Forecasting is a big problem

Rapid progress

Actual v. predicted distances of Atlantic cyclones

General, overlapping approaches

Machine learning

Statistical models

Nonlinear forecasting

"Mechanistic" modeling

DREAM challenges

Inference of gene regulatory networks

from knockout, observational, and synthetic data

Compete Lasso, random forests, Bayesian networks, mutual information, ANOVA, etc.

Ecological niche modeling

An artificial neural network that included microbial interactions performed best.

Nonlinear forecasting

Reconstruct attractor ("library") from time series

Use attractor to make short-term predictions

Forecasting communities

Dynamics may be chaotic

Predictions with chaos: short shelf life

Trajectories in chaotic attractors diverge

$$ \lvert \delta \textbf{Z}(t)\rvert \approx e^{\lambda t}\lvert\delta\textbf{Z}_0\rvert$$

$\lambda$ is the Lyapunov exponent

(so with chaos, $\lambda>0$)

How to forecast

  • Choose an embedding dimension $E$ and lag $\tau$
  • Each point in $E$-dimensional space: $\{x_t,x_{t-\tau},x_{t-2\tau},...,x_{t-(E-1)\tau}\}$
  • Construct these points from the time series
  • Define a point to predict ("predictee")
  • See where predictee's $E+1$ nearest neighbors wind up $t$ steps into the future
  • Measure correlations $\rho$ between predictee's observed future state and neighbors' weighted predictions

Choosing $E$ and $\tau$

An unsolved problem

Use $E$ (and $\tau$) that yield best predictions

Observational noise v. chaos

Predicting flu

Epidemic sizes negatively correlated

Predict based on cumulative incidence

where $I(s)$ is the incidence in week $s$, $h$ is a strain-specific incidence threshold, $T$ is the time of crossing $h$, and $Y$ is the strain's whole-season cumulative incidence proxy.

Predictions v. observations (H3N2)

Predicting flu in Hong King

Aim: Predict peak timing and magnitude

Mechanistic model and particle filter

Achieves 37% accuracy with 1-3 week lead, ~50% at 0 week lead

Epidemic Prediction Initiative

Forecasting SARS-CoV-2

Unusual error

A statistical model

Some precedent: Farr's Law

(U.S.) COVID-19 Forecast Hub

Comparing models

Evaluating performance

Forecasting flu evolution

Vaccine strain selection timeline

Seek to explain change in clade frequencies over 1 year

Fitness models can project clade frequencies

Clade frequencies $X$ derive from the fitnesses $f$ and frequencies $x$ of constituent viruses, such that

$$\hat{X}_v(t+\Delta t) = \sum_{i:v} x_i(t) \, \mathrm{exp}(f_i \, \Delta t)$$

This captures clonal interference between competing lineages

Clonal interference

Predictive fitness models

A simple predictive model estimates the fitness $f$ of virus $i$ as

$$\hat{f}_i = \beta^\mathrm{ep} \, f_i^\mathrm{ep} + \beta^\mathrm{ne} \, f_i^\mathrm{ne}$$

where $f_i^\mathrm{ep}$ measures cross-immunity via substitutions at epitope sites and $f_i^\mathrm{ne}$ measures mutational load via substitutions at non-epitope sites

Model selection


Emergence and spread of SARS-CoV-2 variant viruses

Emergence and spread of SARS-CoV-2 variant viruses

Logistic growth

Exponential growth of fitter variant appears as logistic growth in frequency space

Logistic regression: $$p(x) = \frac{1}{1 + e^{-(\beta_0 + \beta_1 x)}}$$

Multinomial logistic regression fit

What other models would you test?

What limits prediction with other pathogens?