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.