Applying Data Assimilation Tools to COVID Forecasting Models

After earning her PhD in Aerospace Engineering at Delft, Femke spent several years in oceanography, climate research, and subsurface modeling. She developed an expertise in data assimilation that she’s now applying to improve COVID-19 pandemic forecasting models.

Femke explains that data assimilation originated in weather forecasting, where a model is updated with the current day’s weather observations to provide a more accurate forecast for the next day. Data assimilation tools tune the model to provide a more accurate forecast. This concept can be applied in many areas including financial markets, the oil industry, and for COVID-19 research.

To help improve COVID-19 forecasting, she is using a compartmental model where there are compartments for different groups: those susceptible to COVID-19, those exposed to it, those infected, those who recovered, those in quarantine, and those who are deceased. The model is like a set of boxes, and the transition from one box to the other is governed by an ordinary differential equation. Then in those equations, you have parameters, which are typically not well-known.

The data assimilation approach is to work more from the “outside in” instead of from the “inside out”. So, if you know the number of people that have died since the start of COVID, then according to this data, you can determine what the parameters would have looked like three weeks ago. With this type of inverse modeling, you can actually tune the parameters in that compartment model, and find the most likely reproduction number or the likely number of infected in the first place. The approach of having these simple relationships between the different compartments is a good framework for a very complex process. However, you cannot expect the data to tell you the story if you don’t have any prior domain knowledge. In order to take their research to the next level, it will be critical for Femke and her colleagues to collaborate with the medical experts that built the models who know how to express certain relationships.

As she has transitioned from one field to another in her career, Femke has needed to learn how to apply her expertise to entirely different research areas. She says one of the most important skills she has developed is to ask a lot of questions and not worry about being wrong and she advises young researchers to do the same. Sometimes those questions can help people already in the field think differently, and lead to new insights.

Femke’s experience as an endurance athlete has also taught her valuable lessons for her work as a scientist. “People who excel in sports lose more races than they win. You have to make mistakes and fail, that’s the way you actually grow.” It also teaches you perseverance, to hang in there when it gets tough, and be happy with small increments of your own progress rather than always comparing yourself to your competitors.