- 著者
- Ryo Harada Keitaro Kume Kazumasa Horie Takuro Nakayama Yuji Inagaki Toshiyuki Amagasa
- 出版者
- Information Processing Society of Japan
- 雑誌
- IPSJ Transactions on Bioinformatics (ISSN:18826679)
- 巻号頁・発行日
- vol.16, pp.20-27, 2023 (Released:2023-07-25)
- 参考文献数
- 48
Eukaryotic genomes contain exons and introns, and it is necessary to accurately identify exon-intron boundaries, i.e., splice sites, to annotate genomes. To address this problem, many previous works have proposed annotation methods/tools based on RNA-seq evidence. Many recent works exploit neural networks (NNs) as their prediction models, but only a few can be used to generate new genome annotation in practice. In this study, we propose AtLASS, a fully automated method for predicting splice sites from genomic and RNA-seq data using attention-based Bi-LSTM (Bidirectional Long Short-Term Memory). We exploit two-stage training on RNA-seq data to address the problem of biased label problem, thereby reducing the false positives. The experiments on the genomes of three species show that the performance of the proposed method itself is comparable to that of existing methods, but we can achieve better performance by combining the outputs of the proposed method and the existing method. The proposed method is the first program specialized in end-to-end splice site prediction using NNs.
- 著者
- Keisuke MlKI Mari MlKl Yoichi NAKAMURA Yoshihiro SUZUKI Yoshio OKANO Fumitaka OGUSHI Yuji OHTSUKI Takuro NAKAYAMA
- 出版者
- The Japanese Society of Internal Medicine
- 雑誌
- Internal Medicine (ISSN:09182918)
- 巻号頁・発行日
- vol.42, no.9, pp.839-845, 2003 (Released:2006-03-27)
- 参考文献数
- 29
- 被引用文献数
- 13 19
Although cigarette smoking is a recognized cause of acute eosinophilic pneumonia (AEP), and an increase in eosinophils in the lung is a common occurrence in AEP, early-phase neutrophilia in AEP is not well understood. We describe three cases of cigarette smoke (menthol type)-induced AEP with neutrophilia in the lungs or blood. Increased in-vitro production of the neutrophil chemoattractant interleukin (IL)-8 by human bronchial epithelial cells (HBECs) was correlated with neutrophilia. We suggest that IL-8 released from HBECs is involved in neutrophilia in the lung in AEP, and is newly recognized as an important factor in the early phase of AEP development.(Internal Medicine 42: 839-845, 2003)