6,536 research outputs found
Convex Relaxations for Permutation Problems
Seriation seeks to reconstruct a linear order between variables using
unsorted, pairwise similarity information. It has direct applications in
archeology and shotgun gene sequencing for example. We write seriation as an
optimization problem by proving the equivalence between the seriation and
combinatorial 2-SUM problems on similarity matrices (2-SUM is a quadratic
minimization problem over permutations). The seriation problem can be solved
exactly by a spectral algorithm in the noiseless case and we derive several
convex relaxations for 2-SUM to improve the robustness of seriation solutions
in noisy settings. These convex relaxations also allow us to impose structural
constraints on the solution, hence solve semi-supervised seriation problems. We
derive new approximation bounds for some of these relaxations and present
numerical experiments on archeological data, Markov chains and DNA assembly
from shotgun gene sequencing data.Comment: Final journal version, a few typos and references fixe
Effective Graph-Based Content--Based Image Retrieval Systems for Large-Scale and Small-Scale Image Databases
This dissertation proposes two novel manifold graph-based ranking systems for Content-Based Image Retrieval (CBIR). The two proposed systems exploit the synergism between relevance feedback-based transductive short-term learning and semantic feature-based long-term learning to improve retrieval performance. Proposed systems first apply the active learning mechanism to construct users\u27 relevance feedback log and extract high-level semantic features for each image. These systems then create manifold graphs by incorporating both the low-level visual similarity and the high-level semantic similarity to achieve more meaningful structures for the image space. Finally, asymmetric relevance vectors are created to propagate relevance scores of labeled images to unlabeled images via manifold graphs. The extensive experimental results demonstrate two proposed systems outperform the other state-of-the-art CBIR systems in the context of both correct and erroneous users\u27 feedback
Online Metric-Weighted Linear Representations for Robust Visual Tracking
In this paper, we propose a visual tracker based on a metric-weighted linear
representation of appearance. In order to capture the interdependence of
different feature dimensions, we develop two online distance metric learning
methods using proximity comparison information and structured output learning.
The learned metric is then incorporated into a linear representation of
appearance.
We show that online distance metric learning significantly improves the
robustness of the tracker, especially on those sequences exhibiting drastic
appearance changes. In order to bound growth in the number of training samples,
we design a time-weighted reservoir sampling method.
Moreover, we enable our tracker to automatically perform object
identification during the process of object tracking, by introducing a
collection of static template samples belonging to several object classes of
interest. Object identification results for an entire video sequence are
achieved by systematically combining the tracking information and visual
recognition at each frame. Experimental results on challenging video sequences
demonstrate the effectiveness of the method for both inter-frame tracking and
object identification.Comment: 51 pages. Appearing in IEEE Transactions on Pattern Analysis and
Machine Intelligenc
Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes
Similarly to protein folding, the association of two proteins is driven
by a free energy funnel, determined by favorable interactions in some neighborhood of the
native state. We describe a docking method based on stochastic global minimization of
funnel-shaped energy functions in the space of rigid body motions (SE(3)) while accounting
for flexibility of the interface side chains. The method, called semi-definite
programming-based underestimation (SDU), employs a general quadratic function to
underestimate a set of local energy minima and uses the resulting underestimator to bias
further sampling. While SDU effectively minimizes functions with funnel-shaped basins, its
application to docking in the rotational and translational space SE(3) is not
straightforward due to the geometry of that space. We introduce a strategy that uses
separate independent variables for side-chain optimization, center-to-center distance of the
two proteins, and five angular descriptors of the relative orientations of the molecules.
The removal of the center-to-center distance turns out to vastly improve the efficiency of
the search, because the five-dimensional space now exhibits a well-behaved energy surface
suitable for underestimation. This algorithm explores the free energy surface spanned by
encounter complexes that correspond to local free energy minima and shows similarity to the
model of macromolecular association that proceeds through a series of collisions. Results
for standard protein docking benchmarks establish that in this space the free energy
landscape is a funnel in a reasonably broad neighborhood of the native state and that the
SDU strategy can generate docking predictions with less than 5 � ligand interface Ca
root-mean-square deviation while achieving an approximately 20-fold efficiency gain compared
to Monte Carlo methods
Soft peer review: social software and distributed scientific evaluation
The debate on the prospects of peer-review in the Internet age and the
increasing criticism leveled against the dominant role of impact factor
indicators are calling for new measurable criteria to assess scientific quality.
Usage-based metrics offer a new avenue to scientific quality assessment but
face the same risks as first generation search engines that used unreliable
metrics (such as raw traffic data) to estimate content quality. In this article I
analyze the contribution that social bookmarking systems can provide to the
problem of usage-based metrics for scientific evaluation. I suggest that
collaboratively aggregated metadata may help fill the gap between traditional
citation-based criteria and raw usage factors. I submit that bottom-up,
distributed evaluation models such as those afforded by social bookmarking
will challenge more traditional quality assessment models in terms of coverage,
efficiency and scalability. Services aggregating user-related quality indicators
for online scientific content will come to occupy a key function in the scholarly
communication system
Autoencoding the Retrieval Relevance of Medical Images
Content-based image retrieval (CBIR) of medical images is a crucial task that
can contribute to a more reliable diagnosis if applied to big data. Recent
advances in feature extraction and classification have enormously improved CBIR
results for digital images. However, considering the increasing accessibility
of big data in medical imaging, we are still in need of reducing both memory
requirements and computational expenses of image retrieval systems. This work
proposes to exclude the features of image blocks that exhibit a low encoding
error when learned by a autoencoder (). We examine the
histogram of autoendcoding errors of image blocks for each image class to
facilitate the decision which image regions, or roughly what percentage of an
image perhaps, shall be declared relevant for the retrieval task. This leads to
reduction of feature dimensionality and speeds up the retrieval process. To
validate the proposed scheme, we employ local binary patterns (LBP) and support
vector machines (SVM) which are both well-established approaches in CBIR
research community. As well, we use IRMA dataset with 14,410 x-ray images as
test data. The results show that the dimensionality of annotated feature
vectors can be reduced by up to 50% resulting in speedups greater than 27% at
expense of less than 1% decrease in the accuracy of retrieval when validating
the precision and recall of the top 20 hits.Comment: To appear in proceedings of The 5th International Conference on Image
Processing Theory, Tools and Applications (IPTA'15), Nov 10-13, 2015,
Orleans, Franc
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