1,590 research outputs found
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
A Comprehensive Survey on Deep Graph Representation Learning
Graph representation learning aims to effectively encode high-dimensional
sparse graph-structured data into low-dimensional dense vectors, which is a
fundamental task that has been widely studied in a range of fields, including
machine learning and data mining. Classic graph embedding methods follow the
basic idea that the embedding vectors of interconnected nodes in the graph can
still maintain a relatively close distance, thereby preserving the structural
information between the nodes in the graph. However, this is sub-optimal due
to: (i) traditional methods have limited model capacity which limits the
learning performance; (ii) existing techniques typically rely on unsupervised
learning strategies and fail to couple with the latest learning paradigms;
(iii) representation learning and downstream tasks are dependent on each other
which should be jointly enhanced. With the remarkable success of deep learning,
deep graph representation learning has shown great potential and advantages
over shallow (traditional) methods, there exist a large number of deep graph
representation learning techniques have been proposed in the past decade,
especially graph neural networks. In this survey, we conduct a comprehensive
survey on current deep graph representation learning algorithms by proposing a
new taxonomy of existing state-of-the-art literature. Specifically, we
systematically summarize the essential components of graph representation
learning and categorize existing approaches by the ways of graph neural network
architectures and the most recent advanced learning paradigms. Moreover, this
survey also provides the practical and promising applications of deep graph
representation learning. Last but not least, we state new perspectives and
suggest challenging directions which deserve further investigations in the
future
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