What Viterbi Leaves Out - Viterbi Decoding of a CpG-Island HMM Step by Step

A decoded path is a model-based best path, not guaranteed biological truth.

highlighted = computed this step

The best path can hide ties

The final I and N cells are exactly equal at 81/2048. Viterbi returns the first tied state by state order, not every equally good path.

\text{tie value}=\frac{81}{2048}

The HMM is a model, not measured truth

Real CpG-island detection uses richer models over four nucleotides and dinucleotides. The probabilities are model parameters, and practical code uses log-probabilities to avoid underflow; exact fractions sidestep that here.

\text{decoded path} \ne \text{guaranteed biology}