Monitoring Shifts in Flowering Phenology Using Satellite Imagery and
Deep Learning
Abstract
The onset of plant flowering is one of many factors affected by climate
change. This has important consequences for ecosystems, where plants and
pollinators are at risk of a temporal mismatch. This also has
implications for crops. The timing of their highest-sensitivity window
is affected, despite some control exerted by agricultural management.
Current efforts to monitor the onset of flowering rest on numerous but
sparse ground observations, or on proxies like temperature models or
vegetation indices. In crop studies, a time-invariant harvesting
calendar is most widely used to infer the flowering period for crops. We
use spectral data from satellite imagery, combined with convolutional
neural networks, to create a large-scale, high-resolution proxy for the
timing of flowering. We exploit a transfer learning method to overcome
the sparsity of ground truth data on plant phenology. We first train a
temporal convolutional neural network to predict a temperature-based
proxy for flowering (the First Bloom Index from the National Phenology
Network), using as input the 8-day composite from MODIS at a 500m
resolution. This model learns relevant temporal patterns on both short
and long time scales within a year, thanks to a dilated convolution
structure. We then fine-tune the parameters from the last fully
connected layer using ground observations from the National Phenology
Network as training data. The root mean squared error of our model is
about 8.6 days, though this average hides much spatial heterogeneity: in
many places, the model performs well-enough to capture year-to-year
variations, with a prediction within a couple days of the target, while
it performs extremely poorly in a few places. Our model outperforms the
temperature-based proxy since the latter has a root mean squared error
of about 9.3 days on the same testing data. More importantly, our model
extrapolates much better over space: it has a root mean squared error of
about 12 days when predicting outside of our study region, compared to a
35-day error for the temperature-based model. This is a key feature,
since our goal is to fill in the spatial gaps left by the sparse ground
truth observations. These large-scale predictions of annual flowering
times could offer insights into plant-pollinator desynchronization and
crop calendar variation under climate change, and could be used for
further applications like studying the health impacts of shifts in
spring flowering times.