Abstract Motivation Alternative splicing generates multiple isoforms from a single gene, greatly increasing the functional diversity of a genome. Although gene functions have been well studied, little is known about the specific functions of isoforms, making accurate prediction of isoform functions highly desirable. However, the existing approaches to predicting isoform functions are far from satisfactory due to at least two reasons: (i) unlike genes, isoform-level functional annotations are scarce. (ii) The information of isoform functions is concealed in various types of data including isoform sequences, co-expression relationship among isoforms, etc. Results In this study, we present a novel approach, DIFFUSEmore »
This content will become publicly available on April 1, 2023
Structure Meets Sequences: Predicting Network of Co-evolving Sequences
Co-evolving sequences are ubiquitous in a variety of applications, where different sequences are often inherently inter-connected with each other. We refer to such sequences, together with their inherent connections modeled as a structured network, as network of co-evolving sequences (NoCES). Typical NoCES applications in- clude road traffic monitoring, company revenue prediction, motion capture, etc. To date, it remains a daunting challenge to accurately model NoCES due to the coupling between network structure and sequences. In this paper, we propose to modeling NoCES with the aim of simultaneously capturing both the dynamics and the inter- play between network structure and sequences. Specifically, we propose a joint learning framework to alternatively update the network representations and sequence representations as the se- quences evolve over time. A unique feature of our framework lies in that it can deal with the case when there are co-evolving sequences on both network nodes and edges. Experimental evaluations on four real datasets demonstrate that the proposed approach (1) out- performs the existing competitors in terms of prediction accuracy, and (2) scales linearly w.r.t. the sequence length and the network size.
- Publication Date:
- NSF-PAR ID:
- 10332503
- Journal Name:
- WSDM
- Page Range or eLocation-ID:
- 1090 to 1098
- Sponsoring Org:
- National Science Foundation
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