46,328 research outputs found
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
Exploring Student Check-In Behavior for Improved Point-of-Interest Prediction
With the availability of vast amounts of user visitation history on
location-based social networks (LBSN), the problem of Point-of-Interest (POI)
prediction has been extensively studied. However, much of the research has been
conducted solely on voluntary checkin datasets collected from social apps such
as Foursquare or Yelp. While these data contain rich information about
recreational activities (e.g., restaurants, nightlife, and entertainment),
information about more prosaic aspects of people's lives is sparse. This not
only limits our understanding of users' daily routines, but more importantly
the modeling assumptions developed based on characteristics of recreation-based
data may not be suitable for richer check-in data. In this work, we present an
analysis of education "check-in" data using WiFi access logs collected at
Purdue University. We propose a heterogeneous graph-based method to encode the
correlations between users, POIs, and activities, and then jointly learn
embeddings for the vertices. We evaluate our method compared to previous
state-of-the-art POI prediction methods, and show that the assumptions made by
previous methods significantly degrade performance on our data with dense(r)
activity signals. We also show how our learned embeddings could be used to
identify similar students (e.g., for friend suggestions).Comment: published in KDD'1
KGAT: Knowledge Graph Attention Network for Recommendation
To provide more accurate, diverse, and explainable recommendation, it is
compulsory to go beyond modeling user-item interactions and take side
information into account. Traditional methods like factorization machine (FM)
cast it as a supervised learning problem, which assumes each interaction as an
independent instance with side information encoded. Due to the overlook of the
relations among instances or items (e.g., the director of a movie is also an
actor of another movie), these methods are insufficient to distill the
collaborative signal from the collective behaviors of users. In this work, we
investigate the utility of knowledge graph (KG), which breaks down the
independent interaction assumption by linking items with their attributes. We
argue that in such a hybrid structure of KG and user-item graph, high-order
relations --- which connect two items with one or multiple linked attributes
--- are an essential factor for successful recommendation. We propose a new
method named Knowledge Graph Attention Network (KGAT) which explicitly models
the high-order connectivities in KG in an end-to-end fashion. It recursively
propagates the embeddings from a node's neighbors (which can be users, items,
or attributes) to refine the node's embedding, and employs an attention
mechanism to discriminate the importance of the neighbors. Our KGAT is
conceptually advantageous to existing KG-based recommendation methods, which
either exploit high-order relations by extracting paths or implicitly modeling
them with regularization. Empirical results on three public benchmarks show
that KGAT significantly outperforms state-of-the-art methods like Neural FM and
RippleNet. Further studies verify the efficacy of embedding propagation for
high-order relation modeling and the interpretability benefits brought by the
attention mechanism.Comment: KDD 2019 research trac
Conditional network embeddings
Network Embeddings (NEs) map the nodes of a given network into -dimensional Euclidean space . Ideally, this mapping is such that 'similar' nodes are mapped onto nearby points, such that the NE can be used for purposes such as link prediction (if 'similar' means being 'more likely to be connected') or classification (if 'similar' means 'being more likely to have the same label'). In recent years various methods for NE have been introduced, all following a similar strategy: defining a notion of similarity between nodes (typically some distance measure within the network), a distance measure in the embedding space, and a loss function that penalizes large distances for similar nodes and small distances for dissimilar nodes.
A difficulty faced by existing methods is that certain networks are fundamentally hard to embed due to their structural properties: (approximate) multipartiteness, certain degree distributions, assortativity, etc. To overcome this, we introduce a conceptual innovation to the NE literature and propose to create \emph{Conditional Network Embeddings} (CNEs); embeddings that maximally add information with respect to given structural properties (e.g. node degrees, block densities, etc.). We use a simple Bayesian approach to achieve this, and propose a block stochastic gradient descent algorithm for fitting it efficiently.
We demonstrate that CNEs are superior for link prediction and multi-label classification when compared to state-of-the-art methods, and this without adding significant mathematical or computational complexity. Finally, we illustrate the potential of CNE for network visualization
Bayesian Learning of Sum-Product Networks
Sum-product networks (SPNs) are flexible density estimators and have received
significant attention due to their attractive inference properties. While
parameter learning in SPNs is well developed, structure learning leaves
something to be desired: Even though there is a plethora of SPN structure
learners, most of them are somewhat ad-hoc and based on intuition rather than a
clear learning principle. In this paper, we introduce a well-principled
Bayesian framework for SPN structure learning. First, we decompose the problem
into i) laying out a computational graph, and ii) learning the so-called scope
function over the graph. The first is rather unproblematic and akin to neural
network architecture validation. The second represents the effective structure
of the SPN and needs to respect the usual structural constraints in SPN, i.e.
completeness and decomposability. While representing and learning the scope
function is somewhat involved in general, in this paper, we propose a natural
parametrisation for an important and widely used special case of SPNs. These
structural parameters are incorporated into a Bayesian model, such that
simultaneous structure and parameter learning is cast into monolithic Bayesian
posterior inference. In various experiments, our Bayesian SPNs often improve
test likelihoods over greedy SPN learners. Further, since the Bayesian
framework protects against overfitting, we can evaluate hyper-parameters
directly on the Bayesian model score, waiving the need for a separate
validation set, which is especially beneficial in low data regimes. Bayesian
SPNs can be applied to heterogeneous domains and can easily be extended to
nonparametric formulations. Moreover, our Bayesian approach is the first, which
consistently and robustly learns SPN structures under missing data.Comment: NeurIPS 2019; See conference page for supplemen
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