DeepAI AI Chat
Log In Sign Up

Graph-in-Graph Network for Automatic Gene Ontology Description Generation

06/10/2022
by   Fenglin Liu, et al.
Tencent
Peking University
Yale University
University of Washington
0

Gene Ontology (GO) is the primary gene function knowledge base that enables computational tasks in biomedicine. The basic element of GO is a term, which includes a set of genes with the same function. Existing research efforts of GO mainly focus on predicting gene term associations. Other tasks, such as generating descriptions of new terms, are rarely pursued. In this paper, we propose a novel task: GO term description generation. This task aims to automatically generate a sentence that describes the function of a GO term belonging to one of the three categories, i.e., molecular function, biological process, and cellular component. To address this task, we propose a Graph-in-Graph network that can efficiently leverage the structural information of GO. The proposed network introduces a two-layer graph: the first layer is a graph of GO terms where each node is also a graph (gene graph). Such a Graph-in-Graph network can derive the biological functions of GO terms and generate proper descriptions. To validate the effectiveness of the proposed network, we build three large-scale benchmark datasets. By incorporating the proposed Graph-in-Graph network, the performances of seven different sequence-to-sequence models can be substantially boosted across all evaluation metrics, with up to 34.7 ROUGE-L, and METEOR, respectively.

READ FULL TEXT

page 1

page 2

page 3

page 4

05/09/2012

Using the Gene Ontology Hierarchy when Predicting Gene Function

The problem of multilabel classification when the labels are related thr...
06/03/2019

Incorporating Biological Knowledge with Factor Graph Neural Network for Interpretable Deep Learning

While deep learning has achieved great success in many fields, one commo...
05/21/2018

GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

Bioinformatics tools have been developed to interpret gene expression da...
09/01/2016

How Much is 131 Million Dollars? Putting Numbers in Perspective with Compositional Descriptions

How much is 131 million US dollars? To help readers put such numbers in ...
03/25/2022

Feature extraction using Spectral Clustering for Gene Function Prediction

Gene annotation addresses the problem of predicting unknown associations...
10/04/2020

Knowledge-Enhanced Personalized Review Generation with Capsule Graph Neural Network

Personalized review generation (PRG) aims to automatically produce revie...