{"title":"Physical Model to Achieve Virtual Mezzotint","authors":"Daisuke Tasaki, M. Katou, S. Mizuno, M. Okada","doi":"10.2197/IPSJDC.3.244","DOIUrl":"https://doi.org/10.2197/IPSJDC.3.244","url":null,"abstract":"The authors propose a method of producing virtual mezzotint using a physics-based rendering approach. Mezzotint is a traditional copperplate printing technique. An important characteristic is its gradations from black to white. This is acquired in three phases during the plate-making process, i.e., by roughening, scraping, and burnishing. Numerous dots and burrs are created with a rocker in the roughening phase over the entire surface of the copper plate to obtain black areas in the print. The burrs are removed in the second phase with a scraper to yield halftones. The plate surface is finally polished with a burnisher in the last phase to produce the white areas. A method of simulating these phases and physical phenomena is discussed in this paper to make mezzotint enjoyable even for beginners and children. Zigzag-stroke patterns and paraboloidal-dot models are applied to the rocker to simulate the roughening phase. Reducing and smoothing models are applied to the scraper and burnisher to simulate the scraping and burnishing phases. The feasibility of the proposed method is demonstrated by observing and comparing actual and virtual plate surfaces with determined patterns and actual pieces of handcrafted work.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126944154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Retrieving functionally similar bioinformatics workflows using TF-IDF filtering","authors":"Junya Seo, S. Seno, Y. Takenaka, H. Matsuda","doi":"10.2197/IPSJDC.3.164","DOIUrl":"https://doi.org/10.2197/IPSJDC.3.164","url":null,"abstract":"In bioinformatics, dealing with tools to analyze biological data becomes important. Those tools are provided by various institutions and the number of the tools is rapidly increasing. Recently many institutions have been offering those tools and access to databases with Web service technologies. The workflow technology is one of the ways to manage those tools and it is becoming available in bioinformatics. In order to compose workflows, several research groups develop and provide workflow composing tools. And consequently, the concept “Workflow Reuse” is also arisen in order to help workflow composition. Nevertheless it is still difficult to search for the reusable workflows from the repository of workflows in the current situation. In this paper, we propose a method to extract reusable workflows from the repository by using currently available information. We could extract some functionally similar workflows as reusable ones. By extracting reusable workflows efficiently, researchers can compose their workflow more easily.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121859813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"GroupAdaBoost: Accurate Prediction and Selection of Important Genes","authors":"Takashi Takenouchi, M. Ushijima, S. Eguchi","doi":"10.2197/IPSJDC.3.145","DOIUrl":"https://doi.org/10.2197/IPSJDC.3.145","url":null,"abstract":"In this paper, we propose GroupAdaBoost which is a variant of AdaBoost for statistical pattern recognition. The objective of the proposed algorithm is to solve the “ p » n ”problem arisen in bioinformatics. In a microarray experiment, gene expressions are observed to extract any specific pattern of gene expressions related to a disease status. Typically, p is the number of investigated genes and n is number of individuals. The ordinary method for predicting the genetic causes of diseases is apt to over-learn from any particular training dataset because of the“ p » n ” problem. We observed that GroupAdaBoost gave a robust performance for cases of the excess number p of genes. In several real datasets which are publicly available from web-pages, we compared the analysis of results among the proposed method and others, and a small scale of simulation study to confirm the validity of the proposed method. Additionally the proposed method effectively worked for the identification of important genes.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"250 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129996679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Duality between Call-by-value Reductions and Call-by-name Reductions","authors":"D. Kimura","doi":"10.2197/IPSJDC.3.207","DOIUrl":"https://doi.org/10.2197/IPSJDC.3.207","url":null,"abstract":"Wadler proposed the dual calculus, which corresponds to classical sequent calculus LK, and studied the relationship between the λμ-calculus and the dual calculus as equational systems to explain the duality between call-by-value and call-by-name in a purely syntactical way. Wadler left an open question whether one can obtain similar results by replacing the equations with reductions. This paper gives one answer to his question. We first refine the λμ-calculus as reduction systems by reformulating sum types and omitting problematic reduction rules that are not simulated by reductions of the dual calculus. Secondly, we give translations between the call-by-name λμ-calculus and the call-by-name dual calculus, and show that they preserve the call-by-name reductions. We also show that the compositions of these translations become identity maps up to the call-by-name reductions. We also give translations for the call-by-value systems, and show that they satisfy properties similar to the call-by-name translations. Thirdly, we introduce translations between the call-by-value λμ-calculus and the call-by-name one by composing the above translations with duality on the dual calculus. We finally obtain results corresponding to Wadler's, but our results are based on reductions.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122278508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qamar Uddin Khand, Sumudu Dematapitiya, S. Saga, J. Maeda
{"title":"A Multi-Resolution Grid Snapping Technique Based on Fuzzy Theory","authors":"Qamar Uddin Khand, Sumudu Dematapitiya, S. Saga, J. Maeda","doi":"10.2197/IPSJDC.3.198","DOIUrl":"https://doi.org/10.2197/IPSJDC.3.198","url":null,"abstract":"This paper presents a grid snapping technique, called multi-resolution fuzzy grid snapping (MFGS), that enables automatic mouse cursor snapping for a multi-resolution grid system. Quick and frequent switching between high- and low-resolution grid snapping is essential to make geometrical drawings that include both fine and coarse structures when using CAD systems with ordinary single-resolution grid systems. MFGS is intended to relieve users of this tedious manual switching. MFGS dynamically selects an appropriate snapping resolution level from a multi-resolution grid system according to the pointing behavior of the user. MFGS even supports an extremely fine grid resolution level, which is referred to as the no-snapping level. We show experimental results which demonstrate that MFGS is an effective grid snapping technique that speeds up low-resolution grid snapping while retaining the ability to snap to high-resolution grids. Furthermore, we examine the role of fuzziness in MFGS and its effect on snapping performance.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127745063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Hardness Results on Local Multiple Alignment of Biological Sequences","authors":"T. Akutsu, Hiroki Arimura, S. Shimozono","doi":"10.2197/IPSJDC.3.174","DOIUrl":"https://doi.org/10.2197/IPSJDC.3.174","url":null,"abstract":"This paper studies the local multiple alignment problem, which is, given protein or DNA sequences, to locate a region (i.e., a substring) of fixed length from each sequence so that the score determined from the set of regions is optimized. We consider the following scoring schemes: the relative entropy score (i.e., average information content), the sum-of-pairs score and a relative entropy-like score introduced by Li, et al. We prove that multiple local alignment is NP-hard under each of these scoring schemes. In particular, we prove that multiple local alignment is APX-hard under relative entropy scoring. It implies that unless P =NP there is no polynomial time algorithm whose worst case approximation error can be arbitrarily specified(precisely, a polynomial time approximation scheme). Several related theoretical results are also provided.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132387658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shuhei Kimura, Katsuki Sonoda, S. Yamane, Koki Matsumura, M. Hatakeyama
{"title":"Function Approximation Approach to the Inference of Neural Network Models of Genetic Networks","authors":"Shuhei Kimura, Katsuki Sonoda, S. Yamane, Koki Matsumura, M. Hatakeyama","doi":"10.2197/IPSJDC.3.153","DOIUrl":"https://doi.org/10.2197/IPSJDC.3.153","url":null,"abstract":"A model based on a set of differential equations can effectively capture various dynamics. This type of model is therefore ideal for describing genetic networks. Several genetic network inference algorithms based on models of this type have been proposed. Most of these inference methods use models based on a set of differential equations of the fixed form to describe genetic networks. In this study, we propose a new method for the inference of genetic networks. To describe genetic networks, the proposed method does not use models of the fixed form, but uses neural network models. In order to interpret obtained neural network models, we also propose a method based on sensitivity analysis. The effectiveness of the proposed methods is verified through a series of artificial genetic network inference problems.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114744241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A biclustering method for gene expression module discovery using a closed itemset enumeration algorithm","authors":"Yoshifumi Okada, W. Fujibuchi, P. Horton","doi":"10.2197/IPSJDC.3.183","DOIUrl":"https://doi.org/10.2197/IPSJDC.3.183","url":null,"abstract":"A gene expression module (module for short) is a set of genes with shared expression behavior under certain experimental conditions. Discovering of modules enables us to uncover the function of uncharacterized genes or genetic networks. In recent years, several biclustering methods have been suggested to discover modules from gene expression data matrices, where a bicluster is defined as a subset of genes that exhibit a highly correlated expression pattern over a subset of conditions. Biclustering however involves combinatorial optimization in selecting the rows and columns composing modules. Hence most existing algorithms are based on heuristic or stochastic approaches and produce possibly sub-optimal solutions. In this paper, we propose a novel biclustering method, BiModule, based on a closed itemset enumeration algorithm. By exhaustive enumeration of such biclusters, it is possible to select only biclusters satisfying certain criteria such as a user-specified bicluster size, an enrichment of functional annotation terms, etc. We performed comparative experiments to existing salient biclustering methods to test the validity of biclusters extracted by BiModule using synthetic data and real expression data. We show that BiModule provides high performance compared to the other methods in extracting artificially-embedded modules as well as modules strongly related to GO annotations, protein-protein interactions and metabolic pathways.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116580540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Estimating Interruptibility in the Home for Remote Communication Based on Audio-Visual Tracking","authors":"Y. Takemae, Takehiko Ohno, I. Yoda, S. Ozawa","doi":"10.2197/IPSJDC.3.125","DOIUrl":"https://doi.org/10.2197/IPSJDC.3.125","url":null,"abstract":"This paper presents a method for automatically estimating human interruptibility in the home environment. To make online remote communication smoother, determining if it is appropriate to interrupt the remote partner is critical. As a first step in achieving this goal, several audio-visual features, extracted from data streams captured by a camera and a microphone, are correlated to human assessments of own interruptibility. Based on these features, the level of interruptibility is estimated using the trained Support Vector Regression (SVR) technique. Finally, we discuss the potential of our method based on the results of several experiments.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125943110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kazuyoshi Yoshii, Masataka Goto, Kazunori Komatani, T. Ogata, HIroshi G. Okuno
{"title":"Drumix: An Audio Player with Real-time Drum-part Rearrangement Functions for Active Music Listening","authors":"Kazuyoshi Yoshii, Masataka Goto, Kazunori Komatani, T. Ogata, HIroshi G. Okuno","doi":"10.2197/IPSJDC.3.134","DOIUrl":"https://doi.org/10.2197/IPSJDC.3.134","url":null,"abstract":"This paper presents a highly functional audio player, called Drumix, that allows a listener to control the volume, timbre, and rhythmic patterns (drum patterns)of bass and snare drums within existing audio recordings in real time. A demand for active music listening has recently emerged. If the drum parts of popular songs could be manipulated, listeners could have new musical experiences by freely changing their impressions of the pieces (e.g., making the drum performance more energetic)instead of passively listening to them. To achieve this, Drumix provides three functions for rearranging drum parts, i.e., a volume control function that enables users to cut or boost the volume of each drum with a drum-specific volume slider, a timbre change function that allows them to replace the original timbre of each drum with another selected from a drop-down list, and a drum-pattern editing function that enables them to edit repetitive patterns of drum onsets on a graphical representation of their scores. Special musical skills are not required to use these functions. Subjective experiments revealed that Drumix could add a new dimension to the way listeners experience music.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"5 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120983890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}