2472095
Coarse and Reliable Geometric Alignment for Protein Docking
We present an efficient algorithm for generating a small set of coarse alignments between interacting proteins using meaningful features on their surfaces. The proteins are treated as rigid bodies, but the results are more generally useful as the produced configurations can serve as input to local improvement algorithms that allow for protein flexibility. We apply our algorithm to a diverse set of protein complexes from the Protein Data Bank, demonstrating the effectivity of our algorithm, both for bound and for unbound protein docking problems.
312809
Segmenting molecular surfaces
This paper presents a new method for segmentation of molecular surfaces. Topological analysis of a scalar function defined on the surface and its associated gradient field reveals the relationship between the features of interest and critical points of the scalar function. The segmentation is obtained by associating segments with local minima/maxima. Controlled simplification of the function merges segments resulting in a hierarchical segmentation of the molecular surface. This segmentation is used to identify rigid components of protein molecules and to study the role of cavities and protrusions in protein-protein interactions.
47345540
Shape Fitting with Outliers
Given a set $\mathcal{H}$ of n hyperplanes in ${\Bbb R}^d$, we present an algorithm that $\eps$-approximates the extent between the top and bottom k levels of the arrangement of $\mathcal{H}$ in time $O(n + (k/\eps)^c)$, where c is a constant depending on d. The algorithm relies on computing a subset of $\mathcal{H}$ of size $O(k/\eps^{d-1})$, in near linear time, such that the k-level of the arrangement of the subset approximates that of the original arrangement. Using this algorithm, we propose efficient approximation algorithms for shape fitting with outliers for various shapes. These are the first algorithms to handle outliers efficiently for the shape fitting problems considered.
7748348
Shape fitting with outliers
Given a set <i>H</i> of <i>n</i> hyperplanes in <i>R<sup>d</sup></i>, we present an algorithm that <i>e</i>-approximates the extent between the top and bottom <i>k</i> levels of the arrangement of <i>H</i> in time <i>O(n + (k/e)<sup>c</sup>)</i>, where <i>c</i> is a constant depending on <i>d</i>. The algorithm relies on computing a subset of <i>H</i> of size.<i>O(k/e<sup>d-1</sup>)</i>, in near linear time, such that the <i>k</i>-level of the arrangement of the subset approximates that of the original arrangement. Using this algorithm, we propose efficient approximation algorithms for shape fitting with outliers for various shapes. This is the first algorithms to handle outliers efficiently for the shape fitting problems considered.
34251654
Near-Linear Time Approximation Algorithms for Curve Simplification
We consider the problem of approximating a polygonal curve P under a given error criterion by another polygonal curve P? whose vertices are a subset of the vertices of P. The goal is to minimize the number of vertices of P? while ensuring that the error between P? and P is below a certain threshold. We consider two fundamentally different error measures -- Hausdorff and Frechet error measures. For both error criteria, we present near-linear time approximation algorithms that, given a parameter ? > 0, compute a simplified polygonal curve P? whose error is less than ? and size at most the size of an optimal simplified polygonal curve with error ?/2. We consider monotone curves in the case of Hausdorff error measure and arbitrary curves for the Frechet error measure. We present experimental results demonstrating that our algorithms are simple and fast, and produce close to optimal simplifications in practice.
21531236
Towards Unsupervised Segmentation of Semi-rigid Low-Resolution Molecular Surfaces
In this paper, we study a particular type of surface segmentation problem motivated by molecular biology applications. In particular, two input surfaces are given, coarsely modeling two different conformations of a molecule undergoing a semi-rigid deformation. The molecule consists of two subunits that move in a roughly rigid manner. The goal is to segment the input surfaces into these semi-rigid subcomponents. The problem is closely related to non-rigid surface registration problems, although considering only a special type of deformation that exists commonly in macromolecular movements (such as the popular hinge motion). We present and implement an efficient paradigm for this problem, which combines several existing and new ideas. We demonstrate the performance of our new algorithm by some preliminary experimental results in segmenting low-resolution molecular surfaces.
3069530
HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data
MOTIVATION
Recent studies have shown that microarray gene expression data are useful for phenotype classification of many diseases. A major problem in this classification is that the number of features (genes) greatly exceeds the number of instances (tissue samples). It has been shown that selecting a small set of informative genes can lead to improved classification accuracy. Many approaches have been proposed for this gene selection problem. Most of the previous gene ranking methods typically select 50-200 top-ranked genes and these genes are often highly correlated. Our goal is to select a small set of non-redundant marker genes that are most relevant for the classification task.


RESULTS
To achieve this goal, we developed a novel hybrid approach that combines gene ranking and clustering analysis. In this approach, we first applied feature filtering algorithms to select a set of top-ranked genes, and then applied hierarchical clustering on these genes to generate a dendrogram. Finally, the dendrogram was analyzed by a sweep-line algorithm and marker genes are selected by collapsing dense clusters. Empirical study using three public datasets shows that our approach is capable of selecting relatively few marker genes while offering the same or better leave-one-out cross-validation accuracy compared with approaches that use top-ranked genes directly for classification.


AVAILABILITY
The HykGene software is freely available at http://www.cs.dartmouth.edu/~wyh/software.htm


CONTACT
wyh@cs.dartmouth.edu


SUPPLEMENTARY INFORMATION
Supplementary material is available from http://www.cs.dartmouth.edu/~wyh/hykgene/supplement/index.htm.
3331857
Table Detection via Probability Optimization
In this paper, we define the table detection problem as a probability optimization problem. We begin, as we do in our previous algorithm, finding and validating each detected table candidates. We proceed to compute a set of probability measurements for each of the table entities. The computation of the probability measurements takes into consideration tables, table text separators and table neighboring text blocks. Then, an iterative updating method is used to optimize the page segmentation probability to obtain the final result. This new algorithm shows a great improvement over our previous algorithm. The training and testing data set for the algorithm include 1, 125 document pages having 518 table entities and a total of 10, 934 cell entities. Compared with our previous work, it raised the accuracy rate to 95.67% from 90.32% and to 97.05% from 92.04%.
12841371
Implementing the Real-Time Processes of RTPA using Real-Time Java
This paper discusses the implementation of the real-time processes of real-time process algebra (RTPA) using real-time Java. The difficulty in implementing real-time software from formal specifications comes from the fact that some realtime features expressed using a formal specification language cannot be easily transformed into a programming language. The paper shows how a combination of a real-time support library for RTPA (RTPASupportLib) and the recently developed extensions to real-time Java can overcome some of these difficulties. The strategies and techniques employed in implementing RTPA real-time features such as concurrency, interleaving, and interrupt/event/time-driven dispatching of real-time processes are presented. A number of case studies on the implementation of RTPA real-time features show that the approach is a feasible one
40360434
Measurement of the cognitive functional complexity of software
One of the central problems in software engineering is its inherited complexity. It is recognized that cognitive informatics plays an important role in understanding the fundamental characteristics of software. This paper models the cognitive weights of basic control structures of software, and develops a new concept of cognitive functional size for measuring software complexity. Comparative case studies between the cognitive functional size and physical sizes of 20 programs are conducted. It is found that for a given design, although the physical sizes of software may vary in a wide range, the cognitive functional sizes are much stable and independent from implementation technologies and programming languages. Therefore, the cognitive functional size provides a novel, stable and practical software complexity measurement and is helpful to explain the fundamental nature of software complexity in the phase of design, implementation, or maintenance in software engineering.
1333188
Querying approximate shortest paths in anisotropic regions
We present a data structure for answering approximate shortest path queries ina planar subdivision from a fixed source. Let ρ ≥ 1 be a real number.Distances in each face of this subdivision are measured by a possiblyasymmetric convex distance function whose unit disk is contained in aconcentric unit Euclidean disk, and contains a concentric Euclidean disk withradius 1/ρ. Different convex distance functions may be used for differentfaces, and obstacles are allowed. Let ε be any number strictly between 0and 1. Our data structure returns a (1+ε)approximation of the shortest path cost from the fixed source to a querydestination in O(logρn/ε) time. Afterwards, a(1+ε)-approximate shortest path can be reported in time linear in itscomplexity. The data structure uses O(ρ<sup>2</sup> n<sup>4</sup>/ε<sup>2</sup> log ρn/ε) space and can be built in O((ρ<sup>2</sup> n<sup>4</sup>)/(ε<sup>2</sup>)(log ρn/ε)<sup>2</sup>) time. Our time and space bounds do not depend onany geometric parameter of the subdivision such as the minimum angle.