Inbok Lee - Academia.edu (original) (raw)

Papers by Inbok Lee

Research paper thumbnail of Development of Straightforward Method of Estimating LMA and LMR using Computational Fluid Dynamics Technology

Ventilation efficiency has an important role in agricultural facilities such as greenhouse and li... more Ventilation efficiency has an important role in agricultural facilities such as greenhouse and livestock house to keep internally optimum environmental condition. Age-of-air concept allows to assess the ventilation efficiency of an agricultural facility according to estimating the ability of fresh air supply and contaminants emission using LMA and LMR. Most of these methods use a tracer gas method which has some limitations in experiment like dealing unstable and invisible gas. Therefore, the aim of this study was to develop a straightforward method to calculate age-of-air values with CFD simulation which has the advantage of saving computational time and resources and these method can solve the limitations in experiment using tracer gas method. The main idea of LMA computation is to solve the passive scalar transport equation with the assumption that the production of the time scalar throughout the room is uniform. In case of LMR calculation, the transport of the time scalar was re...

Research paper thumbnail of delta-gamma-Parameterized Matching

String Processing and Information Retrieval, 2008

This paper defines a new pattern matching problem by combining two paradigms: δγ–matching and par... more This paper defines a new pattern matching problem by combining two paradigms: δγ–matching and parameterized matching. The solution is essentially obtained by a combination of bitparallel techniques and a reduction to a graph matching problem. The time complexity of the algorithm is O(nm), assuming text size n, pattern size m and a constant size alphabet.

Research paper thumbnail of Finding overlaps within regular expressions with variable-length gaps

Proceedings of the 2013 Research in Adaptive and Convergent Systems on - RACS '13, 2013

ABSTRACT Regular expressions play an important role in various fields in computer science. Howeve... more ABSTRACT Regular expressions play an important role in various fields in computer science. However, handling many regular expressions in parallel requires huge computation resources. Therefore, it is necessary to find and eliminate overlapping regular expressions. In this paper, we consider a special type of regular expressions: expressions comprised of characters and variable-length gaps between such characters. Specifically, we propose a bit-parallel solution to determine whether the languages of two expressions X and Y with variable-length gaps have a common string. The time complexity of our algorithm is O (min (LX 2|Σ|, LX LY)/w) where Σ is the alphabet from which X and Y are drawn, LX and LY are the lengths of the longest strings that respectively match X and Y, and w is the size of the computer word.

Research paper thumbnail of Approximate Function Matching under δ- and γ- Distances

Lecture Notes in Computer Science, 2012

ABSTRACT This paper defines a new string matching problem by combining two paradigms: function ma... more ABSTRACT This paper defines a new string matching problem by combining two paradigms: function matching and δγ-matching. The result is an approximate variant of function matching where two equal-length strings X and Y match if there exists a function that maps X to a string X′ such that X′ and Y are δγ- similar. We propose an O(nm) algorithm for finding all the matches of a pattern P1 …m in a text T1 …n.

Research paper thumbnail of Optimizing Weighted Kernel Function for Support Vector Machine by Genetic Algorithm

Lecture Notes in Computer Science, 2006

The problem of determining optimal decision model is a difficult combinatorial task in the fields... more The problem of determining optimal decision model is a difficult combinatorial task in the fields of pattern classification, machine learning, and especially bioinformatics. Recently, support vector machine (SVM) has shown a better performance than conventional ...

Research paper thumbnail of δγ – Parameterized Matching

Lecture Notes in Computer Science, 2009

I would like to thank my advisor Moshe Lewenstein for his guidance and directions. He taught me a... more I would like to thank my advisor Moshe Lewenstein for his guidance and directions. He taught me a lot and I am grateful for the time and effort he put in this work.

Research paper thumbnail of Extending alignments with k-mismatches and ℓ-gaps

Theoretical Computer Science, 2014

Recently, the problem of extending an alignment with k-mismatches and a single gap for pairwise s... more Recently, the problem of extending an alignment with k-mismatches and a single gap for pairwise sequence alignment was introduced (Flouri et al., 2011). The authors considered the problem of extending an alignment under the Hamming distance model by also allowing the insertion of a single gap; and presented a Θ(mβ)-algorithm to solve it, where m is the length of the shortest sequence to be extended, and β is the maximum allowed length of the single gap. Very recently, it was shown ) that this problem is strongly and directly motivated by the next-generation resequencing application: aligning tens of millions of short DNA sequences against a reference genome. In this article, we consider an extension of this problem: extending an alignment with k-mismatches and two gaps; and present a Θ(mβ)-time algorithm to solve it. This extension is proved to be fundamental in the next-generation re-sequencing application . In addition, we present a generalisation of our solution to solve the problem of extending an alignment with k-mismatches and ℓ-gaps in time Θ(mβℓ). The presented solutions work provided that all gaps in the alignment must occur in one of the two sequences.

Research paper thumbnail of A Simple Algorithm for Finding Exact Common Repeats

IEICE Transactions on Information and Systems, 2007

Given a set of strings U = {T 1 , T 2 , . . . , T }, the longest common repeat problem is to find... more Given a set of strings U = {T 1 , T 2 , . . . , T }, the longest common repeat problem is to find the longest common substring that appears at least twice in each string, considering direct, inverted, and mirror repeats. We define the generalised longest common repeat problem and present a linear time solution.

Research paper thumbnail of Finding Patterns with Variable Length Gaps or Don’t Cares

Lecture Notes in Computer Science, 2006

In this paper we have presented new algorithms to handle the pattern matching problem where the p... more In this paper we have presented new algorithms to handle the pattern matching problem where the pattern can contain variable length gaps. Given a pattern P with variable length gaps and a text T our algorithm works in O(n + m + α log(max 1<=i<=l (bi − ai))) time where n is the length of the text, m is the summation of the lengths of the component subpatterns, α is the total number of occurrences of the component subpatterns in the text and ai and bi are, respectively, the minimum and maximum number of don't cares allowed between the ith and (i+1)st component of the pattern. We also present another algorithm which, given a suffix array of the text, can report whether P occurs in T in O(m + α log log n) time. Both the algorithms record information to report all the occurrences of P in T . Furthermore, the techniques used in our algorithms are shown to be useful in many other contexts.

Research paper thumbnail of Development of Straightforward Method of Estimating LMA and LMR using Computational Fluid Dynamics Technology

Ventilation efficiency has an important role in agricultural facilities such as greenhouse and li... more Ventilation efficiency has an important role in agricultural facilities such as greenhouse and livestock house to keep internally optimum environmental condition. Age-of-air concept allows to assess the ventilation efficiency of an agricultural facility according to estimating the ability of fresh air supply and contaminants emission using LMA and LMR. Most of these methods use a tracer gas method which has some limitations in experiment like dealing unstable and invisible gas. Therefore, the aim of this study was to develop a straightforward method to calculate age-of-air values with CFD simulation which has the advantage of saving computational time and resources and these method can solve the limitations in experiment using tracer gas method. The main idea of LMA computation is to solve the passive scalar transport equation with the assumption that the production of the time scalar throughout the room is uniform. In case of LMR calculation, the transport of the time scalar was re...

Research paper thumbnail of delta-gamma-Parameterized Matching

String Processing and Information Retrieval, 2008

This paper defines a new pattern matching problem by combining two paradigms: δγ–matching and par... more This paper defines a new pattern matching problem by combining two paradigms: δγ–matching and parameterized matching. The solution is essentially obtained by a combination of bitparallel techniques and a reduction to a graph matching problem. The time complexity of the algorithm is O(nm), assuming text size n, pattern size m and a constant size alphabet.

Research paper thumbnail of Finding overlaps within regular expressions with variable-length gaps

Proceedings of the 2013 Research in Adaptive and Convergent Systems on - RACS '13, 2013

ABSTRACT Regular expressions play an important role in various fields in computer science. Howeve... more ABSTRACT Regular expressions play an important role in various fields in computer science. However, handling many regular expressions in parallel requires huge computation resources. Therefore, it is necessary to find and eliminate overlapping regular expressions. In this paper, we consider a special type of regular expressions: expressions comprised of characters and variable-length gaps between such characters. Specifically, we propose a bit-parallel solution to determine whether the languages of two expressions X and Y with variable-length gaps have a common string. The time complexity of our algorithm is O (min (LX 2|Σ|, LX LY)/w) where Σ is the alphabet from which X and Y are drawn, LX and LY are the lengths of the longest strings that respectively match X and Y, and w is the size of the computer word.

Research paper thumbnail of Approximate Function Matching under δ- and γ- Distances

Lecture Notes in Computer Science, 2012

ABSTRACT This paper defines a new string matching problem by combining two paradigms: function ma... more ABSTRACT This paper defines a new string matching problem by combining two paradigms: function matching and δγ-matching. The result is an approximate variant of function matching where two equal-length strings X and Y match if there exists a function that maps X to a string X′ such that X′ and Y are δγ- similar. We propose an O(nm) algorithm for finding all the matches of a pattern P1 …m in a text T1 …n.

Research paper thumbnail of Optimizing Weighted Kernel Function for Support Vector Machine by Genetic Algorithm

Lecture Notes in Computer Science, 2006

The problem of determining optimal decision model is a difficult combinatorial task in the fields... more The problem of determining optimal decision model is a difficult combinatorial task in the fields of pattern classification, machine learning, and especially bioinformatics. Recently, support vector machine (SVM) has shown a better performance than conventional ...

Research paper thumbnail of δγ – Parameterized Matching

Lecture Notes in Computer Science, 2009

I would like to thank my advisor Moshe Lewenstein for his guidance and directions. He taught me a... more I would like to thank my advisor Moshe Lewenstein for his guidance and directions. He taught me a lot and I am grateful for the time and effort he put in this work.

Research paper thumbnail of Extending alignments with k-mismatches and ℓ-gaps

Theoretical Computer Science, 2014

Recently, the problem of extending an alignment with k-mismatches and a single gap for pairwise s... more Recently, the problem of extending an alignment with k-mismatches and a single gap for pairwise sequence alignment was introduced (Flouri et al., 2011). The authors considered the problem of extending an alignment under the Hamming distance model by also allowing the insertion of a single gap; and presented a Θ(mβ)-algorithm to solve it, where m is the length of the shortest sequence to be extended, and β is the maximum allowed length of the single gap. Very recently, it was shown ) that this problem is strongly and directly motivated by the next-generation resequencing application: aligning tens of millions of short DNA sequences against a reference genome. In this article, we consider an extension of this problem: extending an alignment with k-mismatches and two gaps; and present a Θ(mβ)-time algorithm to solve it. This extension is proved to be fundamental in the next-generation re-sequencing application . In addition, we present a generalisation of our solution to solve the problem of extending an alignment with k-mismatches and ℓ-gaps in time Θ(mβℓ). The presented solutions work provided that all gaps in the alignment must occur in one of the two sequences.

Research paper thumbnail of A Simple Algorithm for Finding Exact Common Repeats

IEICE Transactions on Information and Systems, 2007

Given a set of strings U = {T 1 , T 2 , . . . , T }, the longest common repeat problem is to find... more Given a set of strings U = {T 1 , T 2 , . . . , T }, the longest common repeat problem is to find the longest common substring that appears at least twice in each string, considering direct, inverted, and mirror repeats. We define the generalised longest common repeat problem and present a linear time solution.

Research paper thumbnail of Finding Patterns with Variable Length Gaps or Don’t Cares

Lecture Notes in Computer Science, 2006

In this paper we have presented new algorithms to handle the pattern matching problem where the p... more In this paper we have presented new algorithms to handle the pattern matching problem where the pattern can contain variable length gaps. Given a pattern P with variable length gaps and a text T our algorithm works in O(n + m + α log(max 1<=i<=l (bi − ai))) time where n is the length of the text, m is the summation of the lengths of the component subpatterns, α is the total number of occurrences of the component subpatterns in the text and ai and bi are, respectively, the minimum and maximum number of don't cares allowed between the ith and (i+1)st component of the pattern. We also present another algorithm which, given a suffix array of the text, can report whether P occurs in T in O(m + α log log n) time. Both the algorithms record information to report all the occurrences of P in T . Furthermore, the techniques used in our algorithms are shown to be useful in many other contexts.