Decoding Translation-Related Functional Sequences in 5'UTRs Using Interpretable Deep Learning Models

Understanding how 5' untranslated regions (5'UTRs) regulate mRNA translation is critical for controlling protein expression and designing effective therapeutic mRNAs. While recent deep learning models have shown promise in predicting translational efficiency from 5'UTR sequences, most are constrained by fixed input lengths and limited interpretability. We introduce UTR-STCNet, a Transformer-based architecture for flexible and biologically grounded modeling of variable-length 5'UTRs. UTR-STCNet integrates a Saliency-Aware Token Clustering (SATC) module that iteratively aggregates nucleotide tokens into multi-scale, semantically meaningful units based on saliency scores. A Saliency-Guided Transformer (SGT) block then captures both local and distal regulatory dependencies using a lightweight attention mechanism. This combined architecture achieves efficient and interpretable modeling without input truncation or increased computational cost. Evaluated across three benchmark datasets, UTR-STCNet consistently outperforms state-of-the-art baselines in predicting mean ribosome load (MRL), a key proxy for translational efficiency. Moreover, the model recovers known functional elements such as upstream AUGs and Kozak motifs, highlighting its potential for mechanistic insight into translation regulation.

WMFormer++: Nested Transformer for Visible Watermark Removal via Implict Joint Learning

Watermarking serves as a widely adopted approach to safeguard media copyright. In parallel, the research focus has extended to watermark removal techniques, offering an adversarial means to enhance watermark robustness and foster advancements in the watermarking field. Existing watermark removal methods mainly rely on UNet with task-specific decoder branches--one for watermark localization and the other for background image restoration. However, watermark localization and background restoration are not isolated tasks; precise watermark localization inherently implies regions necessitating restoration, and the background restoration process contributes to more accurate watermark localization. To holistically integrate information from both branches, we introduce an implicit joint learning paradigm. This empowers the network to autonomously navigate the flow of information between implicit branches through a gate mechanism. Furthermore, we employ cross-channel attention to facilitate local detail restoration and holistic structural comprehension, while harnessing nested structures to integrate multi-scale information. Extensive experiments are conducted on various challenging benchmarks to validate the effectiveness of our proposed method. The results demonstrate our approach's remarkable superiority, surpassing existing state-of-the-art methods by a large margin.

Benchmarking optimality of time series classification methods in distinguishing diffusions

Performance benchmarking is a crucial component of time series classification (TSC) algorithm design, and a fast-growing number of datasets have been established for empirical benchmarking. However, the empirical benchmarks are costly and do not guarantee statistical optimality. This study proposes to benchmark the optimality of TSC algorithms in distinguishing diffusion processes by the likelihood ratio test (LRT). The LRT is optimal in the sense of the Neyman-Pearson lemma: it has the smallest false positive rate among classifiers with a controlled level of false negative rate. The LRT requires the likelihood ratio of the time series to be computable. The diffusion processes from stochastic differential equations provide such time series and are flexible in design for generating linear or nonlinear time series. We demonstrate the benchmarking with three scalable state-of-the-art TSC algorithms: random forest, ResNet, and ROCKET. Test results show that they can achieve LRT optimality for univariate time series and multivariate Gaussian processes. However, these model-agnostic algorithms are suboptimal in classifying nonlinear multivariate time series from high-dimensional stochastic interacting particle systems. Additionally, the LRT benchmark provides tools to analyze the dependence of classification accuracy on the time length, dimension, temporal sampling frequency, and randomness of the time series. Thus, the LRT with diffusion processes can systematically and efficiently benchmark the optimality of TSC algorithms and may guide their future improvements.