379 research outputs found
A representation learning model based on variational inference and graph autoencoder for predicting lncRNA‑disease associations
Background: Numerous studies have demonstrated that long non-coding RNAs are related to plenty of human diseases. Therefore, it is crucial to predict potential lncRNAdisease associations for disease prognosis, diagnosis and therapy. Dozens of machine learning and deep learning algorithms have been adopted to this problem, yet it is still challenging to learn efficient low-dimensional representations from high-dimensional features of lncRNAs and diseases to predict unknown lncRNA-disease associations accurately. Results: We proposed an end-to-end model, VGAELDA, which integrates variational inference and graph autoencoders for lncRNA-disease associations prediction. VGAELDA contains two kinds of graph autoencoders. Variational graph autoencoders (VGAE) infer representations from features of lncRNAs and diseases respectively, while graph autoencoders propagate labels via known lncRNA-disease associations. These two kinds of autoencoders are trained alternately by adopting variational expectation maximization algorithm. The integration of both the VGAE for graph representation learning, and the alternate training via variational inference, strengthens the capability of VGAELDA to capture efficient low-dimensional representations from high-dimensional features, and hence promotes the robustness and preciseness for predicting unknown lncRNA-disease associations. Further analysis illuminates that the designed co-training framework of lncRNA and disease for VGAELDA solves a geometric matrix completion problem for capturing efficient low-dimensional representations via a deep learning approach. Conclusion: Cross validations and numerical experiments illustrate that VGAELDA outperforms the current state-of-the-art methods in lncRNA-disease association prediction. Case studies indicate that VGAELDA is capable of detecting potential lncRNAdisease associations. The source code and data are available at https:// github. com/ zhang labNKU/ VGAEL DA
Graph Representation Learning in Biomedicine
Biomedical networks are universal descriptors of systems of interacting
elements, from protein interactions to disease networks, all the way to
healthcare systems and scientific knowledge. With the remarkable success of
representation learning in providing powerful predictions and insights, we have
witnessed a rapid expansion of representation learning techniques into
modeling, analyzing, and learning with such networks. In this review, we put
forward an observation that long-standing principles of networks in biology and
medicine -- while often unspoken in machine learning research -- can provide
the conceptual grounding for representation learning, explain its current
successes and limitations, and inform future advances. We synthesize a spectrum
of algorithmic approaches that, at their core, leverage graph topology to embed
networks into compact vector spaces, and capture the breadth of ways in which
representation learning is proving useful. Areas of profound impact include
identifying variants underlying complex traits, disentangling behaviors of
single cells and their effects on health, assisting in diagnosis and treatment
of patients, and developing safe and effective medicines
Enhancing Deep Learning Models through Tensorization: A Comprehensive Survey and Framework
The burgeoning growth of public domain data and the increasing complexity of
deep learning model architectures have underscored the need for more efficient
data representation and analysis techniques. This paper is motivated by the
work of (Helal, 2023) and aims to present a comprehensive overview of
tensorization. This transformative approach bridges the gap between the
inherently multidimensional nature of data and the simplified 2-dimensional
matrices commonly used in linear algebra-based machine learning algorithms.
This paper explores the steps involved in tensorization, multidimensional data
sources, various multiway analysis methods employed, and the benefits of these
approaches. A small example of Blind Source Separation (BSS) is presented
comparing 2-dimensional algorithms and a multiway algorithm in Python. Results
indicate that multiway analysis is more expressive. Contrary to the intuition
of the dimensionality curse, utilising multidimensional datasets in their
native form and applying multiway analysis methods grounded in multilinear
algebra reveal a profound capacity to capture intricate interrelationships
among various dimensions while, surprisingly, reducing the number of model
parameters and accelerating processing. A survey of the multi-away analysis
methods and integration with various Deep Neural Networks models is presented
using case studies in different application domains.Comment: 34 pages, 8 figures, 4 table
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