Choosing a Model for 5′UTR Translation Experiments: Cheap Features, a Small CNN or Frozen UTR-LM
With related sequences kept out of training, a small CNN reduced mean ribosome load MSE by +0.216 [+0.176, +0.252] MRL² against a cheap ridge baseline. For picking the top 1% of 15,004 test sequences the difference was not supported (+0.020 [−0.088, +0.132]). As CNN input, frozen UTR-LM features gave no supported gain over one-hot input on the grouped split and no gain above the practical threshold on either split. One unreplicated assay, about 70,000 training labels, exploratory.
