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We need to design the model that will predict likely degradation rates at each base of an RNA molecule, trained on a subset of an Eterna dataset comprising over 3000 RNA molecules (which span a panoply of sequences and structures) and their degradation rates at each position.
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I have experimented with multiple traditional models including Light GBM, Catboost, and BiLSTM, but the result was quite bad as compare to triple GRU layers. Using simple 3 Bidirectional GRU layer with linear activation. This model is quite simple and derived from xhlulu initial model.
https://deepnote.com/@abid/mRNA-Vaccine-Degradation-Prediction-ZbqWvkGcQXGU3-1fDqb-fQAre you sure you want to delete this access key?
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