A Statistical Model for Automatic Extraction of Korean Transliterated Foreign Words
In this paper, we will describe a Korean transliterated foreign word extraction algorithm. In the proposed method, we reformulate the foreign word extraction problem as a syllable-tagging problem such that each syllable is tagged with a foreign syllable tag or a pure Korean syllable tag. Syllable sequences of Korean strings are modelled by Hidden Markov Model whose state represents a character with binary marking to indicate whether the syllable is part of a transliterated foreign word or not. The proposed method extracts a transliterated foreign word with high recall rate and precision rate. Moreover, our method shows good performance even with small-sized training corpora.

title: Incremental cue phrase learning and bootstrapping method for causality extraction using cue phrase and word pair probabilities
abstract: This work aims to extract possible causal relations that exist between noun phrases. Some causal relations are manifested by lexical patterns like causal verbs and their sub-categorization. We use lexical patterns as a filter to find causality candidates and we transfer the causality extraction problem to the binary classification. To solve the problem, we introduce probabilities for word pair and concept pair that could be part of causal noun phrase pairs. We also use the cue phrase probability that could be a causality pattern. These probabilities are learned from the raw corpus in an unsupervised manner. With this probabilistic model, we increase both precision and recall. Our causality extraction shows an F-score of 77.37%, which is an improvement of 21.14 percentage points over the baseline model. The long distance causal relation is extracted with the binary tree-styled cue phrase. We propose an incremental cue phrase learning method based on the cue phrase confidence score that was measured after each causal classifier learning step. A better recall of 15.37 percentage points is acquired after the cue phrase learning.

title: Effective foreign word extraction for Korean information retrieval
abstract: In Korean text, foreign words, which are mostly transliterations of English words, are frequently used. Foreign words are usually very important index terms in Korean information retrieval since most of them are technical terms or names. So accurate foreign word extraction is crucial for high performance of information retrieval. However, accurate foreign word extraction is not easy because it inevitably accompanies word segmentation and most of the foreign words are unknown. In this paper, we present an effective foreign word recognition and extraction method. In order to accurately extract foreign words, we developed an effective method of word segmentation that involves unknown foreign words. Our word segmentation method effectively utilizes both unknown word information acquired through the automatic dictionary compilation and foreign word recognition information. Our HMM-based foreign word recognition method does not require large labeled examples for the model training unlike the previously proposed method.

title: A Comparison of Different Machine Transliteration Models
abstract: Machine transliteration is a method for automatically converting words in one language into phonetically equivalent ones in another language. Machine transliteration plays an important role in natural language applications such as information retrieval and machine translation, especially for handling proper nouns and technical terms. Four machine transliteration models - grapheme-based transliteration model, phoneme-based transliteration model, hybrid transliteration model, and correspondence-based transliteration model - have been proposed by several researchers. To date, however, there has been little research on a framework in which multiple transliteration models can operate simultaneously. Furthermore, there has been no comparison of the four models within the same framework and using the same data. We addressed these problems by 1) modeling the four models within the same framework, 2) comparing them under the same conditions, and 3) developing a way to improve machine transliteration through this comparison. Our comparison showed that the hybrid and correspondence-based models were the most effective and that the four models can be used in a complementary manner to improve machine transliteration performance.

title: Re-ranking model based on document clusters
abstract: In this paper, we describe a model of information retrieval system that is based on a document re-ranking method using document clusters. In the first step, we retrieve documents based on the inverted-file method. Next, we analyze the retrieved documents using document clusters, and re-rank them. In this step, we use static clusters and dynamic cluster view. Consequently, we can produce clusters that are tailored to characteristics of the query. We focus on the merits of the inverted-file method and cluster analysis. In other words, we retrieve documents based on the inverted-file method and analyze all terms in document based on the cluster analysis. By these two steps, we can get the retrieved results which are made by the consideration of the context of all terms in a document as well as query terms. We will show that our method achieves significant improvements over the method based on similarity search ranking alone.

title: Determining the specificity of terms using inside-outside information: a necessary condition of term hierarchy mining
abstract: This paper introduces new specificity measuring methods of terms using inside and outside information. Specificity of a term is the quantity of domain specific information contained in the term. Specific terms have a larger quantity of domain information than general terms. Specificity is an important necessary condition for building hierarchical relations among terms. If t1 is a hyponym of t2 in a domain term hierarchy, then the specificity of t1 is greater than that of t2. As domain specific terms are commonly compounds of the generic level term and some modifiers, inside information is important to represent the meaning of terms. Outside contextual information is also used to complement the shortcomings of inside information. We propose an information theoretic method to measure the quantity of terms. Experiments showed promising results with a precision of 73.9% when applied to terms in the MeSH thesaurus.

title: Fine-Grained Dynamic Voltage and Frequency Scaling for Precise Energy and Performance Trade-Off Based on the Ratio of Off-Chip Access to On-Chip Computation Times
abstract: This paper presents an intra-process dynamic voltage and frequency scaling (DVFS) technique targeted toward non real-time applications running on an embedded system platform. The key idea is to make use of runtime information about the external memory access statistics in order to perform CPU voltage and frequency scaling with the goal of minimizing the energy consumption while translucently controlling the performance penalty. The proposed DVFS technique relies on dynamically-constructed regression models that allow the CPU to calculate the expected workload and slack time for the next time slot, and thus, adjust its voltage and frequency in order to save energy while meeting soft timing constraints. This is in turn achieved by estimating and exploiting the ratio of the total off-chip access time to the total on-chip computation time. The proposed technique has been implemented on an XScale-based embedded system platform and actual energy savings have been calculated by current measurements in hardware. For memory-bound programs, a CPU energy saving of more than 70% with a performance degradation of 12% was achieved. For CPU-bound programs, 15/spl sim/60% CPU energy saving was achieved at the cost of 5-20% performance penalty.

title: Efficient instruction-level optimization methodology for low-power embedded systems
abstract: For low-power embedded systems, we solve the instruction scheduling and reordering problem as a Precedence Constrained Hamiltonian Path Problem for DAGs and the traveling salesman problem (TSP), both of which are NP-hard (W.J. Cook et al., 1998; V. Jain et al., 1999). We propose an efficient instruction-level optimization algorithm for solving the NP-hard problem. Minimum spanning tree (MST) and simulated annealing (SA) mechanisms are used for the optimization. We describe the methods for generating the control flow and data dependence graph (CDG), power dissipation table (PDT), and weighted strongly connected graph (SCG) for the instruction-level low-power analysis. In addition, confidence limits with error tolerance are considered for the validation of the optimization. Finally, experimental results that demonstrate the effectiveness and efficiency of the proposed algorithms are shown.

title: Nonrandom Clusters of Palindromes in Herpesvirus Genomes
abstract: Palindromes are symmetrical words of DNA in the sense that they read exactly the same as their reverse complementary sequences. Representing the occurrences of palindromes in a DNA molecule as points on the unit interval, the scan statistics can be used to identify regions of unusually high concentration of palindromes. These regions have been associated with the replication origins on a few herpesviruses in previous studies. However, the use of scan statistics requires the assumption that the points representing the palindromes are independently and uniformly distributed on the unit interval. In this paper, we provide a mathematical basis for this assumption by showing that in randomly generated DNA sequences, the occurrences of palindromes can be approximated by a Poisson process. An easily computable upper bound on the Wasserstein distance between the palindrome process and the Poisson process is obtained. This bound is then used as a guide to choose an optimal palindrome length in the analysis of a collection of 16 herpesvirus genomes. Regions harboring significant palindrome clusters are identified and compared to known locations of replication origins. This analysis brings out a few interesting extensions of the scan statistics that can help formulate an algorithm for more accurate prediction of replication origins.

title: Multiple Genome Alignment by Clustering Pairwise Matches
abstract: We have developed a multiple genome alignment algorithm by using a sequence clustering algorithm to combine local pairwisegenome sequence matches produced by pairwise genome alignments, e.g, BLASTZ. Sequence clustering algorithms often generate clusters of sequences such that there exists a common shared region among all sequences in each cluster. To use a sequence clustering algorithm for genome alignment, it is necessary to handle numerous local alignments between a pair of genomes. We propose a multiple genome alignment method that converts the multiple genome alignment problem to the sequence clustering problem. This method does not need to make a guide tree to determine the order of multiple alignment, and it accurately detects multiple homologous regions. As a result, our multiple genome alignment algorithm performs competitively over existing algorithms. This is shown using an experiment which compares the performance of TBA, MultiPipMaker (MPM) and our algorithm in aligning 12 groups of 56 microbial genomes and by evaluating the number of common COGs detected.

title: PLATCOM: Current Status and Plan for the Next Stages
abstract: We have been developing a web-based system for comparing multiple genomes, PLATCOM, where users can choose genomes of their choice freely and perform analysis of the selected genomes with a suite of computational tools. PLATCOM is built on internal databases such as GenBank, COG, KEGG, and Pairwise Comparison Database (PCDB) that contains all pairwise comparisons (97,034 entries) of protein sequence files (.faa) and whole genome sequence files (.fna) of 312 replicons. Since combining multiple tools for sequence analysis requires a significant amount of programming work and knowledge on each tool, we also developed and incorporated high performance sequence data mining tools such as sequence clustering and neighborhood prediction. The next plan includes defining several data types for genome analysis and integrating system modules using data mining tools that operate on the genome data types. PLATCOM is available at http://platcom.informatics.indiana.edu.