4,945 research outputs found
Off the Beaten Path: Let's Replace Term-Based Retrieval with k-NN Search
Retrieval pipelines commonly rely on a term-based search to obtain candidate
records, which are subsequently re-ranked. Some candidates are missed by this
approach, e.g., due to a vocabulary mismatch. We address this issue by
replacing the term-based search with a generic k-NN retrieval algorithm, where
a similarity function can take into account subtle term associations. While an
exact brute-force k-NN search using this similarity function is slow, we
demonstrate that an approximate algorithm can be nearly two orders of magnitude
faster at the expense of only a small loss in accuracy. A retrieval pipeline
using an approximate k-NN search can be more effective and efficient than the
term-based pipeline. This opens up new possibilities for designing effective
retrieval pipelines. Our software (including data-generating code) and
derivative data based on the Stack Overflow collection is available online
Discrete Elastic Inner Vector Spaces with Application in Time Series and Sequence Mining
This paper proposes a framework dedicated to the construction of what we call
discrete elastic inner product allowing one to embed sets of non-uniformly
sampled multivariate time series or sequences of varying lengths into inner
product space structures. This framework is based on a recursive definition
that covers the case of multiple embedded time elastic dimensions. We prove
that such inner products exist in our general framework and show how a simple
instance of this inner product class operates on some prospective applications,
while generalizing the Euclidean inner product. Classification experimentations
on time series and symbolic sequences datasets demonstrate the benefits that we
can expect by embedding time series or sequences into elastic inner spaces
rather than into classical Euclidean spaces. These experiments show good
accuracy when compared to the euclidean distance or even dynamic programming
algorithms while maintaining a linear algorithmic complexity at exploitation
stage, although a quadratic indexing phase beforehand is required.Comment: arXiv admin note: substantial text overlap with arXiv:1101.431
Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks
Complex biological systems have been successfully modeled by biochemical and
genetic interaction networks, typically gathered from high-throughput (HTP)
data. These networks can be used to infer functional relationships between
genes or proteins. Using the intuition that the topological role of a gene in a
network relates to its biological function, local or diffusion based
"guilt-by-association" and graph-theoretic methods have had success in
inferring gene functions. Here we seek to improve function prediction by
integrating diffusion-based methods with a novel dimensionality reduction
technique to overcome the incomplete and noisy nature of network data. In this
paper, we introduce diffusion component analysis (DCA), a framework that plugs
in a diffusion model and learns a low-dimensional vector representation of each
node to encode the topological properties of a network. As a proof of concept,
we demonstrate DCA's substantial improvement over state-of-the-art
diffusion-based approaches in predicting protein function from molecular
interaction networks. Moreover, our DCA framework can integrate multiple
networks from heterogeneous sources, consisting of genomic information,
biochemical experiments and other resources, to even further improve function
prediction. Yet another layer of performance gain is achieved by integrating
the DCA framework with support vector machines that take our node vector
representations as features. Overall, our DCA framework provides a novel
representation of nodes in a network that can be used as a plug-in architecture
to other machine learning algorithms to decipher topological properties of and
obtain novel insights into interactomes.Comment: RECOMB 201
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