Single Sequence Based Feature Engineering for Convolutional Neural Networks Towards RNA Contact Map Prediction

Loading...
Thumbnail Image
File version

Accepted Manuscript (AM)

Author(s)
Rashid, MA
Paliwal, KK
Griffith University Author(s)
Primary Supervisor
Other Supervisors
Editor(s)
Date
2023
Size
File type(s)
Location

Nadi, Fiji

License
Abstract

Features are crucial for deep learning models as they help understand complex data, learn patterns, and make accurate predictions. Feature engineering can sometimes be computationally expensive, but it can speed up the training and inference phases of the deep learning models. By providing a more concise and informative representation, it reduces the number of parameters and computations required in the down-stream operations. Well-chosen features can enhance a model's ability to represent data in a structured and meaningful way. They help learn hierarchical dependencies in data, reduce the dimensionality of the input data, and generalize from the training data to unseen data to make the model robust. In this work, we present a self-supervised learning model for feature generation from RNA sequences towards applying in deep learning models for RNA contact map prediction. We test the efficacy of our extracted features by comparing the prediction performance with the prediction performance obtained by the features extracted using the state-of-the-art language foundation model, RNA-FM. We found our approach promising.

Journal Title
Conference Title

2023 IEEE Asia-Pacific Conference on Computer Science and Data Engineering (CSDE)

Book Title
Edition
Volume
Issue
Thesis Type
Degree Program
School
Publisher link
Patent number
Funder(s)
Grant identifier(s)
Rights Statement
Rights Statement

This work is covered by copyright. You must assume that re-use is limited to personal use and that permission from the copyright owner must be obtained for all other uses. If the document is available under a specified licence, refer to the licence for details of permitted re-use. If you believe that this work infringes copyright please make a copyright takedown request using the form at https://www.griffith.edu.au/copyright-matters.

Item Access Status
Note
Access the data
Related item(s)
Subject

Biomedical and clinical sciences

Neural networks

Deep learning

Data management and data science

Genetics

Persistent link to this record
Citation

Rashid, MA; Paliwal, KK, Single Sequence Based Feature Engineering for Convolutional Neural Networks Towards RNA Contact Map Prediction, 2023 IEEE Asia-Pacific Conference on Computer Science and Data Engineering (CSDE), 2023