Controlling translational elongation is essential for efficient protein synthesis. Ribosome profiling has revealed that the speed of ribosome movement is correlated with translational efficiency in the translational elongation ramp. In this work, we present a new deep learning model, called DeepTESR, to predict the degree of translational elongation short ramp (TESR) from mRNA sequence. The proposed deep learning model exhibited superior performance in predicting the TESR scores for 226 981 TESR sequences, resulting in the mean absolute error (MAE) of 0.285 and a coefficient of determination R 2 of 0.627, superior to the conventional machine learning models (e.g., MAE of 0.335 and R 2 of 0.571 for LightGBM). We experimentally validated that heterologous fluorescence expression of proteins with randomly selected TESR was moderately correlated with the predictions. Furthermore, a genome-wide analysis of TESR prediction in the 4305 coding sequences of Escherichia coli showed conserved TESRs over the clusters of orthologous groups. In this sense, DeepTESR can be used to predict the degree of TESR for gene expression control and to decipher the mechanism of translational control with ribosome profiling. DeepTESR is available at https://github.com/fmblab/DeepTESR.

When a person solves the multi-choice problem, she considers not only what is the answer but also what is not the answer. Knowing what choice is not the answer and utilizing the relationships between choices, she can improve the prediction accuracy. Inspired by this human reasoning process, we propose a new training strategy to fully utilize inter-class relationships, namely LogitMix. Our strategy is combined with recent data augmentation techniques, e.g., Mixup, Manifold Mixup, CutMix, and PuzzleMix. Then, we suggest using a mixed logit, i.e., a mixture of two logits, as an auxiliary training objective. Since the logit can preserve both positive and negative inter-class relationships, it can impose a network to learn the probability of wrong answers correctly. Our extensive experimental results on the image- and language-based tasks demonstrate that LogitMix achieves state-of-the-art performance among recent data augmentation techniques regarding calibration error and prediction accuracy.