5208095
Decomposition of perfect graphs
Abstract We describe composition and decomposition schemes for perfect graphs, which generalize all recent results in this area, e.g., the amalgam and the 2-amalgam split. Our approach is based on the consideration of induced cycles and their complements in perfect graphs (as opposed to the consideration of cycles for defining biconnected or 3-connected graphs). Our notion of 1-inseparable graphs is “parallel” to that of biconnected graphs in that different edges in different inseparable components of a graph are not contained in any induced cycle or any complement of an induced cycle. Furthermore, in a special case which generalizes the join operation, this definition is self-complementary in a natural fashion. Our 2-composition operation, which only creates even induced cycles in the composed graphs, is based on two perfection-preserving vertex merge operations on perfect graphs. As a by-product, some new properties of minimally imperfect graphs are presented.
1312350
Fast algorithms for the dominating set problem on permutation graphs
AnO(n log logn) (resp.O(n2 log2n)) algorithm is presented to solve the minimum cardinality (resp. weight) dominating set problem on permutation graphs, assuming the input is a permutation. The best-known previous algorithm was given by FÄrber and Keil, where they use dynamic programming to get anO(n2 (resp.O(n3)) algorithm. Our improvement is based on the following three factors: (1) an observation on the order among the intermediate terms in the dynamic programming, (2) a new construction formula for the intermediate terms, and (3) efficient data structures for manipulating these terms.
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.
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.
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.
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.
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.
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.
5367915
A Maximum Entropy Approach to Biomedical Named Entity Recognition
Machine learning approaches are frequently used to solve name entity (NE) recognition (NER). In this paper we propose a hybrid method that uses maximum entropy (ME) as the underlying machine learning method incorporated with dictionary-based and rule-based methods for post-processing. Simply using ME for NER, inaccurate boundary detection of NEs and misclassification may occur. Some NEs are partially recognized by ME. In the post-processing stage, we use dictionary-based and rule-based methods to extend boundary of partially recognized NEs and to adjust classification. We use GENIA corpus 3.01 to conduct 10-fold cross-verification experiments. To evaluate the performance, we consider the longest NE annotations. We evaluate our approach using standard precision (P), recall (R), and F-score, where F-score is defined as 2PR/(P+R). The precision, recall and F-score ([P, R, F]) of our ME module for overall 23 categories is [0.512, 0.538, 0.525], and after the post-processing the performance becomes [0.729, 0.711, 0.72] for [P, R, F]. For protein, DNA and RNA classes, our method achieves [P, R, F] of [0.77, 0.80, 0.785], [0.653, 0.748, 0.7], and [0.716, 0.788, 0.752], respectively. The post-processing stage significantly improves the performance of our ME-based NER module.
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.
6185076
Text categorization using automatically acquired domain ontology
In this paper, we describe ontology-based text categorization in which the domain ontologies are automatically acquired through morphological rules and statistical methods. The ontology-based approach is a promising way for general information retrieval applications such as knowledge management or knowledge discovery. As a way to evaluate the quality of domain ontologies, we test our method through several experiments. Automatically acquired domain ontologies, with or without manual editing, have been used for text categorization. The results are quite satisfactory. Furthermore, we have developed an automatic method to evaluate the quality of our domain ontology.