TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants.
IEEE/ACM Trans Comput Biol Bioinform
; 21(3): 472-479, 2024.
Article
en En
| MEDLINE
| ID: mdl-38451770
ABSTRACT
Genome-wide association studies have shown that common genetic variants associated with complex diseases are mostly located in non-coding regions, which may not be causal. In addition, the limited number of validated non-coding functional variants makes it difficult to develop an effective supervised learning model. Therefore, improving the accuracy of predicting non-coding causal variants has become critical. This study aims to build a transfer learning-based machine learning method for predicting regulatory variants to overcome the problem of limited sample size. This paper presents a supervised learning method transfer support vector machine (TSVM) for massively parallel reporter assays (MPRA) validated regulatory variants prediction. First, uses a convolutional neural network to extract features with transfer learning. Second, the extracted features are selected by random forest method. Third, the selected features are used to train support vector machine for classification. We performed scale sensitivity experiments on the MPRA dataset and validated the effectiveness of transfer learning. The model achieves the Mcc of 0.326 and the AUC of 0.720, which are higher than the state-of-the-art method.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Biología Computacional
/
Máquina de Vectores de Soporte
Límite:
Humans
Idioma:
En
Revista:
ACM Trans Comput Biol Bioinform
Asunto de la revista:
BIOLOGIA
/
INFORMATICA MEDICA
Año:
2024
Tipo del documento:
Article
Pais de publicación:
Estados Unidos