15,920 research outputs found
Classifying pairs with trees for supervised biological network inference
Networks are ubiquitous in biology and computational approaches have been
largely investigated for their inference. In particular, supervised machine
learning methods can be used to complete a partially known network by
integrating various measurements. Two main supervised frameworks have been
proposed: the local approach, which trains a separate model for each network
node, and the global approach, which trains a single model over pairs of nodes.
Here, we systematically investigate, theoretically and empirically, the
exploitation of tree-based ensemble methods in the context of these two
approaches for biological network inference. We first formalize the problem of
network inference as classification of pairs, unifying in the process
homogeneous and bipartite graphs and discussing two main sampling schemes. We
then present the global and the local approaches, extending the later for the
prediction of interactions between two unseen network nodes, and discuss their
specializations to tree-based ensemble methods, highlighting their
interpretability and drawing links with clustering techniques. Extensive
computational experiments are carried out with these methods on various
biological networks that clearly highlight that these methods are competitive
with existing methods.Comment: 22 page
Kernel methods in genomics and computational biology
Support vector machines and kernel methods are increasingly popular in
genomics and computational biology, due to their good performance in real-world
applications and strong modularity that makes them suitable to a wide range of
problems, from the classification of tumors to the automatic annotation of
proteins. Their ability to work in high dimension, to process non-vectorial
data, and the natural framework they provide to integrate heterogeneous data
are particularly relevant to various problems arising in computational biology.
In this chapter we survey some of the most prominent applications published so
far, highlighting the particular developments in kernel methods triggered by
problems in biology, and mention a few promising research directions likely to
expand in the future
Identification of functionally related enzymes by learning-to-rank methods
Enzyme sequences and structures are routinely used in the biological sciences
as queries to search for functionally related enzymes in online databases. To
this end, one usually departs from some notion of similarity, comparing two
enzymes by looking for correspondences in their sequences, structures or
surfaces. For a given query, the search operation results in a ranking of the
enzymes in the database, from very similar to dissimilar enzymes, while
information about the biological function of annotated database enzymes is
ignored.
In this work we show that rankings of that kind can be substantially improved
by applying kernel-based learning algorithms. This approach enables the
detection of statistical dependencies between similarities of the active cleft
and the biological function of annotated enzymes. This is in contrast to
search-based approaches, which do not take annotated training data into
account. Similarity measures based on the active cleft are known to outperform
sequence-based or structure-based measures under certain conditions. We
consider the Enzyme Commission (EC) classification hierarchy for obtaining
annotated enzymes during the training phase. The results of a set of sizeable
experiments indicate a consistent and significant improvement for a set of
similarity measures that exploit information about small cavities in the
surface of enzymes
STNet: Selective Tuning of Convolutional Networks for Object Localization
Visual attention modeling has recently gained momentum in developing visual
hierarchies provided by Convolutional Neural Networks. Despite recent successes
of feedforward processing on the abstraction of concepts form raw images, the
inherent nature of feedback processing has remained computationally
controversial. Inspired by the computational models of covert visual attention,
we propose the Selective Tuning of Convolutional Networks (STNet). It is
composed of both streams of Bottom-Up and Top-Down information processing to
selectively tune the visual representation of Convolutional networks. We
experimentally evaluate the performance of STNet for the weakly-supervised
localization task on the ImageNet benchmark dataset. We demonstrate that STNet
not only successfully surpasses the state-of-the-art results but also generates
attention-driven class hypothesis maps
Event-based Vision: A Survey
Event cameras are bio-inspired sensors that differ from conventional frame
cameras: Instead of capturing images at a fixed rate, they asynchronously
measure per-pixel brightness changes, and output a stream of events that encode
the time, location and sign of the brightness changes. Event cameras offer
attractive properties compared to traditional cameras: high temporal resolution
(in the order of microseconds), very high dynamic range (140 dB vs. 60 dB), low
power consumption, and high pixel bandwidth (on the order of kHz) resulting in
reduced motion blur. Hence, event cameras have a large potential for robotics
and computer vision in challenging scenarios for traditional cameras, such as
low-latency, high speed, and high dynamic range. However, novel methods are
required to process the unconventional output of these sensors in order to
unlock their potential. This paper provides a comprehensive overview of the
emerging field of event-based vision, with a focus on the applications and the
algorithms developed to unlock the outstanding properties of event cameras. We
present event cameras from their working principle, the actual sensors that are
available and the tasks that they have been used for, from low-level vision
(feature detection and tracking, optic flow, etc.) to high-level vision
(reconstruction, segmentation, recognition). We also discuss the techniques
developed to process events, including learning-based techniques, as well as
specialized processors for these novel sensors, such as spiking neural
networks. Additionally, we highlight the challenges that remain to be tackled
and the opportunities that lie ahead in the search for a more efficient,
bio-inspired way for machines to perceive and interact with the world
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