Search

Recently, the superiority of Transformer for long-term time series forecasting (LTSF) tasks has been challenged, particularly since recent work has shown that simple models can outperform numerous Transformer-based approaches. This suggests that a notable gap remains in fully leveraging the potential of Transformer in LTSF tasks. Consequently, this study investigates key issues when applying Transformer to LTSF, encompassing aspects of temporal continuity, information density, and multi-channel relationships. We introduce the Placeholder-enhanced Technique (PET) to enhance the computational efficiency and predictive accuracy of Transformer in LTSF tasks. Furthermore, we delve into the impact of larger patch strategies and channel interaction strategies on Transformer's performance, specifically Long Sub-sequence Division (LSD) and Multi-channel Separation and Interaction (MSI). These strategies collectively constitute a novel model termed PETformer. Extensive experiments have demonstrated that PETformer achieves state-of-the-art performance on eight commonly used public datasets for LTSF, surpassing all existing models. The insights and enhancement methodologies presented in this paper serve as valuable reference points and sources of inspiration for future research endeavors.

Motivation: Post-database searching is a key procedure in peptide dentification with tandem mass spectrometry (MS/MS) strategies for refining peptide-spectrum matches (PSMs) generated by database search engines. Although many statistical and machine learning-based methods have been developed to improve the accuracy of peptide identification, the challenge remains on large-scale datasets and datasets with an extremely large proportion of false positives (hard datasets). A more efficient learning strategy is required for improving the performance of peptide identification on challenging datasets. Results: In this work, we present an online learning method to conquer the challenges remained for exiting peptide identification algorithms. We propose a cost-sensitive learning model by using different loss functions for decoy and target PSMs respectively. A larger penalty for wrongly selecting decoy PSMs than that for target PSMs, and thus the new model can reduce its false discovery rate on hard datasets. Also, we design an online learning algorithm, OLCS-Ranker, to solve the proposed learning model. Rather than taking all training data samples all at once, OLCS-Ranker iteratively feeds in only one training sample into the learning model at each round. As a result, the memory requirement is significantly reduced for large-scale problems. Experimental studies show that OLCS-Ranker outperforms benchmark methods, such as CRanker and Batch-CS-Ranker, in terms of accuracy and stability. Furthermore, OLCS-Ranker is 15--85 times faster than CRanker method on large datasets. Availability and implementation: OLCS-Ranker software is available at no charge for non-commercial use at https://github.com/Isaac-QiXing/CRanker., Comment: 16 pages, 3 figures