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2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops最新文献

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A data aggregation framework for cancer subtype discovery 癌症亚型发现的数据聚合框架
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470250
S. N. Nagabhushan, T. Ahn, M. Srikanth, T. Park, Ajit S. Bopardikar, R. Narayanan
Personalized genomic medicine aims to revolutionize healthcare by applying our growing understanding of the molecular basis of disease for effective diagnosis and personalized therapy. Computational research in this arena has major challenges such as handling large volume of highly heterogeneous data sets. To extract knowledge, researchers must integrate data from several sources and efficiently query these large and diverse data sets. This presents daunting informatics challenges such as suitable data representation for computational inference (knowledge representation), linking heterogeneous data sets (data integration) and keeping track of the source of the data to be aggregated. Many of these challenges can be categorized as data integration problems. In this paper, we present relevant methodologies from the field of data integration as potential solution for such challenges encountered by computational biologist while handling diversified data. The work presented in the paper represents the first crucial step towards identifying cancer biomarkers leading to cancer pathways signatures and personalized medicine.
个性化基因组医学旨在通过应用我们对疾病分子基础的不断增长的理解来进行有效的诊断和个性化治疗,从而彻底改变医疗保健。该领域的计算研究面临着重大挑战,例如处理大量高度异构的数据集。为了提取知识,研究人员必须整合多个来源的数据,并有效地查询这些庞大而多样的数据集。这就提出了令人生畏的信息学挑战,例如适合计算推理的数据表示(知识表示)、链接异构数据集(数据集成)以及跟踪要聚合的数据源。这些挑战中的许多都可以归类为数据集成问题。在本文中,我们提出了数据集成领域的相关方法,作为计算生物学家在处理多样化数据时遇到的这些挑战的潜在解决方案。论文中提出的工作代表了确定癌症生物标志物的关键第一步,从而导致癌症途径签名和个性化医疗。
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引用次数: 0
Early classification of multivariate time series using a hybrid HMM/SVM model 基于HMM/SVM混合模型的多变量时间序列早期分类
Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392654
Mohamed F. Ghalwash, Dusan Ramljak, Z. Obradovic
Early classification of time series has been receiving a lot of attention as of late, particularly in the context of gene expression. In the biomédical realm, early classification can be of tremendous help, by identifying the onset of a disease before it has time to fully take hold, or determining that a treatment has done its job and can be discontinued. In this paper we present a state-of-the-art model, which we call the Early Classification Model (ECM), that allows for early, accurate, and patient-specific classification of multivariate time series. The model is comprised of an integration of the widely-used HMM and SVM models, which, while not a new technique per se, has not been used for early classification of multivariate time series classification until now. It attained very promising results on the datasets we tested it on: in our experiments based on a published dataset of response to drug therapy in Multiple Sclerosis patients, ECM used only an average of 40% of a time series and was able to outperform some of the baseline models, which needed the full time series for classification.
时间序列的早期分类近年来受到了广泛的关注,特别是在基因表达方面。在生物医学领域,早期分类可以提供巨大的帮助,通过在疾病有时间完全控制之前识别疾病的发作,或者确定治疗已经发挥了作用,可以停止治疗。在本文中,我们提出了一个最先进的模型,我们称之为早期分类模型(ECM),它允许对多变量时间序列进行早期,准确和患者特定的分类。该模型由广泛使用的HMM模型和SVM模型集成而成,虽然本身不是一种新技术,但迄今为止尚未将其用于多变量时间序列分类的早期分类。在我们测试的数据集上,它获得了非常有希望的结果:在我们基于多发性硬化症患者对药物治疗反应的公开数据集的实验中,ECM平均只使用了40%的时间序列,并且能够优于一些基线模型,这些模型需要完整的时间序列进行分类。
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引用次数: 34
Discovery at a distance: Farther journeys in predication space 远方的发现:预测空间中更远的旅程
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470307
T. Cohen, D. Widdows, R. Schvaneveldt, T. Rindflesch
In this paper we extend the Predication-based Semantic Indexing (PSI) approach to search efficiently across triple-predicate pathways in a database of predications extracted from the biomédical literature by the SemRep system. PSI circumvents the combinatorial explosion of possible pathways by converting the task of traversing individual predications into the task of measuring the similarity between composite concept vectors. Consequently, search time for single, double or triple predicate paths is identical once the relevant concept vectors have been constructed. This paper describes the application of PSI to infer double and triple predicate pathways connecting example pairs of therapeutically related drugs and diseases; and to use these inferred pathways to guide search for treatments for other diseases. In an evaluation of the utility of vector-based dual- and triple-predicate path search in a simulated discovery experiment, these approaches are found to be complementary, with best performance obtained through their application in combination.
在本文中,我们扩展了基于谓词的语义索引(PSI)方法,以便在SemRep系统从生物医学文献中提取的谓词数据库中高效地搜索三谓词路径。PSI通过将遍历单个谓词的任务转换为测量复合概念向量之间相似性的任务,避免了可能路径的组合爆炸。因此,一旦构建了相关的概念向量,单个、两个或三个谓词路径的搜索时间是相同的。本文描述了PSI在推断连接治疗相关药物和疾病的示例对的双和三重谓词通路中的应用;并利用这些推断的途径来指导寻找其他疾病的治疗方法。在模拟发现实验中对基于向量的双谓词和三谓词路径搜索的效用进行了评估,发现这些方法是互补的,通过组合应用可以获得最佳性能。
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引用次数: 16
CryoEM skeleton length estimation using a decimated curve 利用抽取曲线估计CryoEM骨架长度
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470283
Andrew McKnight, Kamal Al-Nasr, Dong Si, Andrey N. Chernikov, N. Chrisochoides, Jing He
Cryo-electron Microscopy (cryoEM) is an important biophysical technique that produces 3-dimensional (3D) images at different resolutions. De novo modeling is becoming a promising approach to derive the atomic structure of proteins from the cryoEM 3D images at medium resolutions. Distance measurement along a thin skeleton in the 3D image is an important step in de novo modeling. In spite of the need of such measurement, little has been investigated about the accuracy of the measurement in searching for an effective method. We propose a new computational geometric approach to estimate the distance along the skeleton. Our preliminary test results show that the method was able to estimate fairly well in eleven cases.
低温电子显微镜(cryoEM)是一种重要的生物物理技术,可以产生不同分辨率的三维(3D)图像。从头建模正在成为一种很有前途的方法,可以从中分辨率的冷冻电镜3D图像中获得蛋白质的原子结构。在三维图像中沿薄骨架的距离测量是从头建模的重要步骤。尽管有这种测量的需要,但在寻找有效方法的过程中,很少对测量的准确性进行研究。我们提出了一种新的计算几何方法来估计沿骨架的距离。我们的初步测试结果表明,该方法能够较好地估计11种情况。
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引用次数: 2
Managing data provenance in genome project workflows 管理基因组计划工作流程中的数据来源
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470215
Renato de Paula, M. Holanda, M. E. Walter, Sérgio Lifschitz
In this article, we propose the application of the PROV-DM model to manage data provenance for workflows designed to support genome projects. This provenance model aims at storing details of each execution of the workflow, which include raw and produced data, computational tools and versions, parameters, and so on. This way, biologists can review details of a particular workflow execution, compare information generated among different executions, and plan new ones more efficiently. In addition, we have created a provenance simulator to facilitate the inclusion of a provenance data model in genome projects. In order to validate our proposal, we discuss a case study of an RNA-Seq project that aims to identify, measure and compare RNA expression levels across liver and kidney RNA samples produced by high-throughput automatic sequencers.
在本文中,我们建议应用provo - dm模型来管理为支持基因组计划而设计的工作流的数据来源。这个溯源模型旨在存储工作流的每个执行的细节,包括原始和生成的数据、计算工具和版本、参数等等。通过这种方式,生物学家可以查看特定工作流执行的细节,比较不同执行之间生成的信息,并更有效地计划新的工作流。此外,我们还创建了一个来源模拟器,以方便在基因组计划中包含来源数据模型。为了验证我们的建议,我们讨论了一个RNA- seq项目的案例研究,该项目旨在鉴定、测量和比较高通量自动测序仪产生的肝脏和肾脏RNA样品中的RNA表达水平。
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引用次数: 3
A novel acupuncture for killing lumbago: Immediate effects of balancing acupuncture for acute lumbar disc herniation 一种治疗腰痛的新针灸:平衡针灸治疗急性腰椎间盘突出症的即时效果
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470356
Xiaohong Xu, Shudong Chen, Xiaoling Xu
[Purpose] This study aimed to evaluate the immediate effects of Balancing acupuncture as adjuvant therapy for patients with acute lumbar disc herniation (ALDH). [Method] We recruited 47 patients with ALDH in Orthopedic therapy center of Guangdong Provincial Hospital of Chinese Medicine in China. McGill pain questionnaire (MPQ) and clinical effects of Balancing acupuncture were measured. [Results] We found that no case showed clinical cure, 42 cases showed improvement, while 5 cases showed ineffectiveness, indicating an improvement rate of 89.4%. Immediate MPQ total score after Balancing acupuncture was lower than before treatment, which showed a statistical significance between them (P=0.0000<;0.05). Differences in PRI, VAS, and PPI reached statistical significance (P<;0.05). A statistically significant difference was found in Pain perception score before and after treatment (P=0.0125<;0.05), while pain emotion score failed to reach statistical significance (P=0.6983>0.05). [Conclusions] The results suggested that Balancing acupuncture may lead to immediate benefits for patients with ALDH.
【目的】本研究旨在评价平衡针刺辅助治疗急性腰椎间盘突出症(ALDH)的即时效果。[方法]选取广东省中医院骨科治疗中心的ALDH患者47例。测量McGill疼痛问卷(MPQ)和平衡针刺的临床效果。【结果】临床无治愈病例,好转42例,无效5例,改善率89.4%。平衡针刺后即刻MPQ总分低于治疗前,差异有统计学意义(P=0.00000.05)。[结论]结果提示,平衡针刺可使ALDH患者立即获益。
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引用次数: 0
The mechanism of acupuncture for obsessive-complusive disorder on TCM heart-gallbladder concept 针刺治疗强迫症的中医心胆观机制探讨
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470328
Nipeng Lin, Changeai Xie, Xiaohong Xu, W. Fu
Obsessive-compulsive disorder (obsessive - compulsive disorder) is a neurotic mental disorders characterized by the uncontrolled obsessions and compulsive behavior. Patients know that the continued obsessive-compulsive symptoms are pointless and unreasonable, but can not get rid of it. Therefore they feel very nervous and suffering. Acupuncture for obsessive - compulsive disorder guided by TCM Heart and Gall Theory can improve the blood supply in brain, adjust the HPA function, regulate immune function, bidirectionally regulate the release of SP and affect the metabolism of NE. Hence, the efficacy and effectiveness of acupuncture for OCD on TCM Heart-Gall Bladder Concept have been widely recognized.
强迫症(obsessive -compulsive disorder)是一种以无法控制的强迫行为和强迫行为为特征的神经性精神障碍。患者知道持续的强迫症症状是毫无意义和不合理的,但却无法摆脱。因此,他们感到非常紧张和痛苦。中医心胆理论指导下针灸治疗强迫症,可改善脑血供,调节HPA功能,调节免疫功能,双向调节SP的释放,影响NE的代谢。因此,针灸治疗强迫症的疗效和效果在中医心胆概念上得到了广泛的认可。
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引用次数: 0
Joint clustering and alignment for nucleosome occupancy analysis 核小体占用分析的联合聚类和排列
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470269
Teng L. Liu, Yu Zhang, J. Dennis
Several studies show that nucleosome occupancy patterns around transcription starting sites provide evolutionary and regulatory information about genes. However, as transcription starting sites may not accurately reflect physical nucleosome occupancy patterns, clustering of nucleosome occupancy patterns centered at transcription starting sites may give rise to inaccurate and blurred cluster centers, leading to potentially inaccurate conclusions. In this paper, we propose a joint clustering and alignment method and apply it to clustering of nucleosome occupancy patterns around transcription starting sites. The experimental results using the human genome-wide data show that alignment affects the significant majority of genes and leads to more pronounced local nucleosome occupancy patterns.
一些研究表明,转录起始位点周围的核小体占用模式提供了基因的进化和调控信息。然而,由于转录起始位点可能不能准确反映核小体的物理占用模式,以转录起始位点为中心的核小体占用模式聚类可能会产生不准确和模糊的聚类中心,从而导致可能不准确的结论。在本文中,我们提出了一种联合聚类和比对方法,并将其应用于转录起始位点周围核小体占用模式的聚类。使用人类全基因组数据的实验结果表明,比对影响了绝大多数基因,并导致更明显的局部核小体占用模式。
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引用次数: 0
Recognizing drosha processing sites by a two-step prediction model with structure and sequence information 基于结构和序列信息的两步预测模型识别drosha加工位点
Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392714
Xingchi Hu, Yanhong Zhou, Chuang Ma
Drosha is a class of RNase III enzyme plays important roles in the microRNA (miRNA) generation by cleaving primary miRNAs to release hairpin-shaped miRNA precursors. Accurately predicting the Drosha cleavage positions (i.e., processing sites) is helpful for the identification of miRNAs and the understanding of miRNA biogenesis mechanisms. In this study, we presented a Drosha processing site predictor, termed DroshaPSP, with a two-step prediction model by integrating structure and sequence features. Testing results on the Drosophila melanogaster miRNA data showed that DroshaPSP obtained a sensitivity of 0.859, a specificity of 0.999, and a Matthew's Correlation Coefficient of 0.864. We also found that the Shannon entropy is a powerful structure feature for DroshaPSP to distinguish true Drosha processing sites from the nearby pseudo processing sites effectively.
Drosha是一类RNase III酶,通过切割初级miRNA释放发夹状miRNA前体,在microRNA (miRNA)的生成中起重要作用。准确预测Drosha切割位置(即加工位点)有助于miRNA的鉴定和对miRNA生物发生机制的理解。在这项研究中,我们提出了一个Drosha加工位点预测器,称为DroshaPSP,具有两步预测模型,通过整合结构和序列特征。对黑腹果蝇miRNA数据的检测结果显示,DroshaPSP敏感性为0.859,特异性为0.999,马修相关系数为0.864。我们还发现Shannon熵是一个强大的结构特征,可以有效地区分真正的Drosha处理点和附近的伪处理点。
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引用次数: 1
Discussion on the improvement of the arteriovenous fistula surgeon's micrological technique 动静脉瘘外科医生显微技术改进的探讨
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470336
K. Bao, Han-guo Peng, P. Su
Arteriovenous fistula (AVF) is so important to hemodialysis patients that it is called their lifeline. In modern society, it is particularly urgent to improve AVF surgeon's micrological technique as patients' vascular condition tending to deteriorate because of increasing population aging and prevalence of hypertension and diabetes. So this paper is made to discuss how to improve the AVF surgeon's micrological technique from the following three aspects: enhancing the capability of hand movement control, establishing the concept of main-secondary hand and surgery airspace.
动静脉瘘(AVF)对血液透析患者非常重要,被称为他们的生命线。在现代社会,随着人口老龄化的加剧和高血压、糖尿病的流行,患者血管状况趋于恶化,提高AVF外科医生的显微技术显得尤为迫切。为此,本文从提高手的运动控制能力、树立主-副手的概念和手术空域三个方面探讨如何提高AVF外科医生的显微技术。
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引用次数: 0
期刊
2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops
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