Abstract: Genome-wide association studies may allow for detection of variants that are statistically significantly associated with disease risk. However, inferring which are the genes underlying these variant associations may be difficult. The presently disclosed approaches utilize machine learning techniques to predict genes from genome-wide association study summary statistics that substantially improves causal gene identification in terms of both precision and recall compared to other techniques.

Abstract: The technology disclosed relates to a deep learning network system for evolutionary conservation prediction. In one implementation, the system includes a first model for processing a first multiple sequence alignment that aligns a query sequence with a masked base at a target position to N non-query sequences and predicting a first identity of the masked base at the target position. The system also includes a second model for processing a second multiple sequence alignment that aligns the query sequence to M non-query sequences, where M>N, and predicting a second identity of the masked base at the target position. The system further includes an evolutionary conservation determination logic configured to measure an evolutionary conservation of the masked base at the target position based on the first and second identities of the masked base.

Abstract: Described herein are systems and techniques for identifying polypeptides using data collected by a protein sequencing device. The protein sequencing device may collect data obtained from detected light emissions by luminescent labels during binding interactions of reagents with amino acids of the polypeptide. The light emissions may result from application of excitation energy to the luminescent labels. The device may provide the data as input to a trained machine learning model to obtain output that may be used to identify the polypeptide. The output may indicate, for each of a plurality of locations in the polypeptide, one or more likelihoods that one or more respective amino acids is present at the location. The output may be matched to an amino acid sequence that specifies a protein.