32,023 research outputs found
Drug-therapy networks and the predictions of novel drug targets
Recently, a number of drug-therapy, disease, drug, and drug-target networks
have been introduced. Here we suggest novel methods for network-based
prediction of novel drug targets and for improvement of drug efficiency by
analysing the effects of drugs on the robustness of cellular networks.Comment: This is an extended version of the Journal of Biology paper
containing 2 Figures, 1 Table and 44 reference
Structural Deep Embedding for Hyper-Networks
Network embedding has recently attracted lots of attentions in data mining.
Existing network embedding methods mainly focus on networks with pairwise
relationships. In real world, however, the relationships among data points
could go beyond pairwise, i.e., three or more objects are involved in each
relationship represented by a hyperedge, thus forming hyper-networks. These
hyper-networks pose great challenges to existing network embedding methods when
the hyperedges are indecomposable, that is to say, any subset of nodes in a
hyperedge cannot form another hyperedge. These indecomposable hyperedges are
especially common in heterogeneous networks. In this paper, we propose a novel
Deep Hyper-Network Embedding (DHNE) model to embed hyper-networks with
indecomposable hyperedges. More specifically, we theoretically prove that any
linear similarity metric in embedding space commonly used in existing methods
cannot maintain the indecomposibility property in hyper-networks, and thus
propose a new deep model to realize a non-linear tuplewise similarity function
while preserving both local and global proximities in the formed embedding
space. We conduct extensive experiments on four different types of
hyper-networks, including a GPS network, an online social network, a drug
network and a semantic network. The empirical results demonstrate that our
method can significantly and consistently outperform the state-of-the-art
algorithms.Comment: Accepted by AAAI 1
edge2vec: Representation learning using edge semantics for biomedical knowledge discovery
Representation learning provides new and powerful graph analytical approaches
and tools for the highly valued data science challenge of mining knowledge
graphs. Since previous graph analytical methods have mostly focused on
homogeneous graphs, an important current challenge is extending this
methodology for richly heterogeneous graphs and knowledge domains. The
biomedical sciences are such a domain, reflecting the complexity of biology,
with entities such as genes, proteins, drugs, diseases, and phenotypes, and
relationships such as gene co-expression, biochemical regulation, and
biomolecular inhibition or activation. Therefore, the semantics of edges and
nodes are critical for representation learning and knowledge discovery in real
world biomedical problems. In this paper, we propose the edge2vec model, which
represents graphs considering edge semantics. An edge-type transition matrix is
trained by an Expectation-Maximization approach, and a stochastic gradient
descent model is employed to learn node embedding on a heterogeneous graph via
the trained transition matrix. edge2vec is validated on three biomedical domain
tasks: biomedical entity classification, compound-gene bioactivity prediction,
and biomedical information retrieval. Results show that by considering
edge-types into node embedding learning in heterogeneous graphs,
\textbf{edge2vec}\ significantly outperforms state-of-the-art models on all
three tasks. We propose this method for its added value relative to existing
graph analytical methodology, and in the real world context of biomedical
knowledge discovery applicability.Comment: 10 page
Encoding Robust Representation for Graph Generation
Generative networks have made it possible to generate meaningful signals such
as images and texts from simple noise. Recently, generative methods based on
GAN and VAE were developed for graphs and graph signals. However, the
mathematical properties of these methods are unclear, and training good
generative models is difficult. This work proposes a graph generation model
that uses a recent adaptation of Mallat's scattering transform to graphs. The
proposed model is naturally composed of an encoder and a decoder. The encoder
is a Gaussianized graph scattering transform, which is robust to signal and
graph manipulation. The decoder is a simple fully connected network that is
adapted to specific tasks, such as link prediction, signal generation on graphs
and full graph and signal generation. The training of our proposed system is
efficient since it is only applied to the decoder and the hardware requirements
are moderate. Numerical results demonstrate state-of-the-art performance of the
proposed system for both link prediction and graph and signal generation.Comment: 9 pages, 7 figures, 6 table
Machine Learning and Integrative Analysis of Biomedical Big Data.
Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues
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