Transfer Learning Allows Accurate RBP Target Site Prediction with Limited Sample Sizes
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F23%3A00131807" target="_blank" >RIV/00216224:14310/23:00131807 - isvavai.cz</a>
Result on the web
<a href="https://www.mdpi.com/2079-7737/12/10/1276" target="_blank" >https://www.mdpi.com/2079-7737/12/10/1276</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3390/biology12101276" target="_blank" >10.3390/biology12101276</a>
Alternative languages
Result language
angličtina
Original language name
Transfer Learning Allows Accurate RBP Target Site Prediction with Limited Sample Sizes
Original language description
RNA-binding proteins are vital regulators in numerous biological processes. Their disfunction can result in diverse diseases, such as cancer or neurodegenerative disorders, making the prediction of their binding sites of high importance. Deep learning (DL) has brought about a revolution in various biological domains, including the field of protein–RNA interactions. Nonetheless, several challenges persist, such as the limited availability of experimentally validated binding sites to train well-performing DL models for the majority of proteins. Here, we present a novel training approach based on transfer learning (TL) to address the issue of limited data. Employing a sophisticated and interpretable architecture, we compare the performance of our method trained using two distinct approaches: training from scratch (SCR) and utilizing TL. Additionally, we benchmark our results against the current state-of-the-art methods. Furthermore, we tackle the challenges associated with selecting appropriate input features and determining optimal interval sizes. Our results show that TL enhances model performance, particularly in datasets with minimal training data, where satisfactory results can be achieved with just a few hundred RNA binding sites. Moreover, we demonstrate that integrating both sequence and evolutionary conservation information leads to superior performance. Additionally, we showcase how incorporating an attention layer into the model facilitates the interpretation of predictions within a biologically relevant context.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
<a href="/en/project/EF18_053%2F0016952" target="_blank" >EF18_053/0016952: Postdoc2MUNI</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Biology
ISSN
2079-7737
e-ISSN
2079-7737
Volume of the periodical
12
Issue of the periodical within the volume
10
Country of publishing house
CH - SWITZERLAND
Number of pages
19
Pages from-to
1-19
UT code for WoS article
001090019100001
EID of the result in the Scopus database
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