Methods, systems, and apparatus, including computer programs encoded on computer storage media, for molecular content analysis. One of the methods includes receiving molecular content data that indicates a molecular content of a portion of a batch of sludge; determining, by a machine learning module included in the system using the molecular content data and multiple parameters, a predicted value for a property of the portion of the batch of sludge; and providing the predicted value for the property of the portion of the batch of sludge.