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2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)最新文献

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Ranking SVM for multiple kernels output combination in protein-protein interaction extraction from biomedical literature 生物医学文献中蛋白质相互作用提取中多核输出组合排序支持向量机
Pub Date : 2010-12-01 DOI: 10.1109/BIBM.2010.5706635
Zhihao Yang, Yuan Lin, Jiajin Wu, Nan Tang, Hongfei Lin, Yanpeng Li
Knowledge about protein-protein interactions unveils the molecular mechanisms of biological processes. This paper presents a multiple kernels learning-based approach to automatically extracting protein-protein interactions from biomedical literature. Experimental evaluations show that our approach can achieve state-of-the-art performance with respect to comparable evaluations, with 64.88% F-score and 88.02% area under the receiver operating characteristics curve (AUC) on the AImed corpus.
蛋白质相互作用的知识揭示了生物过程的分子机制。本文提出了一种基于多核学习的方法从生物医学文献中自动提取蛋白质-蛋白质相互作用。实验评估表明,我们的方法可以达到最先进的性能,在aims语料库上,f得分为64.88%,接收者操作特征曲线(AUC)下面积为88.02%。
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引用次数: 1
Exploring matrix factorization techniques for significant genes identification of microarray dataset 探索矩阵分解技术用于微阵列数据集的重要基因鉴定
Pub Date : 2010-12-01 DOI: 10.1109/BIBM.2010.5706599
Wei Kong, Xiaoyang Mou, Xiaohua Hu
Unsupervised machine learning approaches are efficient analysis tools for DNA microarray technique which can accumulate hundreds of thousands of genes expression levels in a single experiment. In our study, two unsupervised knowledge-based matrix factorization methods, independent component analysis (ICA) and nonnegative matrix factorization (NMF) are explored to identify significant genes and related pathways in microarray gene expression dataset. The advantage of these two approaches is they can be performed as a biclustering method by which genes and conditions can be clustered simultaneously. Furthermore, they can group genes into different categories for identifying related diagnostic pathways and regulatory networks. The difference between these two method lies in ICA assume statistical independence of the expression modes, while NMF need positivity constrains to generate localized gene expression profiles. By combining the significant genes identified by both ICA and NMF, the simulation results show great efficient for finding underlying biological processes and related pathways in Alzheimer's disease (AD) and the activation patterns to AD phenotypes.
无监督机器学习方法是DNA微阵列技术的有效分析工具,可以在单个实验中积累数十万个基因表达水平。在本研究中,我们探索了独立成分分析(ICA)和非负矩阵分解(NMF)两种无监督的基于知识的矩阵分解方法,以识别微阵列基因表达数据集中的重要基因和相关途径。这两种方法的优点是它们可以作为一种双聚类方法来执行,通过这种方法,基因和条件可以同时聚类。此外,他们可以将基因分组成不同的类别,以确定相关的诊断途径和调控网络。这两种方法的区别在于ICA假设表达模式的统计独立性,而NMF需要正性约束来生成局部基因表达谱。通过结合ICA和NMF识别的重要基因,模拟结果显示,在寻找阿尔茨海默病(AD)的潜在生物学过程和相关途径以及AD表型的激活模式方面具有很高的效率。
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引用次数: 1
Gene selection using 1-norm regularization for multi-class microarray data 多类微阵列数据的1范数正则化基因选择
Pub Date : 2010-12-01 DOI: 10.1109/BIBM.2010.5706621
Xiaofei Nan, Nan Wang, P. Gong, Chaoyang Zhang, Yixin Chen, D. Wilkins
Explosive compounds such as TNT and RDX have various toxicological effects on the natural environment. The goal of the earthworm microarray experiment is to unearth the biomarker for toxicity evaluation. We propose a novel recursive gene selection method which can handle the multi-class setting effectively and efficiently. The selection is performed iteratively. In each iteration, a linear multi-class classifier is trained using 1-norm regularization, which leads to sparse weight vectors, i.e., many feature weights are exactly zero. Those zero-weight features are eliminated in the next iteration. The empirical results demonstrate that the selected features (genes) have very competitive discriminative power. In addition, the selection process has fast rate of convergence.
爆炸性化合物如TNT和RDX对自然环境有各种毒理学影响。蚯蚓微阵列实验的目的是发掘用于毒性评价的生物标志物。提出了一种新的递归基因选择方法,可以有效地处理多类设置。选择是迭代地执行的。在每次迭代中,使用1范数正则化训练线性多类分类器,这导致权重向量稀疏,即许多特征权重正好为零。这些零权重特性将在下一次迭代中消除。实证结果表明,被选择的特征(基因)具有很强的竞争辨别能力。此外,选择过程具有较快的收敛速度。
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引用次数: 3
Autoregressive modeling of DNA features for short exon recognition 用于短外显子识别的DNA特征自回归建模
Pub Date : 2010-12-01 DOI: 10.1109/BIBM.2010.5706608
N. Song, Hong Yan
This paper presents a new technique for the detection of short exons in DNA sequences. In this method, we analyze the DNA propeller twist and bending stiffness using the autoregressive (AR) model. The linear prediction matrices for the two features are combined to find the same set of linear prediction coefficients, from which we estimate the spectrum of the DNA sequence and detect protein-coding regions based on the 1/3 frequency component. To overcome the non-stationarity of DNA sequences, we use moving windows of different sizes in the AR model. Experiments on the human genome show that our multi-feature based method is superior in performance to existing exon detection algorithms.
本文提出了一种检测DNA序列短外显子的新技术。在此方法中,我们使用自回归(AR)模型分析DNA螺旋桨的扭转和弯曲刚度。将这两个特征的线性预测矩阵进行组合,得到一组相同的线性预测系数,以此估计DNA序列的频谱,并根据1/3频率分量检测蛋白质编码区。为了克服DNA序列的非平稳性,我们在AR模型中使用了不同大小的移动窗口。在人类基因组上的实验表明,基于多特征的方法在性能上优于现有的外显子检测算法。
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引用次数: 4
A parallel multi-objective ab initio approach for protein structure prediction 蛋白质结构预测的并行多目标从头算方法
Pub Date : 2010-12-01 DOI: 10.1109/BIBM.2010.5706552
David Becerra, A. Sandoval, Daniel Restrepo-Montoya, L. F. Niño
Protein structure prediction is one of the most important problems in bioinformatics and structural biology. This work proposes a novel and suitable methodology to model protein structure prediction with atomic-level detail by using a parallel multi-objective ab initio approach. In the proposed model, i) A trigonometric representation is used to compute backbone and side-chain torsion angles of protein atoms; ii) The Chemistry at HARvard Macromolecular Mechanics (CHARMm) function optimizes and evaluates the structures of the protein conformations; iii) The evolution of protein conformations is directed by optimization of protein energy contributions using the multi-objective genetic algorithm NSGA-II; and iv) The computation process is sped up and its effectiveness improved through the implementation of an island model of the evolutionary algorithm. The proposed model was validated on a set of benchmark proteins obtaining very promising results.
蛋白质结构预测是生物信息学和结构生物学中的重要问题之一。这项工作提出了一种新的和合适的方法来模拟蛋白质结构预测与原子水平的细节,使用并行多目标从头算方法。在该模型中,i)使用三角函数表示来计算蛋白质原子的主链和侧链扭转角;ii)哈佛大学大分子力学(CHARMm)的化学功能优化和评估蛋白质构象的结构;iii)利用多目标遗传算法NSGA-II优化蛋白质能量贡献,指导蛋白质构象的进化;iv)通过实现进化算法的孤岛模型,加快了计算速度,提高了算法的有效性。该模型在一组基准蛋白上进行了验证,获得了非常有希望的结果。
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引用次数: 23
Phylogenetic reconstruction with gene rearrangements and gene losses 基因重排和基因丢失的系统发育重建
Pub Date : 2010-12-01 DOI: 10.1109/BIBM.2010.5706531
Yiwei Zhang, Fei Hu, Jijun Tang
Reconstructing phylogenies from gene-order data has become very attractive in the research of evolution these years. So far, most methods can only treat genomes with equal gene contents with each gene appearing exactly once in each genome. In this paper, we propose a new distance measurement for genomes with inversions and insertions/deletions that comply with triangle inequality. Based on this distance, we develop a new method to solve the median problem of unequal gene content, which are used to reconstruct both phylogenies and ancestral genomes. We test our method on simulated datasets under various conditions and the experimental results show that our distance measurement can produce more accurate phylogenetic trees compared with other popular methods for unequal genomes. Also our median algorithm produces remarkably more accurate ancestral genomes than the only unequal genome median solver that is currently available.
近年来,利用基因序列数据重构系统发育已成为进化研究的热点。到目前为止,大多数方法只能处理基因含量相等的基因组,每个基因在每个基因组中只出现一次。在本文中,我们提出了一种新的符合三角不等式的基因组倒位和插入/缺失的距离测量方法。基于这一距离,我们提出了一种新的方法来解决基因含量不等的中值问题,并将其用于系统发育和祖先基因组的重建。我们在各种条件下的模拟数据集上测试了我们的方法,实验结果表明,与其他流行的不相等基因组方法相比,我们的距离测量方法可以产生更准确的系统发育树。此外,我们的中位数算法比目前可用的唯一不相等基因组中位数求解器产生更准确的祖先基因组。
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引用次数: 9
Detecting SNPs-disease associations using Bayesian networks 利用贝叶斯网络检测snp -疾病关联
Pub Date : 2010-12-01 DOI: 10.1109/BIBM.2010.5706532
Bing Han, Xue-wen Chen
Epistatic interactions play a significant role in improving pathogenesis, prevention, diagnosis and treatment of complex human diseases. A recent study in automatic detection of epistatic interactions showed that Markov Blanket-based methods are capable of finding SNPs (single-nucleotide polymorphism) that have a strong association with common diseases and of reducing false positives when the number of instances is large. Unfortunately, a typical SNP dataset consists of very limited number of examples, where current methods including Markov Blanket-based methods perform poorly. To address small sample problems, we propose a Bayesian network-based approach to detect epistatic interactions. The proposed method also employs a Branch-and-Bound technique for learning. We apply the proposed method to simulated datasets based on four disease models and a real dataset. Experimental results show that our method significantly outperforms Markov Blanket-based methods and other commonly-used methods, especially when the number of samples is small.
上位相互作用在改善人类复杂疾病的发病机制、预防、诊断和治疗方面发挥着重要作用。最近一项关于上位相互作用自动检测的研究表明,基于马尔可夫毯的方法能够发现与常见疾病密切相关的snp(单核苷酸多态性),并在实例数量较大时减少假阳性。不幸的是,典型的SNP数据集由非常有限的示例组成,其中当前的方法包括基于马尔可夫毯子的方法表现不佳。为了解决小样本问题,我们提出了一种基于贝叶斯网络的方法来检测上位性相互作用。该方法还采用了分支定界法进行学习。我们将该方法应用于基于四种疾病模型和一个真实数据集的模拟数据集。实验结果表明,该方法明显优于基于马尔可夫毯子的方法和其他常用方法,特别是在样本数量较少的情况下。
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引用次数: 2
Predicting ligand binding residues using multi-positional correlations and kernel canonical correlation analysis 利用多位置相关和核典型相关分析预测配体结合残基
Pub Date : 2010-12-01 DOI: 10.1109/BIBM.2010.5706556
Alvaro J. González, Li Liao, Cathy H. Wu
We present a new computational method for predicting ligand binding sites in protein sequences. The method uses kernelbased canonical correlation analysis and linear regression to identify binding sites in protein sequences as the residues that exhibit strong correlation between the residues' evolutionary characterization at the sites and the structure based functional classification of the proteins in the context of a functional family. We explore the effect of correlations among multiple positions in the sequences and show that their inclusion enhances the prediction accuracy significantly.
我们提出了一种新的预测蛋白质序列中配体结合位点的计算方法。该方法使用基于核的典型相关分析和线性回归来识别蛋白质序列中的结合位点作为残基,这些残基在这些位点上的进化特征与蛋白质在功能家族中的基于结构的功能分类之间表现出很强的相关性。我们探索了序列中多个位置之间的相关性的影响,并表明它们的包含显著提高了预测精度。
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引用次数: 5
Identification of critical location on a microstructural bone network 骨微结构网络关键位置的识别
Pub Date : 2010-12-01 DOI: 10.1109/BIBM.2010.5706628
Taehyong Kim, Jaehan Koh, Kang Li, M. Ramanathan, A. Zhang
Identification of a critical location in complex structures is one of the most important issues that affects the quality of safety in human life. Specifically, finding high fracture spots of a bone microstructure in our body is a very important research topic; however, it is still not well understood. In this paper, we study on identifying critical locations in a bone microstructure with our bone network model. In fact, about 25 million people in the United States suffer from osteoporosis, which is a systemic skeletal disease characterized by low bone mass and micro-architectural deterioration of bone tissue leading to enhanced bone fragility and a consequent increase in fracture risk. However, currently available techniques for the diagnosis of osteoporosis and the identification of critical locations of bone microstructure are limited. We create a bone network model based on properties of a bone microstructure and we develop a method, called information propagation, to identify critical locations in a bone network. Our paper focuses on detecting important edges as critical locations for the strength of bone microstructure when there are external forces applied to the bone network. Then, we evaluate results of the method in comparison with existing methods including the weighted betweenness centrality and the weighted bridge coefficient. We conclude with the discussion on advantages and disadvantages among those methods.
复杂结构中关键位置的识别是影响人类生活安全质量的最重要问题之一。具体来说,在我们体内寻找骨骼微观结构的高断裂点是一个非常重要的研究课题;然而,它仍然没有得到很好的理解。在本文中,我们研究了用骨网络模型识别骨微观结构中的关键位置。事实上,美国约有2500万人患有骨质疏松症,骨质疏松症是一种全身性骨骼疾病,其特征是骨量低,骨组织的微结构恶化,导致骨骼脆性增强,从而增加骨折风险。然而,目前可用于骨质疏松症诊断和骨微结构关键部位识别的技术是有限的。我们基于骨微观结构的特性创建了骨网络模型,并开发了一种称为信息传播的方法来识别骨网络中的关键位置。本文的重点是在骨网络受到外力作用时,检测重要边缘作为骨微观结构强度的关键位置。然后,我们将该方法的结果与现有方法进行了比较,包括加权中间度中心性和加权桥系数。最后讨论了这些方法的优缺点。
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引用次数: 4
Intracranial pressure level prediction in traumatic brain injury by extracting features from multiple sources and using machine learning methods 基于多源特征提取和机器学习方法的颅内压水平预测
Pub Date : 2010-12-01 DOI: 10.1109/BIBM.2010.5706619
Wenan Chen, Charles Cockrell, Kevin Ward, K. Najarian
This paper proposes a non-intrusive method to predict/estimate the intracranial pressure (ICP) level based on features extracted from multiple sources. Specifically, these features include midline shift measurement and texture features extracted from CT slices, as well as patient's demographic information, such as age. Injury Severity Score is also considered. After aggregating features from slices, a feature selection scheme is applied to select the most informative features. Support vector machine (SVM) is used to train the data and build the prediction model. The validation is performed with 10 fold cross validation. To avoid overfitting, all the feature selection and parameter selection are done using training data during the 10 fold cross validation for evaluation. This results an nested cross validation scheme implemented using Rapidminer. The final classification result shows the effectiveness of the proposed method in ICP prediction.
本文提出了一种基于多源特征提取的非侵入性颅内压(ICP)水平预测/估计方法。具体来说,这些特征包括从CT切片中提取的中线位移测量和纹理特征,以及患者的年龄等人口统计信息。损伤严重程度评分也被考虑在内。在对切片特征进行聚合后,采用特征选择方案选择信息量最大的特征。使用支持向量机(SVM)对数据进行训练并建立预测模型。验证采用10倍交叉验证。为了避免过拟合,所有的特征选择和参数选择都是在10次交叉验证中使用训练数据进行评估。这就产生了使用Rapidminer实现的嵌套交叉验证方案。最后的分类结果表明了该方法在ICP预测中的有效性。
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引用次数: 24
期刊
2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
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