Saliency as Pseudo-Pixel Supervision for Weakly and Semi-Supervised Semantic Segmentation.

Existing studies on semantic segmentation using image-level weak supervision have several limitations, including sparse object coverage, inaccurate object boundaries, and co-occurring pixels from non-target objects. To overcome these challenges, we propose a novel framework, an improved version of Explicit Pseudo-pixel Supervision (EPS++), which learns from pixel-level feedback by combining two types of weak supervision. Specifically, the image-level label provides the object identity via the localization map, and the saliency map from an off-the-shelf saliency detection model offers rich object boundaries. We devise a joint training strategy to fully utilize the complementary relationship between disparate information. Notably, we suggest an Inconsistent Region Drop (IRD) strategy, which effectively handles errors in saliency maps using fewer hyper-parameters than EPS. Our method can obtain accurate object boundaries and discard co-occurring pixels, significantly improving the quality of pseudo-masks. Experimental results show that EPS++ effectively resolves the key challenges of semantic segmentation using weak supervision, resulting in new state-of-the-art performances on three benchmark datasets in a weakly supervised semantic segmentation setting. Furthermore, we show that the proposed method can be extended to solve the semi-supervised semantic segmentation problem using image-level weak supervision. Surprisingly, the proposed model also achieves new state-of-the-art performances on two popular benchmark datasets.

DeepTESR: A Deep Learning Framework to Predict the Degree of Translational Elongation Short Ramp for Gene Expression Control.

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 R2 of 0.627, superior to the conventional machine learning models (e.g., MAE of 0.335 and R2 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.