Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots

. 2022 Nov 18;13(11):2155. doi: 10.3390/genes13112155

Algorithm 1 The stochastic subgradient descent algorithm for structured support vector machines (SSVMs);

η > 0

is the predefined learning rate.

1:
initialize $λ_{k}$ for all $λ_{k} \in λ$
2:
repeat
3:
for all $(x, y) \in D$ do
4:
$\hat{y} \leftarrow arg {max}_{\hat{y}} [f (x, \hat{y}) + Δ (y, \hat{y})]$
5:
for all $λ_{k} \in λ$ do
6:
$λ_{k} \leftarrow λ_{k} - η (γ + 1) \sum_{i < j} \frac{\partial p_{i j}}{\partial λ_{k}} ({\hat{y}}_{i j} - y_{i j})$
7:
end for
8:
end for
9:
until all the parameters converge