Hierarchical classification of transposable elements and protein functions making ...
| Grant number: | 17/19264-9 |
| Support type: | Scholarships abroad - Research Internship - Master's degree |
| Effective date (Start): | November 01, 2017 |
| Effective date (End): | April 30, 2018 |
| Field of knowledge: | Physical Sciences and Mathematics - Computer Science |
| Principal Investigator: | Ricardo Cerri |
| Grantee: | Felipe Kenji Nakano |
| Supervisor abroad: | Celine Vens |
| Home Institution: | Centro de Ciências Exatas e de Tecnologia (CCET). Universidade Federal de São Carlos (UFSCAR). São Carlos , SP, Brazil |
| Local de pesquisa : | University of Leuven, Kulak Kortrijk (KU Leuven), Belgium |
| Associated to the scholarship: | 16/12489-2 - Deep learning for hierarchical classification of transposable elements, BP.MS |
Abstract Tranposable Elements (TEs) are DNA sequences capable of moving within a cell's genome. Such movement causes genetic variability, and changes in gene's functionality. Usually TEs classification is performed using homology tools. Homology tries to find similar sequences by matching then in a string like fashion, however, such method ignores many biochemical and hierarchical properties. Nonetheless, recently, TEs were proposed as Machine Learning (ML) classification problem. More specifically, TEs are classified using Hierarchical Classification(HC) methods. Differently from traditional classification, HC addresses problems whose classes are structured in a hierarchy. Such methods have proved to be more efficient and feasible than homology, however ML methods require labelled data. TEs' labelling is not an easytask. Repbase, the most academic received TEs repository, employs massive validation andmultiple tools for TEs classification. This process is computationally and financially demanding, resulting in plenty of unlabelled sequences. As a countermeasure, the field of Active Learning (AL) provides methods for using unlabelled data. Basically, an AL algorithm employs strategies that select the most valuable unlabelled data to be labelled. Hence the cost of labelling the data is reduced, and classifiers are likely to learn from the most representative instances. In this research, we plan to investigate AL algorithms for HC, in special, we will merge AL into the state-of-art method for HC, Clus-HMC. | |