Abstract: Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for predicting labels for biological sequences. One of the methods includes, in response to receiving a request to identify labels associated with an input biological sequence: determining, for each of a plurality of candidate labels, a score characterizing a likelihood that the input biological sequence is associated with the candidate label. Each score is determined by identifying a plurality of positive biological sequences that are each associated with the candidate label; and processing a network input including the input biological sequence and the plurality of positive biological sequences using a neural network to generate the score characterizing the likelihood that the input biological sequence is associated with the candidate label. The method includes selecting one or more of the candidate labels as labels for the input biological sequence based on the scores.

Abstract: Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for predicting biological functions of proteins. In one aspect, a method comprises: obtaining data defining a sequence of amino acids in a protein; processing the data defining the sequence of amino acids in the protein using a neural network, wherein: the neural network is a convolutional neural network comprising one or more dilated convolutional layers; and the neural network is configured to process the data defining the sequence of amino acids in the protein in accordance with trained parameter values of the neural network to generate a neural network output characterizing at least one predicted biological function of the sequence of amino acids in the protein; and identifying the predicted biological function of the sequence of amino acids in the protein using the neural network output.

Abstract: Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for predicting biological functions of proteins. In one aspect, a method comprises: obtaining data defining a sequence of amino acids in a protein; processing the data defining the sequence of amino acids in the protein using a neural network, wherein: the neural network is a convolutional neural network comprising one or more dilated convolutional layers; and the neural network is configured to process the data defining the sequence of amino acids in the protein in accordance with trained parameter values of the neural network to generate a neural network output characterizing at least one predicted biological function of the sequence of amino acids in the protein; and identifying the predicted biological function of the sequence of amino acids in the protein using the neural network output.