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Table 4 Strengths and weaknesses of the approaches

From: Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships

  Strength Weakness
Association • Fast in implementation
• No need to pre-determine parameters
•Results can be easily validated by hand calculation
• Unsatisfactory in predictive power
•Does not consider the structures all relevant protein-module associations as a whole
•Do not have control for possible over-prediction of associations between frequently occurring domain-disease pairs
MLE • Good in predictive power
•Fast in implementation
•Take into account the structures all relevant protein-module associations as a whole
• Need to pre-determine parameters
•Do not have control for possible over-prediction of associations between frequently occurring domain-disease pairs
DPEA • Satisfactory in predictive power
•No need to pre-determine parameters
•Have control for possible over-prediction of associations between frequently occurring domain-disease pairs
• Slow in implementation when the number of candidate domain-disease associations is large
Bayesian • Excellent in predictive power
•Take into account the structures all relevant protein-module associations as a whole
• Slow in implementation when the number of candidate domain-disease associations is large
•Do not have control for possible over-prediction of associations between frequently occurring domain-disease pairs
•Failure when the log-concave conditions of parameters are not satisfied
PE • Satisfactory in predictive power
•Only one pre-determined parameter
•Have control for possible over-prediction of associations between frequently occurring domain-disease pairs
• Slow in implementation when the number of candidate domain-disease associations is large