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NF2 Tumor Genomics Hackathon

Intro

On June 23rd, SVAI and Accel.ai are kicking off our first Genomics + AI hackathon at Google Launchpad in San Francisco! This hackathon will focus on analyzing Genomic data using AI and Deep Learning. We have the privilege to work with patient data from an ongoing medical case, provided by Onno Faber, an 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.
  • Potentiality advance our understanding of NF2 mutations.
  • Encourage more AI researchers to pursue healthcare and biology problems.
  • Explore this unique, high definition NF2 Tumor dataset.
  • Establish an open source community for future Medical AI collaborative hacking.

 

Problem Tracks

Co-developed with support from UC Berkeley, Stanford University and the NIH. Expanded problem set descriptions will be available soon.

  1. Drug treatment pathways for existing medications, benchmarked by GeneDrop.
  2. Novice Track: Use AI to rank dataset mutations. Benchmarked by UC Berkeley's Computational Genomics Lab.
  3. Advanced Track: Use AI to rank dataset mutations. Benchmarked by UC Berkeley's Computational Genomics Lab.
  4. Use NLP to mine NF2 research and present novel treatment options.
  5. Bonus Challenge: Create a novel drug intervention with DeepChem.

 

About 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.  Request Early Access to the Dataset.

 

Great Reasons Why You Should Come:

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

 

**More Details Coming Soon**

 

Apply to join event: 

Due to limited space, please apply to join this event. We will work diligently to include everyone who is in interested in this event and be accepting participants on a rolling basis through June 23rd.

Everyone is welcome to participate online and remotely.

 
 

Special thanks to Google Launchpad Space for hosting and sponsoring this event! Subscribe here to receive biweekly event updates from Launchpad Space, Google's new event Space in SF where developers and startups can receive free technical training, one-on-one mentoring and more! 

Note: By signing up for this event, you will automatically be added to future SVAI communications.

 
 

 

SPEAKERS and MENTORS:

 

**More Speakers and Mentors being announced soon! Please let us know if you would like to mentor teams during the event.**

Onno Faber

Entrepreneur, NF2 Patient

*The data we are using for this hackathon is Onno's personal genomic data.*  Onno is the Founder & CEO of Tapstack. He previously founded several companies including; ii studio, Hoppakay, MarketMatchers and Ding Dong. “I have been creating things and solving problems for as long as I can remember. I've studied architecture and got my degree in 2006 ( honors). My interest in the internet and entrepreneuring never left me and ever since grew stronger. Now I'm a full-time entrepreneur, enjoying developing new concepts and products. Above all I value connections to other people."

 Twitter   LinkedIn

Laura Montoya

Accel.ai

Laura is Founder and CEO of Accel.ai where she teaches AI and Deep Learning workshops. She is also a chapter director for Women Who Code. - I have been described by my team members as a natural and versatile leader with a passion for Artificial Intelligence, Computer Science, Research, and Psychology. Personal interests include growth & empowerment, diversity, and community outreach. I enjoy extending any extra energy and resources into volunteering for human rights organizations. When I am not volunteering in my free time, I enjoy cycling, running, and dancing.

Twitter   LinkedIn

Rumman Chowhury

Accenture

I am a Senior Data Scientist and Political Science PhD candidate (ABD) at the University of California, San Diego. My fields of study are primarily American Politics, Urban Politics, and Political Theory which have continued to fuel my love for data science. In my spare time, I love to practice and teach yoga. My diverse background in both academia and the private sector focuses on providing real-world solutions using advanced analytical techniques as a team member and as a team leader.

Twitter   LinkedIn

Avanti Shrikumar

Stanford PhD, MIT

Avanti is a second-year Ph.D student in the Department of Computer Science at Stanford, advised by Professor Anshul Kundaje. She has develop broadly-applicable methods to make deep learning models interpretable, and has applied these methods to study regulatory genomics. Avanti has a Bachelor's in Computer Science with Molecular Biology from MIT and spent a year working as a developer for the Healthcare team of Palantir Technologies before starting her PhD. Read more at Avanti's Stanford page.

Twitter   LinkedIn

Keren Gu

Sift Science, MIT

I am a software engineer on the machine learning team at Sift Science, a real time machine learning startup in San Francisco that helps online merchants detect fraud. Previously, I received my bachelor's in math and computer science in 2014 and master's in computer science in 2015 from MIT. I was a member of the Interactive Robotics Group led by professor Julie Shah at CSAIL. My thesis focuses on building mental models for autonomous agents by drawing intuition from effective human behaviors. While an undergraduate at MIT, I worked on a number of research projects at CSAIL and the Media Lab.

Twitter   LinkedIn

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Yad Faeq

Independent Deep Learning Researcher

Yad is an applied researcher in deep learning and AI, with interests in developing deep learning algorithms to improve up on sequence to sequence learning tasks, introducing deep learning to hard sciences and democratization of AI.

Twitter   LinkedIn

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Bharath Ramsundar

Stanford PhD: Pande Lab, UC Berkeley, DeepChem Author

Bharath Ramsundar received a BA and BS from UC Berkeley in EECS and Mathematics and was valedictorian of his graduating class in mathematics. He is currently a PhD student in computer science at Stanford University with the Pande group. His research focuses on the application of deep-learning to drug-discovery. In particular, Bharath is the creator and lead-developer of DeepChem, an open source package that aims to democratize the use of deep-learning in drug-discovery and quantum chemistry. He is supported by a Hertz Fellowship, the most selective graduate fellowship in the sciences.

Twitter   LinkedIn

Gaia Andreoletti

Postdoctoral Fellow,  Brenner Lab, UC Berkeley

Bio coming soon.

Aashish Adhikari

Postdoc, Brenner Lab, UC Berkeley

Bio coming soon.

Andrew Sharo

PhD student, Biophysics, Brenner Lab, UC Berkeley

Bio coming soon.

 

FORMAT:

Weekend Hackathon (Not an overnight event).

 

AGENDA:

Friday Night - June 23rd

18.00: Doors Open

18.30: Welcome!

18.45: Opening Talks 

20.45: Objectives & Team Formation

23.00: Doors Close

Saturday - June 24th

9.00: Doors Open, Breakfast

10.30: Morning Talk

12.30: Lunch

15.00: Afternoon Talk

18.00: Dinner

19.30: Evening Talk

20.00: Submit Models

23.00: Doors Close

Sunday - June 25th

9.00: Doors Open, Breakfast

10.30: Morning Talk

12.00: Lunch

16.00: Final Presentations

17.00: Happy Hour, Celebrate

 

LIVE STREAM:

Available for final presentations, Sunday Afternoon.

 

TECHNICAL LEVEL:

Everyone is welcome! Note, It's going to be pretty technical. Our target audience is AI Researchers and Biologists, Genomics Researchers. 

 

VENUE:

Google

Launchpad Space 

4th floor, 301 Howard, SF

 

TRANSPORTATION:

BART: 0.3 miles from Embarcadero Station. Map

 

FOOD & DRINKS:

Full Food and Drink accommodations provided by Google.

 

 
 

----Standard Event Disclosures----

We have a pretty thorough FAQ, please check it out here: FAQ

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:

We take photos at our events. Some of these photos will be used on our website. We seek to respect your privacy and ask that if you do not want your photo to appear on SVAI to please email us.

COMMUNICATIONS:

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

PROMOTIONS:

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

IMPORTANT: 

This gathering is limited to -- 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? Tweet to us @SVAIresearch.