Network representation learning: from preprocessing, feature extraction to node embedding

J Zhou, L Liu, W Wei, J Fan - ACM Computing Surveys (CSUR), 2022‏ - dl.acm.org
Network representation learning (NRL) advances the conventional graph mining of social
networks, knowledge graphs, and complex biomedical and physics information networks …

Biomedical knowledge graph learning for drug repurposing by extending guilt-by-association to multiple layers

D Bang, S Lim, S Lee, S Kim - Nature Communications, 2023‏ - nature.com
Computational drug repurposing aims to identify new indications for existing drugs by
utilizing high-throughput data, often in the form of biomedical knowledge graphs. However …

Subgraph neural networks

E Alsentzer, S Finlayson, M Li… - Advances in Neural …, 2020‏ - proceedings.neurips.cc
Deep learning methods for graphs achieve remarkable performance on many node-level
and graph-level prediction tasks. However, despite the proliferation of the methods and their …

Knowledge-based biomedical data science

TJ Callahan, IJ Tripodi… - Annual review of …, 2020‏ - annualreviews.org
Knowledge-based biomedical data science involves the design and implementation of
computer systems that act as if they knew about biomedicine. Such systems depend on …

A survey of the recent trends in deep learning for literature based discovery in the biomedical domain

E Cesario, C Comito, E Zumpano - Neurocomputing, 2024‏ - Elsevier
Every day, enormous amounts of biomedical texts discussing various biomedical topics are
produced. Revealing strong semantic connections hidden in those unstructured data is …

Large language model-based natural language encoding could be all you need for drug biomedical association prediction

H Zhang, Y Zhou, Z Zhang, H Sun, Z Pan… - Analytical …, 2024‏ - ACS Publications
Analyzing drug-related interactions in the field of biomedicine has been a critical aspect of
drug discovery and development. While various artificial intelligence (AI)-based tools have …

IPCARF: improving lncRNA-disease association prediction using incremental principal component analysis feature selection and a random forest classifier

R Zhu, Y Wang, JX Liu, LY Dai - BMC bioinformatics, 2021‏ - Springer
Background Identifying lncRNA-disease associations not only helps to better comprehend
the underlying mechanisms of various human diseases at the lncRNA level but also speeds …

[HTML][HTML] Understanding drug repurposing from the perspective of biomedical entities and their evolution: Bibliographic research using aspirin

X Li, JF Rousseau, Y Ding, M Song… - JMIR medical …, 2020‏ - medinform.jmir.org
Background Drug development is still a costly and time-consuming process with a low rate
of success. Drug repurposing (DR) has attracted significant attention because of its …

DECAB-LSTM: Deep Contextualized Attentional Bidirectional LSTM for cancer hallmark classification

L Jiang, X Sun, F Mercaldo, A Santone - Knowledge-Based Systems, 2020‏ - Elsevier
The great number of online scientific publications on cancer research makes large scale
data mining possible. The hallmarks or characteristics of cancer can be used to distinguish …

AGATHA: automatic graph mining and transformer based hypothesis generation approach

J Sybrandt, I Tyagin, M Shtutman, I Safro - Proceedings of the 29th ACM …, 2020‏ - dl.acm.org
Medical research is risky and expensive. Drug discovery requires researchers to efficiently
winnow thousands of potential targets to a small candidate set. However, scientists spend …