31,336 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
Cross-lingual Entity Alignment via Joint Attribute-Preserving Embedding
Entity alignment is the task of finding entities in two knowledge bases (KBs)
that represent the same real-world object. When facing KBs in different natural
languages, conventional cross-lingual entity alignment methods rely on machine
translation to eliminate the language barriers. These approaches often suffer
from the uneven quality of translations between languages. While recent
embedding-based techniques encode entities and relationships in KBs and do not
need machine translation for cross-lingual entity alignment, a significant
number of attributes remain largely unexplored. In this paper, we propose a
joint attribute-preserving embedding model for cross-lingual entity alignment.
It jointly embeds the structures of two KBs into a unified vector space and
further refines it by leveraging attribute correlations in the KBs. Our
experimental results on real-world datasets show that this approach
significantly outperforms the state-of-the-art embedding approaches for
cross-lingual entity alignment and could be complemented with methods based on
machine translation
DeepPermNet: Visual Permutation Learning
We present a principled approach to uncover the structure of visual data by
solving a novel deep learning task coined visual permutation learning. The goal
of this task is to find the permutation that recovers the structure of data
from shuffled versions of it. In the case of natural images, this task boils
down to recovering the original image from patches shuffled by an unknown
permutation matrix. Unfortunately, permutation matrices are discrete, thereby
posing difficulties for gradient-based methods. To this end, we resort to a
continuous approximation of these matrices using doubly-stochastic matrices
which we generate from standard CNN predictions using Sinkhorn iterations.
Unrolling these iterations in a Sinkhorn network layer, we propose DeepPermNet,
an end-to-end CNN model for this task. The utility of DeepPermNet is
demonstrated on two challenging computer vision problems, namely, (i) relative
attributes learning and (ii) self-supervised representation learning. Our
results show state-of-the-art performance on the Public Figures and OSR
benchmarks for (i) and on the classification and segmentation tasks on the
PASCAL VOC dataset for (ii).Comment: Accepted in IEEE International Conference on Computer Vision and
Pattern Recognition CVPR 201
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