Sequential Labelling and DNABERT For Splice Site Prediction in Homo Sapiens DNA

TL;DR

This paper introduces a sequential labelling approach using DNABERT-3 for splice site prediction in human DNA, aiming to identify intron and exon regions regardless of their position, but faces challenges with overfitting.

Contribution

It proposes a novel sequential labelling method with pretrained DNABERT-3 for splice site detection, addressing limitations of fixed-position models.

Findings

High F1 scores on validation data.

Poor test performance due to overfitting.

Model not suitable for practical splice site prediction.

Abstract

Genome sequencing technology has improved significantly in few last years and resulted in abundance genetic data. Artificial intelligence has been employed to analyze genetic data in response to its sheer size and variability. Gene prediction on single DNA has been conducted using various deep learning architectures to discover splice sites and therefore discover intron and exon region. Recent predictions are carried out with models trained on sequence with fixed splice site location which eliminates possibility of multiple splice sites existence in single sequence. This paper proposes sequential labelling to predict splice sites regardless their position in sequence. Sequential labelling is carried out on DNA to determine intron and exon region and thus discover splice sites. Sequential labelling models used are based on pretrained DNABERT-3 which has been trained on human genome. Both fine-tuning and feature-based approach are tested. Proposed model is benchmarked against latest sequential labelling model designed for mutation type and location prediction. While achieving high F1 scores on validation data, both baseline and proposed model perform poorly on test data. Error and test results analysis reveal that model experience overfitting and therefore, model is deemed not suitable for splice site prediction.