Instance-based processing Whenever possible, MolPipeline processes instances independently, achieving an effective parallelization and reduction memory usage. Before execution, we preprocess the computation graph of the MolPipeline and split it into parts where instances can be processed concurrently and parts that need synchronization. For example, the standardization procedure of molecules might comprise multiple subsequent steps, like salt removal, neutralizing charges, and selecting a canonical tautomer. This subsequent standardization process can be handled independently for each molecule, which allows for effective parallelization. In contrast, synchronization is required when applying column-wise standardization, like z-scaling, to a feature matrix, which can only be applied when the entire feature column is constructed. MolPipeline automatically detects when instances can be processed independently and when synchronization is required. In addition, instance-based processing reduces memory usage because memory-intensive intermediate results are only kept in memory as long as needed.