Using the Gene Ontology Hierarchy when Predicting Gene Function

05/09/2012
by   Sara Mostafavi, et al.
0

The problem of multilabel classification when the labels are related through a hierarchical categorization scheme occurs in many application domains such as computational biology. For example, this problem arises naturally when trying to automatically assign gene function using a controlled vocabularies like Gene Ontology. However, most existing approaches for predicting gene functions solve independent classification problems to predict genes that are involved in a given function category, independently of the rest. Here, we propose two simple methods for incorporating information about the hierarchical nature of the categorization scheme. In the first method, we use information about a gene's previous annotation to set an initial prior on its label. In a second approach, we extend a graph-based semi-supervised learning algorithm for predicting gene function in a hierarchy. We show that we can efficiently solve this problem by solving a linear system of equations. We compare these approaches with a previous label reconciliation-based approach. Results show that using the hierarchy information directly, compared to using reconciliation methods, improves gene function prediction.

READ FULL TEXT
POST COMMENT

Comments

There are no comments yet.

Authors

page 1

page 2

page 3

page 4

11/05/2020

Mining Functionally Related Genes with Semi-Supervised Learning

The study of biological processes can greatly benefit from tools that au...
10/30/2017

Gene Ontology (GO) Prediction using Machine Learning Methods

We applied machine learning to predict whether a gene is involved in axo...
05/23/2018

Analysis of Novel Annotations in the Gene Ontology for Boosting the Selection of Negative Examples

Public repositories for genome and proteome annotations, such as the Gen...
03/25/2022

Feature extraction using Spectral Clustering for Gene Function Prediction

Gene annotation addresses the problem of predicting unknown associations...
07/22/2020

Angle-based hierarchical classification using exact label embedding

Hierarchical classification problems are commonly seen in practice. Howe...
06/24/2020

Multilabel Classification by Hierarchical Partitioning and Data-dependent Grouping

In modern multilabel classification problems, each data instance belongs...
07/19/2020

EPGAT: Gene Essentiality Prediction With Graph Attention Networks

The identification of essential genes/proteins is a critical step toward...
This week in AI

Get the week's most popular data science and artificial intelligence research sent straight to your inbox every Saturday.