Abstract: Disclosed herein are methods and systems for automatically generating processing rules to be used for automated decision-making when operating instruments to analyze and process biological samples (e.g., for the presence, absence, or concentration of analytes). For example, some automatically generated processing rules may set forth conditions and criteria in which some test results obtained from the biological samples can be automatically validated and sent out, while other test results are flagged for additional review. The processing rules can be generated based on patterns observed with the actions taken for historical test results associated with similar biological samples.