11,456 research outputs found
Locally embedded presages of global network bursts
Spontaneous, synchronous bursting of neural population is a widely observed
phenomenon in nervous networks, which is considered important for functions and
dysfunctions of the brain. However, how the global synchrony across a large
number of neurons emerges from an initially non-bursting network state is not
fully understood. In this study, we develop a new state-space reconstruction
method combined with high-resolution recordings of cultured neurons. This
method extracts deterministic signatures of upcoming global bursts in "local"
dynamics of individual neurons during non-bursting periods. We find that local
information within a single-cell time series can compare with or even
outperform the global mean field activity for predicting future global bursts.
Moreover, the inter-cell variability in the burst predictability is found to
reflect the network structure realized in the non-bursting periods. These
findings demonstrate the deterministic mechanisms underlying the locally
concentrated early-warnings of the global state transition in self-organized
networks
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
Predicting epidemic risk from past temporal contact data
Understanding how epidemics spread in a system is a crucial step to prevent
and control outbreaks, with broad implications on the system's functioning,
health, and associated costs. This can be achieved by identifying the elements
at higher risk of infection and implementing targeted surveillance and control
measures. One important ingredient to consider is the pattern of
disease-transmission contacts among the elements, however lack of data or
delays in providing updated records may hinder its use, especially for
time-varying patterns. Here we explore to what extent it is possible to use
past temporal data of a system's pattern of contacts to predict the risk of
infection of its elements during an emerging outbreak, in absence of updated
data. We focus on two real-world temporal systems; a livestock displacements
trade network among animal holdings, and a network of sexual encounters in
high-end prostitution. We define the node's loyalty as a local measure of its
tendency to maintain contacts with the same elements over time, and uncover
important non-trivial correlations with the node's epidemic risk. We show that
a risk assessment analysis incorporating this knowledge and based on past
structural and temporal pattern properties provides accurate predictions for
both systems. Its generalizability is tested by introducing a theoretical model
for generating synthetic temporal networks. High accuracy of our predictions is
recovered across different settings, while the amount of possible predictions
is system-specific. The proposed method can provide crucial information for the
setup of targeted intervention strategies.Comment: 24 pages, 5 figures + SI (18 pages, 15 figures
Herb Target Prediction Based on Representation Learning of Symptom related Heterogeneous Network.
Traditional Chinese Medicine (TCM) has received increasing attention as a complementary approach or alternative to modern medicine. However, experimental methods for identifying novel targets of TCM herbs heavily relied on the current available herb-compound-target relationships. In this work, we present an Herb-Target Interaction Network (HTINet) approach, a novel network integration pipeline for herb-target prediction mainly relying on the symptom related associations. HTINet focuses on capturing the low-dimensional feature vectors for both herbs and proteins by network embedding, which incorporate the topological properties of nodes across multi-layered heterogeneous network, and then performs supervised learning based on these low-dimensional feature representations. HTINet obtains performance improvement over a well-established random walk based herb-target prediction method. Furthermore, we have manually validated several predicted herb-target interactions from independent literatures. These results indicate that HTINet can be used to integrate heterogeneous information to predict novel herb-target interactions
Learning Visual Clothing Style with Heterogeneous Dyadic Co-occurrences
With the rapid proliferation of smart mobile devices, users now take millions
of photos every day. These include large numbers of clothing and accessory
images. We would like to answer questions like `What outfit goes well with this
pair of shoes?' To answer these types of questions, one has to go beyond
learning visual similarity and learn a visual notion of compatibility across
categories. In this paper, we propose a novel learning framework to help answer
these types of questions. The main idea of this framework is to learn a feature
transformation from images of items into a latent space that expresses
compatibility. For the feature transformation, we use a Siamese Convolutional
Neural Network (CNN) architecture, where training examples are pairs of items
that are either compatible or incompatible. We model compatibility based on
co-occurrence in large-scale user behavior data; in particular co-purchase data
from Amazon.com. To learn cross-category fit, we introduce a strategic method
to sample training data, where pairs of items are heterogeneous dyads, i.e.,
the two elements of a pair belong to different high-level categories. While
this approach is applicable to a wide variety of settings, we focus on the
representative problem of learning compatible clothing style. Our results
indicate that the proposed framework is capable of learning semantic
information about visual style and is able to generate outfits of clothes, with
items from different categories, that go well together.Comment: ICCV 201
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