Adam J. Riesselman

Adam J Riesselman, Evan M Cofer, Therese LaRue et al.

Quantifying organism-level phenotypes, such as growth dynamics and biomass accumulation, is fundamental to understanding agronomic traits and optimizing crop production. However, quality growing data of plants at scale is difficult to generate. Here we use a mobile robotic platform to capture high-resolution environmental sensing and phenotyping measurements of a large-scale hydroponic leafy greens system. We describe a self-supervised modeling approach to build a map from observed growing data to the entire plant growth trajectory. We demonstrate our approach by forecasting future plant height and harvest mass of crops in this system. This approach represents a significant advance in combining robotic automation and machine learning, as well as providing actionable insights for agronomic research and operational efficiency.

Adam J. Riesselman, John B. Ingraham, Debora S. Marks

The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects. While recent models have relaxed this constraint to also account for pairwise interactions, these approaches do not provide a tractable path towards modeling higher-order dependencies. Here, we show how latent variable models with nonlinear dependencies can be applied to capture beyond-pairwise constraints in biomolecules. We present a new probabilistic model for sequence families, DeepSequence, that can predict the effects of mutations across a variety of deep mutational scanning experiments significantly better than site independent or pairwise models that are based on the same evolutionary data. The model, learned in an unsupervised manner solely from sequence information, is grounded with biologically motivated priors, reveals latent organization of sequence families, and can be used to extrapolate to new parts of sequence space