Patent ID: 11929152
Assignee: AMAZON TECHNOLOGIES, INC.
Field: Computer technology (Electrical engineering)
Classification: CPC G | IPC G

Claim 12:
13. A system comprising:
a first one or more electronic devices including one or more processors and memory storing instructions that upon execution by the one or more processors cause the first one or more electronic devices to:
receive a request to predict a pair of an enzyme primary sequence and a substrate, and an interaction probability for the pair;
generate a substrate vector by:
decomposing the substrate into a 2-D connection matrix with 1-D embeddings for each node of the 2-D connection matrix;
tiling the 1-D embeddings to form 2-D representations for each node of the 2-D connection matrix;
stacking the 2-D connection matrix with the 2-D representations and upsampling, thereby generating a 2-D upsampled stack; and
convolving the 2-D upsampled stack to generate the substrate vector;

combine an enzyme vector, the substrate vector, and an interaction indication for the enzyme and substrate to form a machine learning (ML) model input;
receive, by a multi-headed self-attention ML model executed by the one or more processors, the ML model input;
predict, using the multi-headed self-attention ML model based at least on the ML model input, the pair of an enzyme primary sequence and a substrate, and an interaction probability for the pair; and
output, by the multi-headed self-attention ML model, a result of the predicting using the multi-headed self-attention ML model, the result including the pair of an enzyme primary sequence and a substrate, and an interaction probability for the pair; and

a second one or more electronic devices including one or more processors and memory storing instructions that upon execution by the one or more processors cause the second one or more electronic devices to generate a 3-D representation of an enzyme based on the result.