SEIR model is a widely used model for simulating the spread of infectious diseases. In its simplest form, the SEIR model assumes that individuals in the population can assume any of the four states: Susceptible, Exposed, Infected and Recovered (or Removed), and the evolution of the system is modeled as a system of ordinary differential equations. Although this simple model performs well in modeling large dense populations, it does not capture population substructure and the effect of variation in interactions.
To address these issues, the general SEIR model models the population as a network where nodes are individuals and edges represent interactions between individuals. This model has attracted more attention during the Covid19 pandemic and there are python implementations that run the simulation on a single node.
In this talk, we discuss implementing the generalized SEIR model using Spark and graph analysis libraries such as GraphFrames and use stochastic simulation methods to predict the spread of Covid19 using Databricks.
Amir Kermany is a Health and Life Sciences Solutions Architect at Databricks, where he leverages his expertise in genomics and machine learning to help companies in the space to solve their problems in generating actionable insights from vast amounts of health related datasets. Amir’s past positions include Sr. Staff Scientist at AncestryDNA, Sr. Data Scientist at Shopify, Postdoctoral Scholar at the Howard Hughes Medical Institute and the University of Montreal. He holds a PhD in Mathematical Biology, MSc in Electrical Engineering and BSc. in Physics.