关键词： Quantum chemical topology   Force field   Multipole moment   Polarisation   Atoms in molecules   Machine learning  

摘要： We describe an intramolecularly polarisable multipolar electrostatic potential model for ethanol, which acts as a pilot molecule for this proof-of-concept study. We define atoms via the partitioning prescribed by quantum chemical topology (QCT). A machine learning method called Kriging is employed to capture the way atomic multipole moments vary upon conformational change. The multipole moments predicted by the Kriging models are used in the calculation of atom-atom electrostatic interaction energies. Charge transfer is treated in the same way as dipolar polarisation and the polarisation of higher rank multipole moments. This method enables the development of a new and more accurate force field. (C) 2011 Elsevier B.V. All rights reserved.

摘要： Mass spectrometric based methods for absolute quantification of proteins, such as QconCAT, rely on internal standards of stable-isotope labeled reference peptides, or "Q-peptides," to act as surrogates. Key to the success of this and related methods for absolute protein quantification (such as AQUA) is selection of the Q-peptide. Here we describe a novel method, CONSeQuence (consensus predictor for Q-peptide sequence), based on four different machine learning approaches for Q-peptide selection. CONSeQuence demonstrates improved performance over existing methods for optimal Q-peptide selection in the absence of prior experimental information, as validated using two independent test sets derived from yeast. Furthermore, we examine the physicochemical parameters associated with good peptide surrogates, and demonstrate that in addition to charge and hydrophobicity, peptide secondary structure plays a significant role in determining peptide "detectability" in liquid chromatography-electrospray ionization experiments. We relate peptide properties to protein tertiary structure, demonstrating a counterintuitive preference for buried status for frequently detected peptides. Finally, we demonstrate the improved efficacy of the general approach by applying a predictor trained on yeast data to sets of proteotypic peptides from two additional species taken from an existing peptide identification repository. Molecular & Cellular Proteomics 10: 10.1074/mcp.M110.003384, 1-12, 2011.

关键词： 蛋白质折叠   机器学习   结构预测  

摘要： 蛋白质的生物功能是由它们的空间折叠结构决定的,理解蛋白质的折叠过程是生物信息学领域中极具挑战性的问题之一。近年来,各种优化方法用于蛋白质空间折叠结构预测。这些方法仍存在着不足,算法在变量数目增大时,难以收敛到全局最优解,并容易产生早熟收敛,从而影响求解精度和效率。针对蛋白质结构预测模型多变量多极值的特点,文章采用机器学习方法对蛋白质进行折叠结构预测。

关键词： Artificial Intelligence   Cysteine/chemistry   Disulfides/chemistry   Eukaryota   Proteins/analysis   Proteins/chemistry  

摘要： Motivation: Disulfide bonds stabilize protein structures and play relevant roles in their functions. Their formation requires an oxidizing environment and their stability is consequently depending on the redox ambient potential, which may differ according to the subcellular compartment. Several methods are available to predict cysteine-bonding state and connectivity patterns. However, none of them takes into consideration the relevance of protein subcellular localization. Results: Here we develop DISLOCATE, a two-step method based on machine learning models for predicting both the bonding state and the connectivity patterns of cysteine residues in a protein chain. We find that the inclusion of protein subcellular localization improves the performance of these predictive steps by 3 and 2 percentage points, respectively. When compared with previously developed methods for predicting disulfide bonds from sequence, DISLOCATE improves the overall performance by more than 10 percentage points.

关键词： Prediction Accuracy   Test Inhibitor   Radial Basis Function Kernel   Positive Class   Quadratic Kernel  

摘要： Background: We present a machine learning approach to the problem of protein ligand interaction prediction. We focus on a set of binding data obtained from 113 different protein kinases and 20 inhibitors. It was attained through ATP site-dependent binding competition assays and constitutes the first available dataset of this kind. We extract information about the investigated molecules from various data sources to obtain an informative set of features. Results: A Support Vector Machine (SVM) as well as a decision tree algorithm (C5/See5) is used to learn models based on the available features which in turn can be used for the classification of new kinase-inhibitor pair test instances. We evaluate our approach using different feature sets and parameter settings for the employed classifiers. Moreover, the paper introduces a new way of evaluating predictions in such a setting, where different amounts of information about the binding partners can be assumed to be available for training. Results on an external test set are also provided. Conclusions: In most of the cases, the presented approach clearly outperforms the baseline methods used for comparison. Experimental results indicate that the applied machine learning methods are able to detect a signal in the data and predict binding affinity to some extent. For SVMs, the binding prediction can be improved significantly by using features that describe the active site of a kinase. For C5, besides diversity in the feature set, alignment scores of conserved regions turned out to be very useful.

关键词： 机器学习方法   分子描述符   递归变量消除法   支持向量机   丙型肝炎病毒  

摘要： 在丙型肝炎病毒(HCV)的基因复制和蛋白质成熟的过程中,非结构蛋白5B(NS5B)作为RNA依赖的RNA聚合酶起到了重要的作用.抑制NS5B聚合酶可以阻止丙型肝炎病毒的RNA复制,因此成为一种治疗丙型肝炎的有效方法.通过计算机方法进行虚拟筛选和预测NS5B聚合酶抑制剂已经变得越来越重要.本文主要采用机器学习方法(支持向量机(SVM)、k-最近相邻法(k-NN)和C4.5决策树(C4.5DT))对已知的丙型肝炎病毒NS5B蛋白酶抑制剂与非抑制剂建立分类预测模型.1248个结构多样性化合物(552个NS5B抑制剂与696个非NS5B抑制剂)被用于测试分类预测系统,并用递归变量消除法选择与NS5B抑制剂相关的性质描述符以提高预测精度.独立验证集的总预测精度为84.1%-85.0%,NS5B抑制剂的预测精度为81.4%-91.7%,非NS5B抑制剂的预测精度为78.2%-87.2%.其中支持向量机给出最好的NS5B抑制剂预测精度(91.7%);C4.5决策树给出最好的非NS5B抑制剂预测精度(87.2%);k-最近相邻法给出最好的总预测精度(85.0%).研究表明机器学习方法可以有效预测未知数据集中潜在的NS5B抑制剂,并有助于发现与其相关的分子描述符.

关键词： machine learning in medicine   radiotherapy   prostate cancer   artificial neural networks   support vector machine  

摘要： Purpose: The goal of this study is to investigate the advantages of large scale optimization methods vs conventional classification techniques in predicting acute toxicity for urinary bladder and rectum due to prostate irradiation. Methods: Clinical and dosimetric data of 321 patients undergoing prostate conformal radiotherapy were recorded. Gastro-intestinal and genito-urinary acute toxicities were scored according to the Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer (RTOG/EORTC) scale. Patients were classified in two categories to separate mild (Grade < 2) from severe toxicity levels (Grade > 2). Machine learning methods at different complexity were implemented to predict toxicity as a function of multiple variables. The first approach consisted of a large scale optimization method, based on genetic algorithms (GAs) and artificial neural networks (ANN). The second approach was a binary classifier based on support vector machines (SVM). Results: The ANN and SVM-based solutions showed comparable prediction accuracy, exhibiting an area under the receiver operating characteristic (ROC) curve of 0.7. Different sensitivity and specificity features were measured for the two approaches. The ANN algorithm showed enhanced sensitivity if combined with appropriate classification criteria. Conclusions: The results demonstrate that high sensitivity in toxicity prediction can be achieved with optimized ANNs, that are put forward to represent a valuable support in medical decisions. Future studies will be focused on enlarging the available patient database to increase the reliability of toxicity prediction algorithms and to define optimal classification criteria. (C) 2011 American Association of Physicists in Medicine. [DOI: 10.1118/1.3582947]

关键词： P2P流量   深度包检测   机器学习   传输层检测  

摘要： 如何快速而准确的检测出P2P流量,是如今网络管理中的1个重要的问题。现在常见的检测方法有基于端口检测法,DPI深度包检测,以及根据传输层特征来检测。DPI深度包检测方法需要及时跟新特征库,对于加密协议无法识别等缺陷限制了其应用。机器学习的传输层检测方法通过分析流的统计特征来检测P2P流量。较之DPI,该方法能检测出DPI无法检测出的加密的P2P流量以及特征库外的流量。本文提出了1种新的结合DPI与基于机器学习的传输层检测方法的模型,并通过实验验证该模型能弥补DPI方法的缺陷,提高检测的准确性。

关键词： 数据挖掘   朴素贝叶斯分类   数据预测   鸢尾花(Iris)数据集  

摘要： 朴素贝叶斯分类方法是数据库分类知识挖掘领域的一项基本技术,并具有广泛的应用。使用贝叶斯分类算法实现了对经典数据集Iris的分类。实践表明,朴素贝叶斯分类是一种有效的数据挖掘分类算法。

关键词： Hormone therapy   MRI   Random forest   WHIMS  

摘要： Use of conjugated equine estrogens (CEE) has been linked to smaller regional brain volumes in women aged >= 65 years;however, it is unknown whether this results in a broad-based characteristic pattern of effects. Structural magnetic resonance imaging was used to assess regional volumes of normal tissue and ischemic lesions among 513 women who had been enrolled in a randomized clinical trial of CEE therapy for an average of 6.6 years, beginning at ages 65-80 years. A multivariate pattern analysis, based on a machine learning technique that combined Random Forest and logistic regression with L-1 penalty, was applied to identify patterns among regional volumes associated with therapy and whether patterns discriminate between treatment groups. The multivariate pattern analysis detected smaller regional volumes of normal tissue within the limbic and temporal lobes among women that had been assigned to CEE therapy. Mean decrements ranged as high as 7% in the left entorhinal cortex and 5% in the left perirhinal cortex, which exceeded the effect sizes reported previously in frontal lobe and hippocampus. Overall accuracy of classification based on these patterns, however, was projected to be only 54.5%. Prescription of CEE therapy for an average of 6.6 years is associated with lower regional brain volumes, but it does not induce a characteristic spatial pattern of changes in brain volumes of sufficient magnitude to discriminate users and nonusers. (c) 2011 Elsevier Inc. All rights reserved.