2,051 research outputs found
Building Efficient and Compact Data Structures for Simplicial Complexes
The Simplex Tree (ST) is a recently introduced data structure that can
represent abstract simplicial complexes of any dimension and allows efficient
implementation of a large range of basic operations on simplicial complexes. In
this paper, we show how to optimally compress the Simplex Tree while retaining
its functionalities. In addition, we propose two new data structures called the
Maximal Simplex Tree (MxST) and the Simplex Array List (SAL). We analyze the
compressed Simplex Tree, the Maximal Simplex Tree, and the Simplex Array List
under various settings.Comment: An extended abstract appeared in the proceedings of SoCG 201
Restricted Value Iteration: Theory and Algorithms
Value iteration is a popular algorithm for finding near optimal policies for
POMDPs. It is inefficient due to the need to account for the entire belief
space, which necessitates the solution of large numbers of linear programs. In
this paper, we study value iteration restricted to belief subsets. We show
that, together with properly chosen belief subsets, restricted value iteration
yields near-optimal policies and we give a condition for determining whether a
given belief subset would bring about savings in space and time. We also apply
restricted value iteration to two interesting classes of POMDPs, namely
informative POMDPs and near-discernible POMDPs
A topological approach for protein classification
Protein function and dynamics are closely related to its sequence and
structure. However prediction of protein function and dynamics from its
sequence and structure is still a fundamental challenge in molecular biology.
Protein classification, which is typically done through measuring the
similarity be- tween proteins based on protein sequence or physical
information, serves as a crucial step toward the understanding of protein
function and dynamics. Persistent homology is a new branch of algebraic
topology that has found its success in the topological data analysis in a
variety of disciplines, including molecular biology. The present work explores
the potential of using persistent homology as an indepen- dent tool for protein
classification. To this end, we propose a molecular topological fingerprint
based support vector machine (MTF-SVM) classifier. Specifically, we construct
machine learning feature vectors solely from protein topological fingerprints,
which are topological invariants generated during the filtration process. To
validate the present MTF-SVM approach, we consider four types of problems.
First, we study protein-drug binding by using the M2 channel protein of
influenza A virus. We achieve 96% accuracy in discriminating drug bound and
unbound M2 channels. Additionally, we examine the use of MTF-SVM for the
classification of hemoglobin molecules in their relaxed and taut forms and
obtain about 80% accuracy. The identification of all alpha, all beta, and
alpha-beta protein domains is carried out in our next study using 900 proteins.
We have found a 85% success in this identifica- tion. Finally, we apply the
present technique to 55 classification tasks of protein superfamilies over 1357
samples. An average accuracy of 82% is attained. The present study establishes
computational topology as an independent and effective alternative for protein
classification
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