A Korean-Japanese-Chinese Aligned Wordnet with Shared Semantic Hierarchy
A Korean-Japanese-Chinese aligned wordnet, “CoreNet” is introduced. For the purpose of this paper, the term “wordnet” refers to a network of words. It is constructed based on a shared semantic hierarchy that is originated from NTT Goidaikei (Lexical Hierarchical System). Korean wordnet was constructed through the semantic category assignment to every meaning of Korean words in a dictionary. Verbs and adjectives’ word senses are assigned to the same semantic hierarchy as that of nouns. Each sense of verbs is investigated from corpora for their usage, and compared with Japanese translation. Chinese wordnet with the same semantic hierarchy was built up based on the comparison with Korean wordnet. Each sense of Chinese verb corresponds to Korean with its argument structure. The use of the same semantic hierarchy for nouns and predicates has several advantages. First, the surface forms of nouns and predicates share the similar one, especially in Chinese words. In case of Korean and Japanese, the typical formation is like “do+Noun” in English like “Noun+suru” in Japanese and “Noun+hada” in Korean. Second, the language generation from conceptual structures takes freedom to choose the surface form whether it chooses noun phrases or verb phrases. CoreNet has been constructed by the following principles: word sense mapping to concept, corpus-based, multi-lingualism, and single concept system for multi-languages. The overall flow of construction is based on dictionary-based bootstrapping, incremental similarity-based classification and manual post-editing. Among consideration points, the followings are introduced: multiple concept mapping, verbal noun, and concept splitting. For multiple concept mapping, a word is mapped into numerous concepts that comprise respective meanings of the word. For example, school is an “institution for the instruction of students.” The word school is mapped into three concepts such as location, organization, and facility. For verbal noun, a word that is a verb is assigned to concepts after it is transformed to a noun. For example, “write” is transformed to its noun form “writing” that is mapped into a concept writing falling under event. For concept splitting, every time inconsistency among nodes of concepts is discovered, a node may be added. What differs between CoreNet and NTT Goidaikei is that CoreNet features mapping between word senses (not just words) and concepts. These works have lasted since 1994.

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: A Statistical Model for Automatic Extraction of Korean Transliterated Foreign Words
abstract: 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: Implicit ambiguity resolution using incremental clustering in cross-language information retrieval
abstract: This paper presents a method to implicitly resolve ambiguities using dynamic incremental clustering in cross-language information retrieval (CLIR) such as Korean-to-English and Japanese-to-English CLIR. The main objective of this paper shows that document clusters can effectively resolve the ambiguities tremendously increased in translated queries as well as take into account the context of all the terms in a document. In the framework we propose, a query in Korean/Japanese is first translated into English by looking up bilingual dictionaries, then documents are retrieved for the translated query terms based on the vector space retrieval model or the probabilistic retrieval model. For the top-ranked retrieved documents, query-oriented document clusters are incrementally created and the weight of each retrieved document is recalculated by using the clusters. In the experiment based on TREC CLIR test collection, our method achieved 39.41% and 36.79% improvement for translated queries without ambiguity resolution in Korean-to-English CLIR, and 17.89% and 30.46% improvements in Japanese-to-English CLIR, on the vector space retrieval and on the probabilistic retrieval, respectively. Our method achieved 12.30% improvement for all translation queries, compared with blind feedback for the probabilistic retrieval in Korean-to-English CLIR. These results indicate that cluster analysis help to resolve ambiguity.

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: Palindromes in SARS and Other Coronaviruses
abstract: With the identification of a novel coronavirus associated with the severe acute respiratory syndrome (SARS), computational analysis of its RNA genome sequence is expected to give useful clues to help elucidate the origin, evolution, and pathogenicity of the virus. In this paper, we study the collective counts of palindromes in the SARS genome along with all the completely sequenced coronaviruses. Based on a Markov-chain model for the genome sequence, the mean and standard deviation for the number of palindromes at or above a given length are derived. These theoretical results are complemented by extensive simulations to provide empirical estimates. Using a z score obtained from these mathematical and empirical means and standard deviations, we have observed that palindromes of length four are significantly underrepresented in all the coronaviruses in our data set. In contrast, length-six palindromes are significantly underrepresented only in the SARS coronavirus. Two other features are unique to the SARS sequence. First, there is a length-22 palindrome TCTTTAACAAGCTTGTTAAAGA spanning positions 25962-25983. Second, there are two repeating length-12 palindromes TTATAATTATAA spanning positions 22712-22723 and 22796-22807. Some further investigations into possible biological implications of these palindrome features are proposed.

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.

title: PLATCOM: a Platform for Computational Comparative Genomics
abstract: As more whole genome sequences become available, comparing multiple genomes at the sequence level can provide insight into new biological discovery. However, there are significant challenges for genome comparison. The challenge includes requirement for computational resources owing to the large volume of genome data. More importantly, since the choice of genomes to be compared is entirely subjective, there are too many choices for genome comparison. For these reasons, there is pressing need for bioinformatics systems for comparing multiple genomes where users can choose genomes to be compared freely.



PLATCOM (Platform for Computational Comparative Genomics) is an integrated system for the comparative analysis of multiple genomes. The system is built on several public databases and a suite of genome analysis applications are provided as exemplary genome data mining tools over these internal databases. Researchers are able to visually investigate genomic sequence similarities, conserved gene neighborhoods, conserved metabolic pathways and putative gene fusion events among a set of selected multiple genomes.



http://platcom.informatics.indiana.edu/platcom

title: PA-ZSA (Power-Aware Zero-Slack Algorithm): A Graph-Based Timing Analysis for Ultra-Low Power CMOS VLSI
abstract: This paper describes a slack budget distribution algorithm for ultra-low power CMOS logic circuits in a VLSI design environment. We introduce Power-Aware Zero-Slack Algorithm (PA-ZSA), which distributes the surplus time slacks into the most power-hungry modules. The PA-ZSA ensures that the total slack budget is near-maximal and the total power is minimal as a power-aware version of the well-known zero-slack algorithm (ZSA). Based on these time slacks, we have conducted the low-power optimization at gate level by using technology scaling technique. The experimental results show that our strategy reduces average 36% of the total (static and dynamic) power over the conventional slack budget distribution algorithms.

title: Sensitivity analysis and efficient method for identifying optimal spaced seeds
abstract: The novel introduction of spaced seed idea in the filtration stage of sequence comparison by Ma et al. (Bioinformatics 18 (2002) 440) has greatly increased the sensitivity of homology search without compromising the speed of search. Finding the optimal spaced seeds is of great importance both theoretically and in designing better search tool for sequence comparison. In this paper, we study the computational aspects of calculating the hitting probability of spaced seeds; and based on these results, we propose an efficient algorithm for identifying optimal spaced seeds.