Baw-Jhiune Liu

National Chiao Tung University, Hsinchu, Taiwan, Taiwan

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Publications (71)48.69 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Asthma is one of the most common chronic diseases in children. It is caused by complicated coactions between various genetic factors and environmental allergens. The study aims to integrate the concept of implementing adaptive neuro-fuzzy inference system (ANFIS) and classification analysis methods for forecasting the association of asthma susceptibility genes on 3 serum IgE groups. The ANFIS model was trained and tested with data sets obtained from 425 asthmatic subjects and 483 non-asthma subjects from the Taiwanese population. We assessed 13 single-nucleotide polymorphisms (SNPs) in seven well-known asthma susceptibility genes; firstly, the proposed ANFIS model learned to reduce input features from the 13 SNPs. And secondly, the classification will be used to classify the serum IgE groups from the simulated SNPs results. The performance of the ANFIS model, classification accuracies and the results confirmed that the integration of ANFIS and classified analysis has potential in association discovery.
    Journal of Medical Systems 02/2012; 36(1):175-85. · 1.78 Impact Factor
  • Kuo-Hung Tseng, Chen-Chung Liu, Baw-Jhiune Liu
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    ABSTRACT: Recently, many forms of e-book readers such as iPad and Kindles are becoming widely-spread. However, simply adopting e-books readers does not necessarily guarantee the improvement of reading process. Educators advocate that learning to read should not be a solitary activity. Instead, it should be a participatory learning activity that engages learners in active reading process. However, due to the less experience in reading, children at the learning-to-read stage need a different set of tools and scaffolds to involve in participatory reading activities than such annotation or tagging systems developed for adults. In this vein, this study proposes a scaffolded participatory reading model addresses the role of e-book readers in strengthen the relationship between reading strategies, child-parent collaboration, and experience sharing in communities. A participatory reading activity was designed based on the model. This study found that tablet-based e-book readers can facilitate child-parent collaboration and afford variety forms of interactions. In particular, the storytelling activity on such tablets helped the parents provide different guidance including dialogic reading strategies and those related to story structure, helping the children to reflect on the book read. The result of this study also suggests that a persistent platform that can record and demonstrate the reading experience is a critical element to facilitate participatory reading among children Educators may find it useful to apply such approach in other reading context.
    01/2012;
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    ABSTRACT: Social media on the World Wide Web, such as Wiki, are increasingly applied to support collaborative learning for students to conduct a project together. However, recent studies indicated that students, learning in the collaborative project, may not actively contribute to the collaborative work and are involved only in a limited level of positive interdependence due to the ambiguous ownership on the collaborative work. To this end, this study proposes an approach to support collaborative learning based on the notion of Creative Commons (CC). CC may be helpful to enhance positive interdependency because it provides a mechanism which protects individual creations while encouraging remixing and deriving new creations from them. This study conducted an empirical evaluation to examine how students react to the collaborative learning with CC notions. The results showed that CC can significantly improve participants' attitude to the derivative works, the satisfaction level of remix outcomes, perception to the peer interaction and the sense of work ownership. Such results suggest that CC may be a potential avenue for increasing individuals' responsibilities and motivating them to participate in the collaborative learning activity.
    Behaviour and Information Technology 06/2011; 2011(iFirst article). · 0.86 Impact Factor
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    ABSTRACT: Storytelling is an imperative and innovative pathway to enhance learning due to the fact that such activity prompts learners to reflect to construct meaning based on their observations and knowledge. Therefore, to develop and enhance students’ storytelling ability has become an important issue for both educators and researchers. Since storytelling involves complex cognitive processes, this study proposed an enhanced concept map approach featured with story grammars to help children develop stories. By gathering the stories developed by 114 third-graders, this study aimed to investigate whether the concept map approach can enhance their storytelling ability. It is found that the children, who used the concept map with story grammars, can develop stories with more complex structure, clearer subjects, more creative ideas, and abundant contents than those only using the concept map without the grammars. Such findings support that the concept map and story grammars can be an effective approach for developing learner-centered storytelling tools which help students develop and apply the knowledge about storytelling.
    Computers & Education 04/2011; · 2.78 Impact Factor
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    Chen-Ming Hsu, Chien-Yu Chen, Baw-Jhiune Liu
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    ABSTRACT: Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards) are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions) that incorporates several pruning strategies to largely reduce the mining cost. WildSpan is shown to efficiently find W-patterns containing conserved residues that are far separated in sequences. We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. The protein-based mining mode of WildSpan is developed for discovering functional regions of a single protein by referring to a set of related sequences (e.g. its homologues). The discovered W-patterns are used to characterize the protein sequence and the results are compared with the conserved positions identified by multiple sequence alignment (MSA). The family-based mining mode of WildSpan is developed for extracting sequence signatures for a group of related proteins (e.g. a protein family) for protein function classification. In this situation, the discovered W-patterns are compared with PROSITE patterns as well as the patterns generated by three existing methods performing the similar task. Finally, analysis on execution time of running WildSpan reveals that the proposed pruning strategy is effective in improving the scalability of the proposed algorithm. The mining results conducted in this study reveal that WildSpan is efficient and effective in discovering functional signatures of proteins directly from sequences. The proposed pruning strategy is effective in improving the scalability of WildSpan. It is demonstrated in this study that the W-patterns discovered by WildSpan provides useful information in characterizing protein sequences. The WildSpan executable and open source codes are available on the web (http://biominer.csie.cyu.edu.tw/wildspan).
    Algorithms for Molecular Biology 03/2011; 6(1):6. · 1.61 Impact Factor
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    ABSTRACT: The accurate identification of potential poly(A) sites has contributed to all many studies with regard to alternative polyadenylation. The aim of this study was the development of a machine-learning methodology that will help to discriminate real polyadenylation signals from randomly occurring signals in genomic sequence. Since previous studies have revealed that RNA secondary structure in certain genes has significant impact, the authors tried to computationally pinpoint common structural patterns around the poly(A) sites and to investigate how RNA secondary structure may influence polyadenylation. This involved an initial study on the impact of RNA structure and it was found using motif search tools that hairpin structures might be important. Thus, it was propose that, in addition to the sequence pattern around poly(A) sites, there exists a widespread structural pattern that is also employed during human mRNA polyadenylation. In this study, the authors present a computational model that uses support vector machines to predict human poly(A) sites. The results show that this predictive model has a comparable performance to the current prediction tool. In addition, it was identified common structural patterns associated with polyadenylation using several motif finding programs and this provides new insight into the role of RNA secondary structure plays in polyadenylation.
    Medical & Biological Engineering 02/2011; 49(4):463-72. · 1.76 Impact Factor
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    ABSTRACT: Students' affections in learning have a significant impact on engagement and learning outcomes. When students have negative emotions, they usually do not learn well. But current e-learning systems often lack many features of profound affection, and fail to provide suitable emotional interaction. In this paper, we evaluate some studies of affective interaction e-learning systems. We also proposed our approach to develop an emotionally interactive learning system.
    Advanced Learning Technologies (ICALT), 2010 IEEE 10th International Conference on; 08/2010
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    ABSTRACT: Small non-coding RNA genes have been shown to play important regulatory roles in a variety of cellular processes, but prediction of non-coding RNA genes is a great challenge, using either an experimental or a computational approach, due to the characteristics of sRNAs, which are that sRNAs are small in size, are not translated into proteins and show variable stability. Most known sRNAs have been identified in Escherichia coli and have been shown to be conserved in closely related organisms. We have developed an integrative approach that searches highly conserved intergenic regions among related bacterial genomes for combinations of characteristics that have been extracted from known E. coli sRNA genes. Support vector machines (SVM) were then used with these characteristics to predict novel sRNA genes.
    Expert Systems with Applications 08/2010; 37:5549-5557. · 1.85 Impact Factor
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    ABSTRACT: There have been little studies on providing collaborative discovery on the web search results contributed by peers in one-to-one environments. This study therefore proposes an integrative groupware, CELL (Contributing, Exchanging, and Linking for Learning), which utilizes both personal mobile computers and a shared display in support of one-to-one Web co-discovery. Through gathering small group activity, facilitated by CELL groupware, it was found that this design was indeed useful in supporting students in their efforts to search the Web autonomously while simultaneously engaging in joint discussion of the emerging web search results. In addition, this study identified three collaborative discovery patterns of student groups in the use of the CELL groupware: iterative envisioning discovery, fixed framework discovery, and framework development impediment. Most student groups demonstrated the iterative envisioning discovery pattern which indicates that the CELL groupware did help students to integrate their findings on the Web and thus gradually to broaden their understanding toward the open-ended problem.
    Educational Technology & Society. 01/2010; 13:126-139.
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    ABSTRACT: Collaborative storytelling is an imperative and innovative pathway to children's learning. Collaborative storytelling can be developed in linear and nonlinear approaches. Linear stories contain exactly one begin, one middle and one end. All children collaborate on a shared story in the form of relay and no branches can be developed. Children deeply rely on evaluating the relationship, continuality and coherence of story path before sequentially participating in building up the story. By contrast, nonlinear stories enable children to link and orchestrate different ideas. Children can thus integrate other's episodes to develop different branches of stories. Since the linear and nonlinear approaches facilitate children to develop stories in different manners, children's perception towards linear and nonlinear approaches may be different, which may affect their motivation and ultimate success in collaborative storytelling. However, research which has empirically documented the children's perception of linear and nonlinear approaches is scant. In order to explore whether children's perception and learning behaviors about linear and nonlinear collaborative storytelling approaches are different, a Web2.0 storytelling platform featuring animated picture books is designed for the study. The platform implements multimedia elements such as texts, pictures, images, music and narration to increase children's engagement and collaboration. More specifically, children are facilitated to collaboratively sketch pictures, create animations and share comments of works. The study involved a four-week empirical study, comprised of a questionnaire concerning four factors: derivation, remix, ownership and positive interdependence. Two intact classes of 57 participants, the 3rd graders were randomly assigned and treated as linear group and nonlinear group. The quantitative analysis of the questionnaires was conducted through an independent t-test to analyze and compare children's perception between the two approaches. Children's onscreen activity and collaboration process were also logged and screen videoed for further analysis. Results showed children in nonlinear group performed superior to those of linear group in all four factors. To conclude, this study may be of importance in providing a deep understanding of how children's perception about linear and nonlinear approaches in collaborative storytelling activities.
    Procedia - Social and Behavioral Sciences 01/2010; 2(2):4787-4792.
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    ABSTRACT: This study applied the features of social media to implement a picture book in facilitating the students collaborative creative activity. Based on Amabile's componential theory, this study evaluated the influences of social media in students' creativity behaviors. The results showed that the students were more active to present multi-thinking, as well as revealed higher significant satisfaction in the perceptions of the ownership of working and peers' mutual support. Moreover, the collaborative creative environment engaged the students in developing creative works.
    01/2010;
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    ABSTRACT: Riboswitches are cis-acting genetic regulatory elements within a specific mRNA that can regulate both transcription and translation by interacting with their corresponding metabolites. Recently, an increasing number of riboswitches have been identified in different species and investigated for their roles in regulatory functions. Both the sequence contexts and structural conformations are important characteristics of riboswitches. None of the previously developed tools, such as covariance models (CMs), Riboswitch finder, and RibEx, provide a web server for efficiently searching homologous instances of known riboswitches or considers two crucial characteristics of each riboswitch, such as the structural conformations and sequence contexts of functional regions. Therefore, we developed a systematic method for identifying 12 kinds of riboswitches. The method is implemented and provided as a web server, RiboSW, to efficiently and conveniently identify riboswitches within messenger RNA sequences. The predictive accuracy of the proposed method is comparable with other previous tools. The efficiency of the proposed method for identifying riboswitches was improved in order to achieve a reasonable computational time required for the prediction, which makes it possible to have an accurate and convenient web server for biologists to obtain the results of their analysis of a given mRNA sequence. RiboSW is now available on the web at http://RiboSW.mbc.nctu.edu.tw/.
    RNA 06/2009; 15(7):1426-30. · 5.09 Impact Factor
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    ABSTRACT: Collaborative learning is extensively applied in classroom activities, but the screens on handheld devices are designed for individual-user mobile applications and may constrain interaction among group learners. The small screen size may lead to fragmented and tête-à-tête communication patterns and frequently obstruct the externalization of the learning process. This study compares two learning scenarios, one using only handheld devices and the other integrating handheld devices with LCD shared displays, in order to explore whether shared displays in classrooms can augment handheld devices to facilitate articulation and communication among participants. This study involved 15 graduate students enrolled in a Statistics and Data Mining course. Data were collected on the course over a period of eight weeks. Students were required to solve problems collaboratively and content analysis was performed on student dialogue and nonverbal interactions in the two different learning scenarios. In the environment with shared displays, each discussion thread attracted more students and demonstrated more shared visual focus than in the one-to-one setting by a significant margin. Students, when studying in an environment with shared displays, exhibited more lively interaction with each other, including frequent hand-pointing behavior. Furthermore, students proposed more arguments and positions in the Shared- Display environment than in the environment without shared displays. Therefore, shared displays can not only improve articulation processes, but can also promote student engagement by establishing a social workspace for learning with handheld devices.
    Educational Technology & Society 01/2009; 12:127-142. · 1.01 Impact Factor
  • Conference Paper: RiboSW .
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    ABSTRACT: Riboswitches are cis-acting genetic regulatory elements within a specific mRNA, and can regulate both transcription and translation by interacting with their corresponding metabolites. Recently, more and more riboswitches were identified and investigated about their roles in regulatory functions in different species. Both of the sequence contexts and structural conformations are important characteristics of riboswitches. None of previous developed tools, such Covariance Models (CMs), Riboswitch finder, and RibEx, provides a web server for efficiently searching homologous instances to known riboswitches and considers two crucial characteristics of each riboswitch, such as structural conformations and sequence contexts of functional regions. Therefore, we developed a systematic method to identify twelve kinds of riboswitches. The method is implemented and provided as a web server, RiboSW, to efficiently and conveniently identify riboswitches within messenger RNA sequences. RiboSW is now available on the web at http://bioinfo.csie.ncu.edu.tw/RiboSW/. The predictive accuracy of the proposed method is comparable with other previous tools. The efficiency of the proposed method for identifying riboswitches was improved in order to achieve a reasonable computational time required for the prediction. That makes it possible to have an accurate and convenient web server for biologists to obtain their analyzing results in a given mRNA sequence.
    Ninth IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2009, June 22-24, 2009, Taichung, Taiwan; 01/2009
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    ABSTRACT: During gene expression, transcription factors are unable to bind to a transcription binding site (TFBS) involved in regulation if DNA methylation has occurred at the TFBS. Methyl-CpG-binding proteins may also occupy the TFBS and prevent the functioning of a transcription factor. Thus, the methylation status of CpG sites is an important issue when trying to understand gene regulation and shows strong correlation with the TFBS involved. In addition, CpG islands would seem to undergo cell-specific and tissue-specific methylation. Such differential methylation is presented at numerous genetic loci that are essential for development. Current DNA methylation site prediction tools need to be improved so that they include TFBS features and have greater accuracy in terms of the DNA region that is involved in methylation. We developed models that compare the differences across these regions and tissues. The TFBSs, DNA properties and DNA distribution were used as features for this classification. From the results, we found some TFBSs that were able to discriminate whether a sequence was methylated or not. The sensitivity, specificity and accuracy estimated using 10-fold cross validation were 90.8%, 80.54%, and 86.07%, respectively. Thus, for these four regions and twelve tissues, the performance levels (ACC) were all greater than 80%. We propose that the differential features or methylations vary between the different regions because the features common to each DNA region made up only 50% of the top 70 features. An online predictor based on EpiMeP is available at http://140.115.51.41/EpiMeP/. Supplementary file is available at http://140.115.51.41/EpiMeP/supplementary.doc.
    Ninth IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2009, June 22-24, 2009, Taichung, Taiwan; 01/2009
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    ABSTRACT: Studies indicate that making learners feel good is important only minor to clear knowledge transformation. Many studies have tried to use virtual humans as a part of interface in learning systems to increase the effect of instructions. Based on social interaction and pedagogical theories, many e-learning systems use animated films or virtual reality to boost human-computer engagement and ease their negative emotions. However, affective learning systems still need much research to improve their functionalities and usability. This study proposed a convenient approach to develop an emotionally interactive learning system; learners can express their emotions by mouse-clicking while learning. A virtual human was created to empathically react to learners in proactive and reactive ways to encourage and persuade them into persistent learning and help achieve their goals. Experimental results show that, averagely, subjects can tell virtual human's emotions and agree to its empathic reactions. Persuasion conducted by virtual human could not increase subjects' learning time, but could significantly increase their completion rate of exercises.
    01/2009;
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    ABSTRACT: From the review of many literatures, it is considered that there are still prevailing obstacles for second language learners due to insufficient vocabulary. Fortunately, there is a way to increase onepsilas vocabulary by means of extensive reading realizing stories. The research tries to utilize robot as a medium to design a pressure-free and intriguing learning system. It is a learning method imitating TPRS that enables learners to design a personal storytelling robot. The learners proceed with extensive reading during the process of designing a storytelling robot and achieve vocabulary acquisition through designing the movements of robots corresponded to the vocabulary by themselves. Our research is in a preliminary stage of realizing userspsila responses. Ten learners from graduate school students of National Central University Department of Computer Science and Information Engineering, the result of tests and interviews will be the basis of further mass amount experiments and improvement.
    Advanced Learning Technologies, 2008. ICALT '08. Eighth IEEE International Conference on; 08/2008
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    ABSTRACT: Selecting transparently a proper network connection for voice communication will be a fundamental requirement in future multi-mode heterogeneous wireless network. This paper extends always best connected (ABC) to a fine-grain paradigm called always best network connection (ABNC) to address this issue. Instead of selecting a best access network as in conventional ABC, ABNC enable users to select a best network connection, which consists of source and destination access network pair, to satisfy quality constraint and users' preference. To support ABNC, we develop a user profile to specify network connection priority. Meanwhile we extend SIP and propose a network selection information service (NSIS) based on MIH (media independent handover) to collect information of both source and destination access networks for decision making. Finally, analytic hierarchy process (AHP) is used to recommend a network connection with assistance of user profile and NSIS. An example is illustrated to show that AHP can successfully select a good network connection that fulfill the requirement of users.
    Advanced Information Networking and Applications, 2008. AINA 2008. 22nd International Conference on; 04/2008
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    ABSTRACT: This study proposed a groupware and a flow of learning activity to guide students in learning arithmetic word problem with handheld devices. Appropriating the concept of semi-situated learning which was aided by the 4-frame comic embedded into the PDA, this study expected the comic to play as a catalyst to trigger students in articulating some theme associated with the content of the 4-frame comic. The scenario and features of this groupware are presented in the paper and a preliminary study at an elementary school is also described and discussed.
    Wireless, Mobile, and Ubiquitous Technology in Education, 2008. WMUTE 2008. Fifth IEEE International Conference on; 04/2008
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    Chen-Ming Hsu, Chien-Yu Chen, Baw-Jhiune Liu
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    ABSTRACT: This paper presents a web service named MAGIICPRO,which aims to discover functional signatures of a query protein by sequential pattern mining. Automatic discovery of patterns from unaligned biological sequences is an important problem in molecular biology. MAGIIC-PRO is different from several previously established methods performing similar tasks in two major ways. The first remarkable feature of MAGIIC-PRO is its efficiency in delivering long patterns. With incorporating a new type of gap constraints and some of the state-of-theart data mining techniques, MAGIIC-PRO usually identifies satisfied patterns within an acceptable response time. The efficiency of MAGIIC-PRO enables the users to quickly discover functional signatures of which the residues are not from only one region of the protein sequences or are only conserved in few members of a protein family. The second remarkable feature of MAGIIC-PRO is its effort in refining the mining results. Considering large flexible gaps improves the completeness of the derived functional signatures. The users can be directly guided to the patterns with as many blocks as that are conserved simultaneously. In this paper,we show by experiments that MAGIIC-PRO is efficient and effective in identifying ligand-binding sites and hot regions in protein-protein interactions directly from sequences. The web service is availableat http://biominer.bime.ntu.edu.tw/magiicproand a mirror site at http://biominer.cse.yzu.edu.tw/magiicpro.
    Nucleic Acids Research 04/2008; 36(4):1400-6. · 8.81 Impact Factor

Publication Stats

234 Citations
48.69 Total Impact Points

Institutions

  • 2011
    • National Chiao Tung University
      • Institute of Bioinformatics and Systems Biology
      Hsinchu, Taiwan, Taiwan
  • 2000–2011
    • Yuan Ze University
      • Department of Computer Science and Engineering
      Tainan, Taiwan, Taiwan
  • 1993–2011
    • National Taiwan University
      • • Department of Bio-Industrial Mechatronics Engineering
      • • Department of Computer Science and Information Engineering
      Taipei, Taipei, Taiwan
  • 2007
    • National University of Tainan
      臺南市, Taiwan, Taiwan
  • 2006
    • National Yang Ming University
      T’ai-pei, Taipei, Taiwan
  • 1994–2006
    • National Central University
      • Department of Computer Science & Information Engineering
      Taoyuan City, Taiwan, Taiwan