FaceBook Group and share some photos of the event (In-person and remote). We plan on periodically live streaming short interviews and broadcasting what people are working on through Facebook. 

SVAI Facebook & AI Deep Learning Enthusiasts

 

YOUTUBE

The opening and closing talks will be live streamed on SVAI's Youtube account.

  • June 23rd 18.40: Opening Talks.
  • June 25th 16.00: Closing Talks and Final Presentations.

 

 


 

Friday Night - June 23rd

18.00: Doors Open, Pizza Served!

18.30: Welcome!

  • Silicon Valley Artificial Intelligence

  • Accel.AI

  • Google

  • Sponsors

19.00: Onno Faber, Entrepreneur

  • NF2 Patient Story 

19:30: Marco Giovannini, MD, PhD

  • Introduction to NF2

20.00: Anita Brede, CEO @ Iris.ai

  • Identifying Quality Research Papers

20.30: Berton Earnshaw, Director of Data Science Research @ Recursion Pharmaceuticals

  • AI for Drug Discovery

20.45: Objectives & Team Formation

23.00: Doors Close

 

Saturday - June 24th

9.00: Doors Open, Breakfast

10.00: Hacking Begins

12.00: Lunch - Bun Mee

13.30: Mo Rahmann, Bioinformatics & Pharmacogenomics CSO @ GeneDrop

  • Genomics Workshop

15.00: Focused Work

17.30: Dinner - Taco Bar

23.00: Doors Close

 

Sunday - June 25th

9.00: Doors Open, Breakfast

10.00: Hacking Begins

12.00: Lunch - Mediterranean Bistro

13.00: Focused Work

15.30: Final Submissions

16.00: Presentations & Judging

18.00: Sliders & Happy Hour, Celebrate!

 

LOCATION

Google Launchpad Space
301 Howard St, 4th Floor
San Francisco, CA 94105
 

TRANSPORTATION

BART: 0.3 miles from Embarcadero Station. Map

 

FAQ

Why are you doing this?

We think it's a good idea to bring together the smartest people in AI / ML, Biology and Genomics to hack on difficult medical cases.

Is this an overnight Hackathon?

Nope. We believe in healthy sleep.

Do I need to provide my own computational power?

No. Google has you covered. We will be issuing Google Cloud credits at the event.

Who is the target Audience?

Computer scientists, AI researchers, Computational Biologists and eager learners around the world.

Can I participate remotely?

Absolutely! Join here.

Will there be opportunities to continue collaborating on this project after the hackathon?

Yes. Please get in touch with us if you'd like to continue working with Onno's dataset.


Standard Event Disclosures

CODE OF CONDUCT:

Our conference is dedicated to providing a harassment-free conference experience for everyone, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, ethnicity, religion (or lack thereof), or technology choices. We do not tolerate harassment of conference participants in any form. Sexual language and imagery is not appropriate for any conference venue, including talks, workshops, parties, Twitter and other online media. Conference participants violating these rules may be sanctioned or expelled from the conference without a refund at the discretion of the conference organizers.

For full version, please see: confcodeofconduct.com.

PHOTOGRAPHY & VIDEOGRAPHY:

We take photos and video at our events. Some of these images will be used on our website. We seek to respect your privacy and ask that if you do not want your likeness to appear on Accel.AI, SVAI, or NF2Dataproject to please email us.

COMMUNICATIONS:

By signing up for this event, you will automatically be added to future Accel.AI, SVAI, and NF2Dataproject announcements.

PROMOTIONS:

We do not make announcements for non-related events or conferences at our gatherings. Distribution of flyers, printed media or other non related materials is not allowed at our events. 

IMPORTANT: 

This gathering is limited to 150 people. You MUST be pre-registered to attend. Registration must include your First and Last name, and some of our venues require ID for entry. You do not need to print a paper ticket. We will be checking people in the building lobby. Questions or comments? Contact us!