Deep Learning in the Life Sciences

Organizer(s):

  • Shawn O'Neil
  • Christopher Sullivan

Workshop type:

  • Workshop

Registration Deadline:

  • July 20, 2018

Workshop Abstract:

The Center for Genome Research and Biocomputing (CGRB) and IBM are partnering to host a 2 1/2-day workshop introducing the fundamentals of deep learning for life-science applications. Participants will access IBM's PowerAI architecture and learn from IBM professionals, including logistic and multinomial regression, deep recurrent and convolutional neural networks, and tools such as Tensorflow and CAFFE. Potential examples to be covered include DNA sequence analysis for protein prediction, mining health analytics data, and textual analysis. 

The 1/2-day "pre-workshop" will also cover relevant background knowledge, including scripting in Python and using Jupyter notebooks.

CGRB Logo    IBM Logo

 

Topics:

The workshop will be a hands-on introduction to deep learning, including worked examples and helpers circulating to answer questions.

  • Python review, Jupyter Notebook Introduction
  • Overview of HPC and Distributed Computing for Deep Learning
  • Introduction to Linear Regression
  • Introduction to Tensorflow
  • Logistic Regression, Multinomial Logistic Regression, Softmax Regression
  • Introduction to Fully Connected Neural Networks
  • Convolutional Neural Networks, ImageNet, and CAFFE
  • Recurrent Neural Networks and Long Short-Term Memory (LSTM) Models
  • Example Application: DNA Sequence Analysis for Protein Prediction
  • Example Application: Mining Health Analytics Data
  • Example Application: Natural Language Processing

     

    Schedule and Registration:

    • August 10: 2:30p to 5:30p: Background topics (Jupyter notebooks, Python scripting, access to PowerAI platform)
    • August 11: 9:00am to 5:30p: Deep Learning topics with IBM (details coming soon)
    • August 12: 9:00am to 5:30p: Deep Learning topics with IBM (details coming soon)

    Standard registration is $900, please register here and select either "ICBO + ML Workshop" if attending both ICBO and this workshop, or just "ML Workshop" to attend just this workshop: Register Here

    The CGRB and ICBO are offering a number of $450 scholarships for students and early-career professionals. Apply for a scholarship here: https://goo.gl/forms/yWRW7D4xZTXC898h1 We'll notify those selected by July 1 and provide a discount code for registration. 

    Note: The scholarship is applied via a discount code that will be provided for use during payment. It is possible to register to reserve a spot now, but defer payment until after July 1 when scholarship notifications are sent. To do so, when the registration form asks for payment information, select “Mail a check.” You’ll get an invoice, and be able to pay with some other method later if you wish, using the code during payment should you be selected.

    The deadline for scholarship applications has passed.

    Logistics:

    Registration includes lunch (on Aug 11 and 12), snacks, and coffee. Dinner and housing is not included. 

    For local accomodations, including hotels and cheaper campus residence hall options, please see the ICBO accommodations page

    Please direct questions about the workshop to shawn.oneil@cgrb.oregonstate.edu or chris@cgrb.oregonstate.edu

    Attendees should bring a laptop with a web browser capable of running modern web-based applications and an SSH client such as Putty.exe if using Windows (Mac users can use built-in tools.) Please email if you don't have a laptop to bring.

     

    Rationale:

    Deep learning is making inroads in many fields, including bioinformatics and life sciences. We hope to highlight the work the CGRB and OSU are doing in this field, as well as generate new ideas for how Deep Learning can be applied to not only image-based data, but also sequence-based and ontology-based.

     

    Funding:

    IBM, CGRB, ICBO