• Title/Summary/Keyword: Similarity Searches

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Identification Performance of Low-Molecular Compounds by Searching Tandem Mass Spectral Libraries with Simple Peak Matching

  • Milman, Boris L.;Zhurkovich, Inna K.
    • Mass Spectrometry Letters
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    • v.9 no.3
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    • pp.73-76
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    • 2018
  • The number of matched peaks (NMP) is estimated as the spectral similarity measure in tandem mass spectral library searches of small molecules. In the high resolution mode, NMP provides the same reliable identification as in the case of a common dot-product function. Corresponding true positive rates are ($94{\pm}3$) % and ($96{\pm}3$) %, respectively.

Isomer Differentiation Using in silico MS2 Spectra. A Case Study for the CFM-ID Mass Spectrum Predictor

  • Milman, Boris L.;Ostrovidova, Ekaterina V.;Zhurkovich, Inna K.
    • Mass Spectrometry Letters
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    • v.10 no.3
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    • pp.93-101
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    • 2019
  • Algorithms and software for predicting tandem mass spectra have been developed in recent years. In this work, we explore how distinct in silico $MS^2$ spectra are predicted for isomers, i.e. compounds having the same formula and similar molecular structures, to differentiate between them. We used the CFM-ID 2.0/3.0 predictor with regard to (a) test compounds, whose experimental mass spectra had been randomly sampled from the MassBank of North America (MoNA) collection, and to (b) the most widespread isomers of test compounds searched in the PubChem database. In the first validation test, in silico mass spectra constitute a reference library, and library searches are performed for test experimental spectra of "unknowns". The searches led to the true positive rate (TPR) of ($46-48{\pm}10$)%. In the second test, in silico and experimental spectra were interchanged and this resulted in a TPR of ($58{\pm}10$)%. There were no significant differences between results obtained with different metrics of spectral similarity and predictor versions. In a comparison of test compounds vs. their isomers, a statistically significant correlation between mass spectral data and structural features was observed. The TPR values obtained should be regarded as reasonable results for predicting tandem mass spectra of related chemical structures.

Moving Objects Modeling for Supporting Content and Similarity Searches (내용 및 유사도 검색을 위한 움직임 객체 모델링)

  • 복경수;김미희;신재룡;유재수;조기형
    • Journal of Korea Multimedia Society
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    • v.7 no.5
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    • pp.617-632
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    • 2004
  • Video Data includes moving objects which change spatial positions as time goes by. In this paper, we propose a new modeling method for a moving object contained in the video data. In order to effectively retrieve moving objects, the proposed modeling method represents the spatial position and the size of a moving object. It also represents the visual features and the trajectory by considering direction, distance and speed or moving objects as time goes by. Therefore, It allows various types of retrieval such as visual feature based similarity retrieval, distance based similarity retrieval and trajectory based similarity retrieval and their mixed type of weighted retrieval.

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Efficient Processing of Subsequence Searching in Sequence Databases (시퀀스 데이터베이스를 위한 서브시퀀스 탐색의 효율적인 처리)

  • Park, Sang-Hyun;Kim, Sang-Wook;Park, Jeong-Il
    • Journal of Industrial Technology
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    • v.21 no.A
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    • pp.155-166
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    • 2001
  • This paper deals with the subsequence searching problem under time-warping. Our work is motivated by the observation that subsequence searches slow down quadratically as the average length of data sequences increases. To resolve this problem, the Segment-Based Approach for Subsequence Searches (SBASS) is proposed. The SBASS divides data and query sequences into a series of segments, and retrieves all data subsequences. Our segmentation scheme allows segments to have different lengths; thus we employ the time warping distance as a similarity measure for each segment pair. For efficient retrieval of similar subsequences, we extract feature vectors from all data segments exploiting their monotonically changing properties, and build a spatial index using feature vectors. The effectiveness of our approach is verified through extensive experiments.

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Wine Label Recognition System using Image Similarity (이미지 유사도를 이용한 와인라벨 인식 시스템)

  • Jung, Jeong-Mun;Yang, Hyung-Jeong;Kim, Soo-Hyung;Lee, Guee-Sang;Kim, Sun-Hee
    • The Journal of the Korea Contents Association
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    • v.11 no.5
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    • pp.125-137
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    • 2011
  • Recently the research on the system using images taken from camera phones as input is actively conducted. This paper proposed a system that shows wine pictures which are similar to the input wine label in order. For the calculation of the similarity of images, the representative color of each cell of the image, the recognized text color, background color and distribution of feature points are used as the features. In order to calculate the difference of the colors, RGB is converted into CIE-Lab and the feature points are extracted by using Harris Corner Detection Algorithm. The weights of representative color of each cell of image, text color and background color are applied. The image similarity is calculated by normalizing the difference of color similarity and distribution of feature points. After calculating the similarity between the input image and the images in the database, the images in Database are shown in the descent order of the similarity so that the effort of users to search for similar wine labels again from the searched result is reduced.

Approximate Top-k Labeled Subgraph Matching Scheme Based on Word Embedding (워드 임베딩 기반 근사 Top-k 레이블 서브그래프 매칭 기법)

  • Choi, Do-Jin;Oh, Young-Ho;Bok, Kyoung-Soo;Yoo, Jae-Soo
    • The Journal of the Korea Contents Association
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    • v.22 no.8
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    • pp.33-43
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    • 2022
  • Labeled graphs are used to represent entities, their relationships, and their structures in real data such as knowledge graphs and protein interactions. With the rapid development of IT and the explosive increase in data, there has been a need for a subgraph matching technology to provide information that the user is interested in. In this paper, we propose an approximate Top-k labeled subgraph matching scheme that considers the semantic similarity of labels and the difference in graph structure. The proposed scheme utilizes a learning model using FastText in order to consider the semantic similarity of a label. In addition, the label similarity graph(LSG) is used for approximate subgraph matching by calculating similarity values between labels in advance. Through the LSG, we can resolve the limitations of the existing schemes that subgraph expansion is possible only if the labels match exactly. It supports structural similarity for a query graph by performing searches up to 2-hop. Based on the similarity value, we provide k subgraph matching results. We conduct various performance evaluations in order to show the superiority of the proposed scheme.

Proposal of Memory Information Extension Model Using Adaptive Resonance Theory (ART를 이용한 기억 정보 확장 모델 제시)

  • 김주훈;김성주;김용택;전홍태
    • Proceedings of the IEEK Conference
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    • 2003.07d
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    • pp.1283-1286
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    • 2003
  • Human can update the memory with new information not forgetting acquired information in the memory. ART(Adaptive Resonance Theory) does not need to change all information. The methodology of ART is followed. The ART updates the memory with the new information that is unknown if it is similar with the memorized information. On the other hand, if it is unknown information the ART adds it to the memory not updating the memory with the new one. This paper shows that ART is able to classify sensory information of a certain object. When ART receives new information of the object as an input, it searches for the nearest thing among the acquired information in the memory. If it is revealed that new information of the object has similarity with the acquired object, the model is updated to reflect new information to the memory. When new object does not have similarity with the acquired object, the model register the object into new memory

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Video Data Modeling for Supporting Structural and Semantic Retrieval (구조 및 의미 검색을 지원하는 비디오 데이타의 모델링)

  • 복경수;유재수;조기형
    • Journal of KIISE:Databases
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    • v.30 no.3
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    • pp.237-251
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    • 2003
  • In this paper, we propose a video retrieval system to search logical structure and semantic contents of video data efficiently. The proposed system employs a layered modelling method that orBanifes video data in raw data layer, content layer and key frame layer. The layered modelling of the proposed system represents logical structures and semantic contents of video data in content layer. Also, the proposed system supports various types of searches such as text search, visual feature based similarity search, spatio-temporal relationship based similarity search and semantic contents search.

A Study on Audio Indexing Using Wavelet Transform for Content-based Retrieval in Audio Database (소파변환을 사용한 오디오 데이터 베이스 검색 기반에서의 오디오 색인에 관한 연구)

  • 최귀열;곽칠성
    • Journal of the Korea Institute of Information and Communication Engineering
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    • v.4 no.2
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    • pp.461-468
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    • 2000
  • Amounts of audio data used in several computer application have necessitated the development of audio database systems with newer features such as content-based queries and similarity searches to manage and use such data. Fast and accurate retrievals for content-based queries are crucial for such systems to be useful. Efficient content-based indexing and similarity searching schemes are keys to providing fast and relevant data retrievals. This paper present a method for indexing of Korean Traditional Music audio data based on wavelets. Also this paper present possibility of wavelet based audio indexing.

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A Method for Measuring Inter-Utterance Similarity Considering Various Linguistic Features (다양한 언어적 자질을 고려한 발화간 유사도 측정 방법)

  • Lee, Yeon-Su;Shin, Joong-Hwi;Hong, Gum-Won;Song, Young-In;Lee, Do-Gil;Rim, Hae-Chang
    • The Journal of the Acoustical Society of Korea
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    • v.28 no.1
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    • pp.61-69
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    • 2009
  • This paper presents an improved method measuring inter-utterance similarity in an example-based dialogue system, which searches the most similar utterance in a dialogue database to generate a response to a given user utterance. Unlike general inter-sentence similarity measures, the inter-utterance similarity measure for example-based dialogue system should consider not only word distribution but also various linguistic features, such as affirmation/negation, tense, modality, sentence type, which affects the natural conversation. However, previous approaches do not sufficiently reflect these features. This paper proposes a new utterance similarity measure by analyzing and reflecting various linguistic features to improve performance in accuracy. Also, by considering substitutability of the features, the proposed method can utilize limited number of examples. Experimental results show that the proposed method achieves 10%p improvement in accuracy compared to the previous method.