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Deep Learning for Cytometry Data In-Person

Overview

Cytometry technologies are essential tools for immunology research, providing high-throughput measurements of the immune cells at the single-cell level. In this workshop, we will build and test a deep convolutional neural network to diagnose the latent cytomegalovirus (CMV) in healthy individuals using CyTOF data. In addition, we will developed a permutation-based method for interpreting the deep convolutional neural network model and identify key immune cells associated with the CMV infection.

Learning Objectives

  • Understand basic concepts in neural networks
  • Learn to build and train neural networks using Keras
  • Design customized deep learning models for cytometry data (CyTOF and flow cytometry data)
  • Apply techniques to interpret deep learning models

Prerequisites / Preparation

Knowledge of several concepts in machine learning: logistic regression, cross-validation, ROC curves, and decision trees. Familiarity with Jupyter notebooks and basic Python 3 data structures including: dictionary, NumPy arrays, and pandas data frames will help if you would like to follow the code examples after the workshop (see the materials section below).

Software

This workshop will be a demonstration of how to use Python and Jupyter notebooks to perform deep learning. If you would like to install software that will allow you to run the code on your own, installation instructions are linked below. You will not need these during the actual workshop.

Materials

Workshop materials are available here.

Instructors

Zicheng Hu is a Research Scientist in the Butte Lab at the Bakar Computational Health Sciences Institute at UCSF.

Sanchita Bhattacharya is a Bioinformatics Project Leader in the Butte Lab at the Bakar Computational Health Sciences Institute at UCSF.

 

Related LibGuide: Bioinformatics and Statistics Resources by Ariel Deardorff

Date:
Thursday, Apr 30 2020
Time:
1:00pm - 4:00pm
Time Zone:
Pacific Time - US & Canada (change)
Campus:
Online
Categories:
  Data Science > Bioinformatics and Statistics     Data Science     Data Science > Programming  
Registration has closed.

Event Organizer

Profile photo of Karla Lindquist
Karla Lindquist