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

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The role of Eigen-matrix translation in classification of biological datasets 特征矩阵翻译在生物数据集分类中的作用
Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392701
Hao Jiang, W. Ching
Driven by the challenge of integrating large amount of experimental data obtained from biological research, computational biology and bioinformatics are growing rapidly. Machine learning methods, especially kernel methods with Support Vector Machines (SVMs) are very popular tools. In the perspective of kernel matrix, a technique namely Eigen-matrix translation has been introduced for protein data classification. The Eigen-matrix translation strategy owns a lot of nice properties while the nature of which needs further exploration. We propose that its importance lies in the dimension reduction of predictor attributes within the data set. This can therefore serve as a novel perspective for future research in dimension reduction problems.
在整合从生物学研究中获得的大量实验数据的挑战的驱动下,计算生物学和生物信息学正在迅速发展。机器学习方法,特别是核方法与支持向量机(svm)是非常流行的工具。从核矩阵的角度出发,引入特征矩阵翻译技术对蛋白质数据进行分类。特征矩阵翻译策略具有许多优良的性质,但其性质有待进一步探讨。我们认为它的重要性在于数据集中预测属性的降维。因此,这可以为未来降维问题的研究提供一个新的视角。
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引用次数: 2
A model of cellular decision making in photodynamic therapy of cancer 肿瘤光动力治疗中的细胞决策模型
Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392704
I. Gkigkitzis, Xin-Hua Hu
The aim of this report is to provide a mathematical model of the mechanism for making binary fate decisions about cell death or survival, during and after type II photodynamic therapy (PDT) treatment, and to supply the logical design for this decision mechanism as an application of rate distortion theory to the biochemical processing of information by the physical system of a cell. Based on system biology models of the molecular interactions involved in the PDT processes previously established, and regarding a cellular decision-making system as a noisy communication channel, we use rate distortion theory to design a time dependent three dimensional Blahut-Arimoto algorithm where the input is a stimulus vector composed of the time dependent concentrations of three PDT related cell death signaling molecules and a cell fate decision as output. The molecular concentrations are determined by a group of rate equations. The output is the cell decision with a probability of cell survival or death. The optimality of the cell decision strategy is assessed by the cell survival probability, which might be modified to account for heterogeneous cell resistance to therapy.
本报告的目的是提供在II型光动力治疗(PDT)治疗期间和之后关于细胞死亡或生存的二元命运决策机制的数学模型,并提供该决策机制的逻辑设计,作为速率畸变理论在细胞物理系统对信息的生化处理中的应用。基于先前建立的PDT过程中涉及的分子相互作用的系统生物学模型,并将细胞决策系统视为一个有噪声的通信通道,我们使用速率失真理论设计了一个时间依赖的三维Blahut-Arimoto算法,其中输入是由三个PDT相关细胞死亡信号分子的时间依赖浓度组成的刺激向量,输出是细胞命运决定。分子浓度由一组速率方程决定。输出是带有细胞存活或死亡概率的细胞决策。细胞决策策略的最优性是通过细胞生存概率来评估的,这可能会被修改以考虑异质细胞对治疗的抵抗。
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引用次数: 1
Aligning ligand binding cavities by optimizing superposed volume 通过优化叠加体积来排列配体结合腔
Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392629
Ruobing Chen, K. Scheinberg, B. Chen
We describe an optimization-based method that seeks the superposition of ligand binding cavities that maximizes their overlapping volume. Our method, called DFO-VASP, iteratively uses Boolean set operations to evaluate overlapping volume in intermediate superpositions while searching for the maximal one. Our results verify that the superpositions identified are biologically relevant, and demonstrate that DFO-VASP generally discovers cavity superpositions with similar or occasionally larger overlapping volume than those of superpositions generated with existing means.
我们描述了一种基于优化的方法,寻求配体结合腔的叠加,使其重叠体积最大化。我们的方法,称为DFO-VASP,迭代地使用布尔集合运算来评估中间叠加的重叠量,同时搜索最大的重叠量。我们的研究结果证实了所识别的叠加具有生物学相关性,并表明DFO-VASP通常发现与现有方法产生的叠加相似或偶尔更大的重叠体积的腔体叠加。
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引用次数: 3
Jumping low, jumping high: Controlling hopping in the protein energy surface 低跳、高跳:控制蛋白能量面跳跃
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470276
Brian S. Olson, Amarda Shehu
The protein conformational space is characterized as a multi-dimensional funnel-like energy surface with conformations corresponding to the native state around the energy basin. The dimensionally and ruggedness of this energy surface are primary why computationally determining the biologically active or native state of a protein remains a difficult challenge. A common template among structure prediction protocols begins by sampling many local minima in the energy surface. Basin Hopping (BH) has emerged as a suitable framework for effectively sampling these coarse grained local minima. BH consists of a series structural perturbations followed by minimizations, forming a trajectory of local minima with the Metropolis criterion biasing it towards increasingly low-energy minima.
蛋白质构象空间的特征是一个多维的漏斗状能量面,其构象与能量盆周围的天然状态相对应。这种能量表面的尺寸和坚固性是计算确定蛋白质的生物活性或天然状态仍然是一项艰巨挑战的主要原因。在结构预测协议中,一个常用的模板是从能量表面的许多局部极小值采样开始的。盆地跳跃(BH)已成为有效采样这些粗粒度局部极小值的合适框架。黑洞由一系列结构扰动和最小化组成,形成了一个局部极小的轨迹,Metropolis准则使其趋向于越来越低能量的极小值。
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引用次数: 0
A supervised solution for redundant feature detection depending on instances 基于实例的冗余特征检测的监督解决方案
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470320
Xue-Qiang Zeng, Guozheng Li
As a high dimensional problem, analysis of microarray data sets is a challenging task, where many weakly relevant or redundant features hurt generalization performance of classifiers. The previous works used redundant feature detection methods to select discriminative compact gene set, which only considered the relationship among features, not the redundancy of classification ability among features. Here, we propose a novel algorithm named RESI (Redundant fEature Selection depending on Instance), which considers label information in the measure of feature subset redundancy. Experimental results on benchmark data sets show that RESI performs better than the previous state-of-arts algorithms on redundant feature selection methods like mRMR.
作为一个高维问题,微阵列数据集的分析是一项具有挑战性的任务,其中许多弱相关或冗余的特征会影响分类器的泛化性能。以往的研究采用冗余特征检测方法选择判别紧凑基因集,只考虑特征之间的关系,没有考虑特征之间分类能力的冗余性。本文提出了一种基于实例的冗余特征选择(RESI)算法,该算法在特征子集冗余度度量中考虑了标签信息。在基准数据集上的实验结果表明,RESI算法在mRMR等冗余特征选择方法上的表现优于现有算法。
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引用次数: 1
Quantitative models for statistical nucleosome occupancy prediction 统计核小体占用预测的定量模型
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470270
Yu Zhang, Xiuwen Liu, J. Dennis
Nucleosome is the basic unit of DNA in eukaryotic cells. As nucleosomes limit the accessibility of the wrapped DNA to transcription factors and other DNA-binding proteins, their positions play an essential role in regulations of gene activities. Experiments have indicated that DNA sequence strongly influences nucleosome positioning by enhancing or reducing their binding affinity to nucleosomes, therefore providing an intrinsic cell regulatory mechanism. While some sequence features are known to be nucleosome forming or nucleosome inhibiting, however, existing models have limited accuracy in predicting quantitatively nucleosomes occupancy (i.e., statistical nucleosome positioning) based on DNA sequence. In this paper, we propose new quantitative models for DNA sequence-based nucleosome-occupancy prediction based on dinucleotide-matching features, where the parameters are learned through regression algorithms. Experimental results on a genome-wide set of yeast dataset show that our models give more accurate predictions than existing models.
核小体是真核细胞中DNA的基本单位。由于核小体限制了被包裹的DNA对转录因子和其他DNA结合蛋白的接近,它们的位置在基因活动的调控中起着至关重要的作用。实验表明,DNA序列通过增强或降低核小体与核小体的结合亲和力来强烈影响核小体的定位,因此提供了一种内在的细胞调节机制。虽然已知一些序列特征是形成核小体或抑制核小体,但是,现有模型在基于DNA序列定量预测核小体占用(即统计核小体定位)方面的准确性有限。在本文中,我们提出了基于二核苷酸匹配特征的DNA序列核小体占用预测的新定量模型,其中参数是通过回归算法学习的。在酵母全基因组数据集上的实验结果表明,我们的模型比现有模型给出了更准确的预测。
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引用次数: 1
Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma 重建肝细胞癌发生过程的动态基因调控网络
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470298
Hailong Zhu, R. Rao, Luonan Chen
A crucial work of investigating the mechanisms of cancer development is to unraveling the dynamic nature of gene regulation during the disease process. However, reconstruction of dynamic gene regulatory network requires time-sequence samples of a biological process, which are not available for many bio-medical problems. In this paper, we propose a dynamic cascaded method to reconstruct dynamic gene networks from sample-based transcriptional data. Our method is based on two biologically plausible assumptions, which can characterise the dynamic and continuous nature of gene transcription. Our approach was successfully applied to reconstruct the dynamic gene networks of hepatocellular carcinoma (HCC) progression. The derived HCC networks were verified by functional analysis and network enrichment analysis.
研究癌症发展机制的一项关键工作是揭示疾病过程中基因调控的动态性质。然而,动态基因调控网络的重建需要生物过程的时间序列样本,这是许多生物医学问题无法获得的。在本文中,我们提出了一种动态级联方法,从基于样本的转录数据重建动态基因网络。我们的方法是基于两个生物学上合理的假设,这可以表征基因转录的动态和连续性。我们的方法被成功地应用于重建肝细胞癌(HCC)进展的动态基因网络。通过功能分析和网络富集分析验证了衍生的HCC网络。
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引用次数: 1
Clinical research on rule of acupoint heat-sensitization within patients suffer Bell's palsy 贝尔氏麻痹患者穴位热敏化规律的临床研究
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470351
Qingsheng Yang, Z. Gu, Zhenhua Xu, Quanxin Chen
This study is to explore the rule of acupoint heat-sensitization within patients who suffer Bell's palsy. Probe the rule of acupoint heat-sensitization within patients suffer Bell's palsy by recording the phenomenon and contrasting the frequency of acupoints, meridians, patterns of manifestation between healthy control volunteers and patients. We found that there was statistical difference between two groups on the frequency of acupoint heat-sensitization phenomenon (P<;0.01), but not among different types of TCM syndrome when compared on the occurrence rate, patterns of manifestation (the top five patterns: blended sense, diathermanous sense, thermolytic sense, orderly transmission along channels, enjoying the thermal sensation), distribution of meridians (the top five channels: meridian of FOOT-YANG MING, HAND-SHAO YANG, FOOT-SHAO YANG, HAND-TAI YANG, HAND-YANG MING) and distribution of acupuncture points (the five top points: YIFENG(SJ17), XIAGUAN(ST7), QUANLIAO(SL18), YANGBAI(GB14), HEGU(LM)) (P>0.05). Thus we conclude that the frequency of acupoint heat-sensitization phenomenon within Bell's palsy patients is higher than normal volunteers, and the difference of patterns of manifestation, distribution of acupoints and meridians are all associated with channels, but not with the TCM syndromes.
本研究旨在探讨贝尔氏麻痹患者穴位热敏化的规律。通过记录贝尔麻痹患者的穴位热敏现象,对比健康对照志愿者与患者的穴位频率、经络、表现模式,探讨贝尔麻痹患者的穴位热敏规律。两组患者穴位热敏现象发生频率比较,差异有统计学意义(P0.05)。因此,我们得出贝尔氏麻痹患者的穴位热敏现象频率高于正常志愿者,其表现模式、穴位分布和经络的差异均与经络有关,而与中医证候无关。
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引用次数: 2
A neural network approach to the identification of b-/y-ions in MS/MS spectra MS/MS光谱中b-/y-离子识别的神经网络方法
Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392625
J. P. Cleveland, J. Rose
The effectiveness of de novo peptide sequencing algorithms depends on the quality of MS/MS spectra. Since most of the peaks in a spectrum are uninterpretable `noise' peaks it is necessary to carefully pre-filter the spectra to identify the `signal' peaks that likely correspond to b-/y-ions. Selecting the optimal set of peaks for candidate peptide generation is essential for obtaining accurate results. A careful balance must be maintained between the precision and recall of peaks that are selected for further processing and candidate peptide generation. If too many peaks are selected the search space will be too large and the problem becomes intractable. If too few peaks are selected cleavage sites will be missed, the resulting candidate peptides will have large gaps, and sequencing results will be poor. For this reason pre-filtering of MS/MS spectra and accurate selection of peaks for peptide candidate generation is essential to any de novo peptide sequencing algorithm. We present a novel neural network approach for the selection of b-/y-ions using known fragmentation characteristics, and leveraging neural network probability estimates of flanking and complementary ions. We show a significant improvement in precision and recall of peaks corresponding to b-/y-ions and a reduction in search space over approaches used by other de novo peptide sequencing algorithms.
从头开始的肽测序算法的有效性取决于质谱/质谱的质量。由于光谱中的大多数峰是不可解释的“噪声”峰,因此有必要仔细地对光谱进行预滤波,以识别可能对应于b-/y-离子的“信号”峰。为候选肽生成选择最佳的峰集对于获得准确的结果至关重要。必须在选择用于进一步处理和候选肽生成的峰的精度和召回率之间保持仔细的平衡。如果选择的峰值太多,则搜索空间太大,问题变得难以处理。如果选择的峰过少,则会错过选择的裂解位点,得到的候选肽将有很大的间隙,测序结果将很差。因此,MS/MS谱的预滤波和候选肽生成峰的准确选择对于任何新的肽测序算法都是必不可少的。我们提出了一种新的神经网络方法,利用已知的碎片特征来选择b-/y离子,并利用神经网络对侧翼和互补离子的概率估计。与其他从头开始的肽测序算法相比,我们在b-/y-离子对应的峰的精度和召回率方面有了显着提高,并且减少了搜索空间。
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引用次数: 4
Keyword annotation of biomedicai documents with graph-based similarity methods 基于图的相似度方法的生物医学文献关键词标注
Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392698
Shuguang Wang, M. Hauskrecht
In this paper, we present a new approach that lets us extract, and represent relations among terms (concepts) in the documents and uses these relations to support various document analysis applications. Our approach works by building a graph of local co-occurrence relations among terms that are extracted directly from text and by defining a global similarity metric among these terms and sets of terms using the graph and its connectivity. We demonstrate the benefit of the approach on the problem of MeSH keyword annotation of documents based on their abstracts.
在本文中,我们提出了一种新的方法,它允许我们提取和表示文档中术语(概念)之间的关系,并使用这些关系来支持各种文档分析应用程序。我们的方法通过构建直接从文本中提取的术语之间的局部共现关系图,并使用图及其连接性在这些术语和术语集之间定义全局相似性度量来工作。我们演示了该方法在基于摘要的文档网格关键字标注问题上的优势。
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引用次数: 2
期刊
2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops
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