2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)最新文献

{"title":"Unsupervised analysis of leukemia and normal hematopoiesis by joint clustering of gene expression data","authors":"Liviu Badea","doi":"10.1109/BIBE.2012.6399647","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399647","url":null,"abstract":"Leukemia is a very heterogeneous cancer of the hematopoietic system. Since its main cause consists of genomic defects in the hematopoietic stem or progenitor cells and given the high complexity of the hematopoietic system, it may seem an important task to investigate the transcriptomic similarities and differences between leukemia subtypes and hematopoietic cells (stem cells, progenitors and differentiated cells). In this paper, we integrate the largest publicly available gene expression datasets of leukemia and normal hematopoiesis with the aim of uncovering the main gene modules involved in normal hematopoiesis as well as in the various leukemia subtypes. Using a joint consensus clustering algorithm, we have been able to relate the major leukemia types to their putative cells of origin in an unsupervised manner. While the normal hematopoietic cell modules are also active in leukemias of the corresponding cell type, our approach has determined leukemia-specific modules comprising genes with a known involvement in leukemogenesis. The expression modules uncovered implicate an unusually large number of transcription factors. This speaks against very simple models of normal hematopoiesis and leukemogenesis that involve just a handful of critical TFs, arguing for the interplay of complex transcription factor networks, in line with the findings of the FANTOM consortium for leukemia and Novershtern et al. for normal hematopoiesis.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"71 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114729404","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":"Heterogeneous data fusion and selection in high-volume molecular and imaging datasets","authors":"K. Moutselos, Ilias Maglogiannis, A. Chatziioannou","doi":"10.1109/BIBE.2012.6399761","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399761","url":null,"abstract":"In this work, two disparate datasets, concerning the study of the same physiological type of cutaneous melanoma but derived from different donors, one of image (dermatoscopy) and the other of molecular (trascriptomic expression) origin are utilized, so as to form an expanded in description depth, integrative dataset. Four different imputation methods are employed in order to derive the unified dataset, prior the application of backward selection together with ensemble classifiers (random forests). The various imputation schemes applied, manage to emulate the effect of biological noise on the unified dataset, adding realistic signal variation. Thus, they immunize the discovery process in the integrative dataset, from false positive artifacts, which do not have a true differential effect. The results suggest that the expansion of the feature space through the data integration and the exploitation of elaborate imputation schemes in general, aid the classification task, imparting stability as regards the derivation of the putative classifiers.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"79 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123951657","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":"Method of extracting sentences about protein interaction from the literature on protein structure analysis using selective transfer learning","authors":"Shun Koyabu, Riku Kyogoku, T. Ohkawa","doi":"10.1109/BIBE.2012.6399705","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399705","url":null,"abstract":"With the progress of research on structural analysis of proteins, a large number of studies have been conducted on extracting the protein interaction information from literature. For automatic extraction of interaction information, the machine learning approach is useful. Generally, linguistic features obtained directly from the literature are used for learning, but a non-linguistic feature such as the atomic distance calculated from the protein structure data is often very effective for learning and classification. We call this type of feature a “key feature” in this study. In the machine learning approach, preparing enough training instances to train the classifier is important, but this often requires great cost. In such a situation, transfer learning is one of the better approaches. However, it is difficult to apply a simple transfer learning algorithm to a task in which the key feature cannot be prepared in the source domain. In this study, we propose a new transfer learning method called STEK (Selective Transfer learning based on Effectiveness of a Key feature). In this method, we focus on the effectiveness of the key feature, and divide a set of instances into two categories. One is a set of instances applying transfer learning and the other is a set of instances avoiding the use of transfer learning. The proposed method with the InstPrune algorithm showed stably high precision, recall and F-measure on average.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124048685","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":"Detection and registration of vessels of fundus and OCT images using curevelet analysis","authors":"M. Golabbakhsh, H. Rabbani, Mahdad Esmaeili","doi":"10.1109/BIBE.2012.6399739","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399739","url":null,"abstract":"In recent years, advanced analysis of retinal images, has built automatic systems for diagnosis of various diseases. These devices help us save both time and money. The new techniques of 3D-Optical Coherence Tomography (OCT) imaging is very useful for detecting retinal pathologic changes in various diseases and determining retinal thickness abnormalities. Fundus color images have been used for several years for detecting retinal abnormalities too. If the two image modalities were combined, the resulted image would be more informative because some abnormalities such as drusen, geographic atrophy, and macular hemorrhages are detected in color fundus images but the exact morphology and localization of these abnormalities are released in OCT images. The first step to combine the different modalities is to register color fundus images with OCT projection. Ten eyes were imaged in this study with Topcon 3D OCT-1000 instrument. This instrument is used to observe the retina, take fundus and tomograms and record them. An en face representation of OCT reflectivity can be registered with color fundus photography. In this study curvelet transform is used to extract vessels for both modalities. Then the extracted vessels from two modalities are registered together. In this way more blood vessels can be obtained and the results would be more informative.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127342451","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":"Development and evaluation of an open source wearable navigation aid for visually impaired users (CYCLOPS)","authors":"Barbara Salonikidou, Dimitris Savvas, Georgios Diamantis, A. Astaras","doi":"10.1109/BIBE.2012.6399659","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399659","url":null,"abstract":"A wearable computing navigation aid for the visually impaired was designed, tested and evaluated in a series of pilot experiments. The system comprises an ultrasonic transceiver, a digital compass with a built-in accelerometer, sound playback electronics, a vibration motor and a microcontroller, all integrated inside a glove. The system prototype is power autonomous for about an hour and interfaces with the user through both audio and tactile output. The system design goals were reliability, wearability, power autonomy, an intuitive user interface, and open source architecture, low cost and rapid prototyping. A total of 16 pilot testers participated in evaluation experiments, in which they had to use CYCLOPS (http://cyclops-eye.yolasite.com) to navigate an unfamiliar obstacle course towards a goal destination designated by an audio target. 5 of the pilot testers were visually impaired, and 11 were blindfolded seeing individuals. Post-experiment interviews were used to collect qualitative data from all participants. Results indicate that pilot testers of both groups found CYCLOPS to be intuitive to use for blind navigation, even after a brief 5min familiarization period. Several functional corrections and requirements were extracted from the experimental and qualitative data, which will be used to drive the design of future CYCLOPS prototypes.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129975022","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":"Posterior ECG: Producing a new electrocardiogram signal from vectorcardiogram using partial linear transformation","authors":"A. M. Dehnavi, Niloofar Salehpour, H. Rabbani, M. Behjati","doi":"10.1109/BIBE.2012.6399714","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399714","url":null,"abstract":"Various techniques are used in diagnosing cardiac diseases. One of these techniques is using electrocardiogram (ECG) tool. In special cardiac cases like atrial fibrillation and posterior myocardial infraction the cardiologist need some information from posterior side of the patient heart, that it can be achieved by using right-posterior ECG method (17 lead ECG). In right-posterior method, position of the patient must be changed in his/her side, so time is waste and patient would be more tired because of taking ECG signals two times. In this study vectorcardiogram (VCG) signals are used as a tool for providing posterior information of the heart. However because for cardiologists is much easier to work with ECG signals for detecting some cardiac diseases, in this study a new method using partial linear transformation is introduced to get posterior ECG leads (V7, V8, V9) from VCG signal. VCG and ECG signals that were used in this study obtained from 30 healthy persons. We presented a statistical approach to transform 3-lead Frank VCG to 15-lead ECG signals and vice versa, based on partial linear transformation (Least Square Method). Also our linear transformation function would be compared with affine transformation functions. The recorder device was Cardiax digital recorder system. The results show that for healthy subjects, the partial linear transformation (least square method) that is presented in this paper maps 3-lead VCG to15-lead ECG, is more accurate than affine transformation function. Regarding the obtained results in this study, ECG signals that derived from VCG signals by using our method was more similar to measured ECG signals than ones derived by using affine transformation. Therefore, by using this transformation function achieving to posterior information of the case heart would be more accurate and useful.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131023452","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":"Clustering microarray data using fuzzy clustering with viewpoints","authors":"K. Karayianni, G. Spyrou, K. Nikita","doi":"10.1109/BIBE.2012.6399651","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399651","url":null,"abstract":"This paper studies the application of fuzzy clustering with viewpoints in order to cluster cell samples according to their gene expression profile. This method combines fuzzy clustering with external domain knowledge represented by the so-called viewpoints. The viewpoints that we employ are obtained from previously available expression data. The method was compared to the clustering algorithms of k-means, fuzzy c-means, affinity propagation, as well as a method of clustering microarray data that is based on prior biological knowledge, and has shown comparable/improved results over them.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123349125","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":"Microarray classification with hierarchical data representation and novel feature selection criteria","authors":"Mattia Bosio, Pau Bellot, P. Salembier, Albert Oliveras-Vergés","doi":"10.1109/BIBE.2012.6399648","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399648","url":null,"abstract":"Microarray data classification is a challenging problem due to the high number of variables compared to the small number of available samples. An effective methodology to output a precise and reliable classifier is proposed in this work as an improvement of the algorithm in [1]. It considers the sample scarcity problem and the lack of data structure typical of microarrays. Both problem are assessed by a two-step approach applying hierarchical clustering to create new features called metagenes and introducing a novel feature ranking criterion, inside the wrapper feature selection task. The classification ability has been evaluated on 4 publicly available datasets from Micro Array Quality Control study phase II (MAQC) classified by 7 different endpoints. The global results have showed how the proposed approach obtains better prediction accuracy than a wide variety of state of the art alternatives.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115949949","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":"Towards an era of epidemiological databases for autoimmune diseases","authors":"Vassiliki Gkantouna, Zafeiria-Marina Ioannou, A. Tsakalidis, Emmanouil Viennas, K. Poulas, J. Tsaknakis, Giannis Tzimas","doi":"10.1109/BIBE.2012.6399709","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399709","url":null,"abstract":"Nowadays, autoimmune diseases are among the leading causes of death for a remarkable number of patients all around the world. Recent studies have witnessed that the epidemiological indices for a specific disease can vary according to ethnic and geographical parameters. As a result, the genetic epidemiology of autoimmune diseases is a major matter of study for the worldwide scientific community. We have previously reported the development of dAUTObase (www.dAUTObase.org), a database recording solely epidemiological data of autoimmune diseases in various populations around the globe. Here, we present an important upgrade of the dAUTObase system focused on the development of new data visualization tools oriented to further assist the effective data querying and the mining process.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126977535","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":"The effects of applying cell-suppression and perturbation to aggregated genetic data","authors":"A. Antoniades, J. Keane, Aristos Aristodimou, Christa Philipou, A. Constantinou, Christos Georgousopoulos, F. Tozzi, K. Kyriacou, A. Hadjisavvas, M. Loizidou, C. Demetriou, C. Pattichis","doi":"10.1109/BIBE.2012.6399777","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399777","url":null,"abstract":"The key test for confidence in any association discovered within the medical domain is replication testing. That is, the ability of the association to be detected in independent populations. At the same time, in order to increase the likelihood of discovering statistically significant associations there is a clear need to increase the statistical power of any given study. A key methodology for increasing statistical power is through the use of as many subjects as possible that match a study's inclusion criteria. Thus many have attempted to merge data from multiple independent sources/sites/studies that contain the same inclusion criteria for subjects as a way of creating a much larger study with significantly more statistical power. For these approaches to work though data from multiple sites need to be made available to a single analysis. This practice is significantly limited by the need to respect legal and ethical requirements that are often complicated, ambiguous and inconsistent across different countries. The common approach to achieve merging of data is by sharing aggregated data rather than subject's personal data. Aggregated data however may still in some cases be reverse engineered, therefore traditionally cells within the aggregated data with small values were suppressed, and some or all of the aggregated data were perturbed in order to add noise inhibiting any attempts at identifying personal information of a specific person or sub-group in the original data. In this paper we study the effects of cell-suppression and perturbation on the results of the data analysis. Each approach is looked at by itself as well as in combination using the typical settings documented in the literature. The tests are based on a real dataset that looks for associations between phenotypes and genetic markers. This work is part of the Linked2Safety project that aims to dynamically interconnect distributed patients' data to better enable medical research efforts, whilst respecting patients' anonymity, as well as European and national legislation.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127690329","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}