38278026
A Simple Test for the Consecutive Ones Property
A (0,1)-matrix satisfies the consecutive ones property if there exists a column permutation such that the ones in each row of the resulting matrix are consecutive. Booth and Lueker (1976, J. Comput. System Sci.13, 335?378) designed a linear time-testing algorithm for this property based on a data structure called “PQ-trees.” This procedure is quite complicated and the linear-time-amortized analysis is also rather involved. We developed an off-line linear time test for the consecutive ones property without using PQ-trees and the corresponding template matching, which makes ours considerably simpler. A simplification of the consecutive ones test will immediately simplify algorithms (and computer codes) for interval-graph and planar-graph recognition. Our approach is based on a decomposition technique that separates the rows into prime subsets, each of which admits essentially a unique column ordering that realizes the consecutive ones property. The success of this approach is based on finding a good “row ordering” to be tested iteratively.
2987495
Independent Sets in Circular-Arc Graphs
This paper presents a linear time algorithm for the independent set problem on circular-arc graphs. previous algorithms for this problem have assumed that the input is a set of circular-arcs and solve the problem in O(n) time. However, the fastest known algorithm for constructing the circular-are representation from a set of adjacency lists takes O(n2) time. We show that we can solve the problem in O(n + m) time, when we are given the circular-arc graph as a set of adjacency lists.
6232755
Algorithms for minimum covering by cliques and maximum clique in claw-free perfect graphs
An algorithm is given for determining a minimum cardinality clique cover ongraphs that do not contain claws, odd holes or odd anti-holes. These graphs are also shown to be perfect so that we obtain a new proof of the strong perfect graph theorem for claw-free graphs. A by-product of our analysis is an algorithm for determining a maximum cardinality clique on claw-free perfect graphs.
17795095
A Simple Test for the Consecutive Ones Property
A (0,1)-matrix satisfies the consecutive ones property if there exists a column permutation such that the one's in each row of the resulting matrix are consecutive. Booth and Lueker [1976] designed a linear time testing algorithm for this property based on a data structure called “PQ-trees”. This procedure is very complicated and the linear time amortized analysis is also rather involved. We develop an off-line testing algorithm for the consecutive ones property without using PQ-trees. Our approach is based on a decomposition technique which separates the rows into “prime” subsets which admit unique column orderings that realize the consecutive ones property. The success of this approach is based on finding a good “row ordering” to be tested iteratively.
208691
Coloring planar perfect graphs by decomposition
This paper describes a decomposition scheme for coloring perfect graphs. Based on this scheme, one need only concentrate on coloring highly connected (at least 3-connected) perfect graphs. This idea is illustrated on planar perfect graphs, which yields a straightforward coloring algorithm. We suspect that, under appropriate definition, highly connected perfect graphs might possess certain regular properties that are amenable to coloring algorithms.
2164726
A New Planarity Test
Abstract Given an undirected graph, the planarity testing problem is to determine whether the graph can be drawn in a plane without any crossing edges. Linear time planarity testing algorithms have previously been designed by Hopcroft and Tarjan, and by Booth and Lueker. However, their approaches are quite involved. Several other approaches have also been developed for simplifying the planarity test. In this paper, we developed a very simple linear time testing algorithm based only on a depth-first search tree. When the given graph is not planar, our algorithm immediately produces explicit Kuratowski's subgraphs. A new data structure, PC -trees, is introduced, which can be viewed as abstract subembeddings of actual planar embeddings. A graph-reduction technique is adopted so that the embeddings for the planar biconnected components constructed at each iteration never have to be changed. The recognition and embedding are actually done simultaneously in our algorithm (Booth and Lueker, 1976). The implementation of our algorithm is quite straightforward.
1049682
An Empirical Comparison of Runtime Systems for Conservative Parallel Simulation
A main consideration when implementing a parallel simulation application is the choice of the parallel simulation protocol (conservative vs. optimistic). Given a particular protocol, the application programmer then has to determine a suitable parallel runtime system to implement the application. If the choice is an optimistic protocol, there are several parallel simulation libraries intended for application programmers (e.g. GTW, Warped). For a conservative protocol, the most effective approach is for the programmer to use a general parallel runtime library, and implement optimizations specific to the simulation application and/or model. In this paper, we selected four general parallel runtime libraries potentially relevant to parallel simulations, and implemented a conservative protocol on each of them. We study the four libraries on three main aspects: (a) programmability; (b) performance, and (c) mechanisms for performance tuning. Our target platforms are machines supporting shared address spaces (e.g. SGI Origin200, Sun Enterprise 3000), and we obtained performance figures from a 4-CPU Ultra2 Sun Enterprise 3000. From our experiments, we find that POSIX, though an industry standard, still has relatively high overheads, and cannot efficiently support a protocol with fine-grain LPs. The research libraries all show speedups on 4 processors, but to different extents. Cilk speedup curves improves with larger thread granularity, while Active threads show relatively good speedup even for small thread granularity. BSP processes are naturally coarse-grained, and thus good speedup is achieved in our simulation application.
32109322
RIBRA-An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem
We develop an iterative relaxation algorithm, called RIBRA, for NMR protein backbone assignment. RIBRA applies nearest neighbor and weighted maximum independent set algorithms to solve the problem. To deal with noisy NMR spectral data, RIBRA is executed in an iterative fashion based on the quality of spectral peaks. We first produce spin system pairs using the spectral data without missing peaks, then the data group with one missing peak, and finally, the data group with two missing peaks. We test RIBRA on two real NMR datasets: hb-SBD and hbLBD, and perfect BMRB data (with 902 proteins) and four synthetic BMRB data which simulate four kinds of errors. The accuracy of RIBRA on hbSBD and hbLBD are 91.4% and 83.6%, respectively. The average accuracy of RIBRA on perfect BMRB datasets is 98.28%, and 98.28%, 95.61%, 98.16% and 96.28% on four kinds of synthetic datasets, respectively.
17603178
A Linear Time Algorithm for Finding a Maximal Planar Subgraph Based on PC-Trees
In Shih & Hsu, a planarity test was introduced utilizing a data structure called PC-trees, generalized from PQ-trees. They illustrated that a PC-tree is more natural in representing planar graphs. Their algorithm starts by constructing a depth-first-search tree and adds all back edges to a vertex one by one. An important feature in the S&H algorithm is that, at each iteration, at most two terminal nodes need to be computed and the unique tree path between these two nodes provides essentially the boundary path of the newly formed biconnected component. 
 
In this paper we modify their PC-tree algorithm and introduce the deferred planarity test (DPT), which has the added benefit of finding a maximal planar subgraph (MPS) in linear time when the given graph is not planar. DPT is an incremental algorithm, which only computes a partial terminal path at each iteration. DPT continually deletes back edges that could create a violation to the formation of those partial terminal paths so that, at the end, the subgraph constructed is guaranteed to be planar. 
 
The key to the efficiency of the S&H and the DPT algorithms lies in their management on the creation and destruction of biconnected components in which the PC-tree plays a major role. Previously, there have been reports that the MPS problem can be solved in linear time. However, there was no concrete data structure realizing them.
341424
Domain Event Extraction and Representation with Domain Ontology
With domain ontology, a meaningful index of document indexing, such as the domain events structure in this paper, can be defined. Since the construction of domain ontology is costly, an automatic domain ontology acquisition is preferred. We find that named entity can be a clue of domain event acquisition from the training corpus. Therefore , we add the named entity recognition module into the automatic domain ontology acquisition process. Thus, a subject-verb-object-modifier (SVOM) indexing can be constructed. Our experimental results demonstrate that the automatic event extraction and ontology acquisition can be good resources for text categorization and further information processing.
16227528
Fast image retrieval using color-spatial information
Abstract. In this paper, we present an image retrieval system that employs both the color and spatial information of images to facilitate the retrieval process. The basic unit used in our technique is a single-colored cluster, which bounds a homogeneous region of that color in an image. Two clusters from two images are similar if they are of the same color and overlap in the image space. The number of clusters that can be extracted from an image can be very large, and it affects the accuracy of retrieval. We study the effect of the number of clusters on retrieval effectiveness to determine an appropriate value for “optimal'' performance. To facilitate efficient retrieval, we also propose a multi-tier indexing mechanism called the Sequenced Multi-Attribute Tree (SMAT). We implemented a two-tier SMAT, where the first layer is used to prune away clusters that are of different colors, while the second layer discriminates clusters of different spatial locality. We conducted an experimental study on an image database consisting of 12,000 images. Our results show the effectiveness of the proposed color-spatial approach, and the efficiency of the proposed indexing mechanism.