基于离散小波变换提取脑机接口中脑电特征

在脑机接口中，针对脑电特征提取利用单一种类信息、使用数据量大、分类性能较差等缺点，提出一种新颖的基于离散小波变换的方法。分析了小波变换特征提取的特点和特征表示方式，用Daubechies类db4小波函数对脑电信号进行6层分解，抽取小波变换各子带关键的部分逼近系数、小波系数、小波子带系数均值组成特征向量。以分类正确率为指标检验了提取特征的性能。实验结果表明，这种方法能够利用少量数据提取脑电信号本质特征，具有较高的分类性能，为利用脑电识别人的不同意图提供了快速而有效的手段。     

Application of laser capture microdissection and proteomics in colon cancer.

AIMS: Laser capture microdissection is a recent development that enables the isolation of specific cell types for subsequent molecular analysis. This study describes a method for obtaining proteome information from laser capture microdissected tissue using colon cancer as a model. METHODS: Laser capture microdissection was performed on toluidine blue stained frozen sections of colon cancer. Tumour cells were selectively microdissected. Conditions were established for solubilising proteins from laser microdissected samples and these proteins were separated by two dimensional gel electrophoresis. Individual protein spots were cut from the gel, characterised by mass spectrometry, and identified by database searching. These results were compared with protein expression patterns and mass spectroscopic data obtained from bulk tumour samples run in parallel. RESULTS: Proteins could be recovered from laser capture microdissected tissue in a form suitable for two dimensional gel electrophoresis. The solubilised proteins retained their expected electrophoretic mobility in two dimensional gels as compared with bulk samples, and mass spectrometric analysis was also unaffected. CONCLUSION: A method for performing two dimensional gel electrophoresis and mass spectrometry using laser capture microdissected tissue has been developed.     

基于小波变换的心电信号准无损压缩算法

提出了基于小波变换的心电信号准无损压缩算法。在对原始信号进行一级小波分解的基础上，根据高频分量和低频分量所占位数的不同分别进行无损压缩。实验结果表明该方法失真度非常小，而且算法简单，运算速度快。     

Research of fetal ECG extraction using wavelet analysis and adaptive filtering

Extracting clean fetal electrocardiogram (ECG) signals is very important in fetal monitoring. In this paper, we proposed a new method for fetal ECG extraction based on wavelet analysis, the least mean square (LMS) adaptive filtering algorithm, and the spatially selective noise filtration (SSNF) algorithm. First, abdominal signals and thoracic signals were processed by stationary wavelet transform (SWT), and the wavelet coefficients at each scale were obtained. For each scale, the detail coefficients were processed by the LMS algorithm. The coefficient of the abdominal signal was taken as the original input of the LMS adaptive filtering system, and the coefficient of the thoracic signal as the reference input. Then, correlations of the processed wavelet coefficients were computed. The threshold was set and noise components were removed with the SSNF algorithm. Finally, the processed wavelet coefficients were reconstructed by inverse SWT to obtain fetal ECG. Twenty cases of simulated data and 12 cases of clinical data were used. Experimental results showed that the proposed method outperforms the LMS algorithm: (1) it shows improvement in case of superposition R-peaks of fetal ECG and maternal ECG; (2) noise disturbance is eliminated by incorporating the SSNF algorithm and the extracted waveform is more stable; and (3) the performance is proven quantitatively by SNR calculation. The results indicated that the proposed algorithm can be used for extracting fetal ECG from abdominal signals.     

基于数据非依赖采集的无色谱数据处理软件系统

目的如何高效准确地定量蛋白质一直是蛋白质组学的主要关注点,基于液相色谱-数据依赖模式进行谱图采集的质谱方法是目前主流的蛋白质测定方式。但是,当面对复杂样本中蛋白质定量的对比实验,为了使肽段得到有效分离,使用较长时间色谱洗脱的方法占据了谱图生成的大量时间。为了解决此问题,并且能够高效、准确地定性定量肽段,提出一个基于数据非依赖采集(data-independent acquisition,DIA)的无色谱数据处理软件系统。方法基于以肽段为中心的蛋白质定量理念,利用现有解决混合图谱的方法对无色谱DIA质谱数据进行定性,随后仿照DIA方法下色谱面积的计算方法完成定量;最后基于分类模型,对最终结果给出统计分析控制。结果本系统能够处理生成无色谱的DIA质谱数据,并且在12 min内从海拉(Henrietta Lacks,Hela)蛋白质样本中定性定量出1954个肽段。结论使用本系统处理无色谱质谱数据,相比于DIA质谱数据,能够在更短的时间内准确定量出足够的肽段,对于在有限时间内测定大规模蛋白质样本有重要的意义。     

An Adaptive Run Length Encoding method for the compression of electrocardiograms

A compression method, based on the choice of a wavelet that minimizes the distortion of compression for each electrocardiogram considered, is proposed in this paper. The scaling filter used on the determination of the wavelet function is obtained from the resolution of an optimization problem, which is unconstrained since the scaling filter is parametrized in a way that the constraints applied to the scaling filter are embedded on the parameters. The coefficients of projection of the signal over the wavelet subspaces are calculated and only the most significant ones are retained, being the significant coefficients determined in order to satisfy a pre-specified distortion measure. The bitmap that informs the positions of the retained coefficients is encoded along with the values of the coefficients by using an improved version of the Run Length Encoding technique. Experiments that compare the proposed approach with other techniques illustrate the efficiency of the method.     

Comparison between liquid chromatography-time of-flight mass spectrometry and selected reaction monitoring liquid chromatography-mass spectrometry for quantitative determination of idoxifene in human plasma.

This study compares HPLC electrospray time-of-flight mass spectrometry and selected reaction monitoring (SRM) LC-MS for high throughput quantitative determination of a small molecule drug in biological samples. A high throughput LC-MS method was developed for quantitatative determination of idoxifene in human plasma and the evaluation was accomplished with the cross-validation of the developed LC-MS method between the time-of-flight mass spectrometer, and a triple quadrupole mass spectrometer operated in the SRM mode. A simple one-step semi-automated 96-well liquid-liquid extraction procedure was used to prepare 96 samples in approximately 30 min and a rapid gradient was used to shorten the LC run time. Time-of-flight mass spectrometry provides acquisition of full-scan mass spectra and extracted ion current chromatograms, which may be extracted from the total ion current chromatogram for peak area determination. The limit of quantitation for idoxifene in human plasma obtained with the time-of-flight mass spectrometer was 5 ng/ml based on 100-microl aliquots of human plasma, and the linear dynamic range was from 5 ng/ml to 2000 ng/ml. The quantitative LC-MS results from the time-of-flight mass spectrometer demonstrated that precision did not exceed 7.1% and accuracy did not exceed 1.7% with reference to quality control samples at three concentration levels in replicates of six. In contrast, the limit of quantitation for idoxifene in human plasma using a tandem triple quadrupole mass spectrometer was 0.5 ng/ml with a linear dynamic range to 1000 ng/ml. The results from the triple quadrupole instrument show that the precision did not exceed 2.2% and accuracy did not exceed 2.9%. The overall results suggest time-of-flight mass spectrometry may be a viable technique for high throughput bioanalytical work for the quantitative determination of a representative small molecule drug in the low ng/ml range in human plasma.     

Digital Radiographic Image Denoising Via Wavelet-Based Hidden Markov Model Estimation

This paper presents a technique for denoising digital radiographic images based upon the wavelet-domain Hidden Markov tree (HMT) model. The method uses the Anscombes transformation to adjust the original image, corrupted by Poisson noise, to a Gaussian noise model. The image is then decomposed in different subbands of frequency and orientation responses using the dual-tree complex wavelet transform, and the HMT is used to model the marginal distribution of the wavelet coefficients. Two different correction functions were used to shrink the wavelet coefficients. Finally, the modified wavelet coefficients are transformed back into the original domain to get the denoised image. Fifteen radiographic images of extremities along with images of a hand, a line-pair, and contrast–detail phantoms were analyzed. Quantitative and qualitative assessment showed that the proposed algorithm outperforms the traditional Gaussian filter in terms of noise reduction, quality of details, and bone sharpness. In some images, the proposed algorithm introduced some undesirable artifacts near the edges.     

一种基于卷积神经网络的DIA数据预处理模型

目的数据非依赖性采集(data independent acquisition,DIA)是目前针对大通量蛋白质组学分析常用的一种数据采集方式。在对DIA数据无目标的分析方式中,由于无法预测肽段出现在DIA数据中的位置,需要对谱中所有的峰进行分析。但谱中含有大量的噪声峰,这些峰会严重影响后续蛋白质定性定量分析的效率与效果,所以在DIA数据的无目标分析过程中先进行预处理以去除噪声峰就成了很重要的一步。为了能充分利用从DIA数据中提取出来的肽段在一级质谱(first stage of mass spectrometry,MS1)和二级质谱(second stage of mass spectrometry,MS2)中的峰信息,提出质谱卷积神经网络(mass spectrometry convolutional neural network,MSCNN)模型。方法不同于传统的方法,本文首先提出适用于MSCNN网络结构的样本提取流程,然后利用MSCNN对样本进行训练和学习,该模型可以最大限度利用肽在MS1和MS2中的特征,最后通过观察模型在测试集中的结果来验证模型的效果。结果和传统算法相比,在保证真峰处理效果大致相同的情况下,MSCNN模型过滤噪声峰的数量提高了约11.2%。结论本文提出的MSCNN模型可以更有效地去除DIA数据中的噪声峰。     

Image de-noising by integer wavelet transforms and generalized cross validation

De-noising algorithms based on wavelet thresholding replace small wavelet coefficients by zero and keep or shrink the coefficients with absolute value above the threshold. The optimal threshold minimizes the error of the result as compared to the unknown, exact data. To estimate this optimal threshold, we use Generalized Cross Validation. This procedure has linear complexity and is fully automatic, i.e., it does not require an estimate for the noise energy. This paper uses the method for wavelet transforms that map integer gray-scale pixel values to integer wavelet coefficients. An image with artificial noise is used to illustrate the optimality properties of the estimator. Not all theoretical requirements for a successful application of the method are strictly fulfilled in the integer transform case. However, this has little influence on practical results.     

基于空间频率与时间序列信息的多类运动想象脑电分类

结合共同空间模式（CSP）、离散小波变换（DWT）和长短期记忆网络（LSTM）方法,提出一种基于空间频率与时间序列信息的多类运动想象脑电特征提取方法。首先利用滑动矩形窗获得时间序列脑电信号,并采用DWT从每一段脑电信号提取运动想象脑电相关的子带小波系数,其次将小波系数通过一对多CSP进一步特征提取,得到的特征作为LSTM的输入,然后对LSTM的时间序列输出在时间步上进行平均,最后使用Softmax分类器进行分类。实验结果显示,新算法取得92.23%的准确率,相比CSP特征以及结合频率或时间序列信息的CSP特征有较大提升,表明空间、频率、时间序列信息的互补性和有效性。     

一种基于小波变换的医学图像量化编码算法的研究

医学图像压缩是远程医疗和PACS系统中的重要研究课题，研究了小波子带图像系数的统计分布，发现小波子带图像系数分布和拉普拉斯分布非常相似，继而提出了一种基于其统计特征的图像量化编码算法，该算法以小波子带图像样本标准差为选择量化编码阈值的重要依据。实验表明，该算法具有计算简单，不同阈值范围待编码系数可预测以及易于获得较高压缩效率的优点，在远程医疗和PACS系统等领域的医学图像压缩中有重要的潜在应用价值。     

结合小波分解和径向基神经网络进行事件相关电位的单次提取

从单次实验记录中提取事件相关电位，无论在临床诊断上还是在大脑高级功能的研究中都起着重要的作用。介绍了一种将小波多分辨率分解和重建与径向基神经网络结合起来进行事件相关电位单次提取的方法。它基于事件相关电位主要是低频信号的事实，发挥径向基神经网络对连续函数的逼近能力，从信号的小波分解系数中提取出与低频响应相关的成分，构造了一种新的时频域滤波的方法，实验表明本方法较好地从单次记录中提取出了事件相关电位。     

Phase Spectral Analysis of EEG Signals

A new method of phase spectral analysis of EEG is proposed for the comparative analysis of phase spectra between normal EEG and epileptic EEG signals based on the wavelet decomposition technique. By using multiscale wavelet decomposition, the original EEGs are mapped to an orthogonal wavelet space, such that the variations of phase can be observed at multiscale. It is found that the phase (and phase difference) spectra of normal EEGs are distinct from that of epileptic EEGs. That is the variations of phase (and phase difference) of normal EEGs have a distinct periodic pattern with the electrical activity proceeds in the brain, but do not the epileptic EEGs. For epileptic EEGs, only at those transient points, the phase variations are obvious. In order to verify these results with the observational data, the phase variations of EEGs in principal component space are observed and found that, the features of phase spectra is in correspondence with that the wavelet space. These results make it possible to view the behavior of EEG rhythms as a dynamic spectrum.     

Novel approaches to visualization and data mining reveals diagnostic information in the low amplitude region of serum mass spectra from ovarian cancer patients

The ability to identify patterns of diagnostic signatures in proteomic data generated by high throughput mass spectrometry (MS) based serum analysis has recently generated much excitement and interest from the scientific community. These data sets can be very large, with high-resolution MS instrumentation producing 1-2 million data points per sample. Approaches to analyze mass spectral data using unsupervised and supervised data mining operations would greatly benefit from tools that effectively allow for data reduction without losing important diagnostic information. In the past, investigators have proposed approaches where data reduction is performed by a priori "peak picking" and alignment/warping/smoothing components using rule-based signal-to-noise measurements. Unfortunately, while this type of system has been employed for gene microarray analysis, it is unclear whether it will be effective in the analysis of mass spectral data, which unlike microarray data, is comprised of continuous measurement operations. Moreover, it is unclear where true signal begins and noise ends. Therefore, we have developed an approach to MS data analysis using new types of data visualization and mining operations in which data reduction is accomplished by culling via the intensity of the peaks themselves instead of by location. Applying this new analysis method on a large study set of high resolution mass spectra from healthy and ovarian cancer patients, shows that all of the diagnostic information is contained within the very lowest amplitude regions of the mass spectra. This region can then be selected and studied to identify the exact location and amplitude of the diagnostic biomarkers.     

Analysis and localization of epileptic events using wavelet packets.

This article compares results obtained in previous studies using time-frequency representations (Wigner-Ville, Choi-Williams and Parametric) and the wavelet transform with those obtained with wavelet packet functions to show new findings about their quality in the analysis of ECoG recordings in human intractable epilepsy: data from 21 patients have been analyzed and processed with four types of wavelet functions, including Orthogonal, Biorthogonal and Non-Orthogonal basis. These functions were compared in order to test their quality to represent spikes in the ECoG. The energy based on the wavelet coefficients to different scales was also calculated. The best results were found with the biorthogonal-6.8 wavelet on 5-7 scales, which gave 0.92 sensitivity, but with a high percentage of false positives; this representation was highly correlated with spike events on time and duration. To improve these results we have studied the wavelet packet coefficients energy. We found that reconstruction wavelet packet coefficients at 4 and 9 nodes contain significant information to characterize the spike event. These nodes' reconstruction coefficients were multiplied and this product was highly correlated with spikes events on time and duration. With this procedure we improved the sensitivity up to 0.96 with the same biorthogonal-6.8 wavelet at four levels. With this technique we do not sacrifice computation time: 896 samples are processed at only 0.16 s, so that it is possible to show the spike scattering path on line, because 896 samples (7 s)/16 channels are processed at 3.13 s.     

A wavelet-based data pre-processing analysis approach in mass spectrometry

Recently, mass spectrometry analysis has a become an effective and rapid approach in detecting early-stage cancer. To identify proteomic patterns in serum to discriminate cancer patients from normal individuals, machine-learning methods, such as feature selection and classification, have already been involved in the analysis of mass spectrometry (MS) data with some success. However, the performance of existing machine learning methods for MS data analysis still needs improving. The study in this paper proposes a wavelet-based pre-processing approach to MS data analysis. The approach applies wavelet-based transforms to MS data with the aim of de-noising the data that are potentially contaminated in acquisition. The effects of the selection of wavelet function and decomposition level on the de-noising performance have also been investigated in this study. Our comparative experimental results demonstrate that the proposed de-noising pre-processing approach has potentials to remove possible noise embedded in MS data, which can lead to improved performance for existing machine learning methods in cancer detection.     

An automated GCxGC‐TOF‐MS protocol for batch‐wise extraction and alignment of mass isotopomer matrixes from differential 13C‐labelling experiments: a case study for photoautotrophic‐mixotrophic grown Chlamydomonas reinhardtii cells

Two dimensional gas chromatography coupled to time‐of‐flight mass spectrometry (GCxGC‐TOF‐MS) is a promising technique to overcome limits of complex metabolome analysis using one dimensional GC‐TOF‐MS. Especially at the stage of data export and data mining, however, convenient procedures to cope with the complexity of GCxGC‐TOF‐MS data are still in development. Here, we present a high sample throughput protocol exploiting first and second retention index for spectral library search and subsequent construction of a high dimensional data matrix useful for statistical analysis. The method was applied to the analysis of ¹³C‐labelling experiments in the unicellular green alga Chlamydomonas reinhardtii. We developed a rapid sampling and extraction procedure for Chlamydomonas reinhardtii laboratory strain (CC503), a cell wall deficient mutant. By testing all published quenching protocols we observed dramatic metabolite leakage rates for certain metabolites. To circumvent metabolite leakage, samples were directly quenched and analyzed without separation of the medium. The growth medium was adapted to this rapid sampling protocol to avoid interference with GCxGC‐TOF‐MS analysis. To analyse batches of samples a new software tool, MetMax, was implemented which extracts the isotopomer matrix from stable isotope labelling experiments together with the first and second retention index (RI1 and RI2). To exploit RI1 and RI2 for metabolite identification we used the Golm metabolome database (GMD [1] with RI1/RI2‐reference spectra and new search algorithms. Using those techniques we analysed the dynamics of ¹³CO₂ and ¹³C‐acetate uptake in Chlamydomonas reinhardtii cells in two different steady states namely photoautotroph and mixotroph growth conditions. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

小波变换在人体血流灌注信号分析中的应用

目的：激光多普勒血流仪测得的皮肤平均血流灌注量和血流速度等这些传统的评估微循环的参数指标在电磁场对人体微循环影响的研究中并没有得到跟其在动物实验中相似的结果。因而本研究欲利用时频分析技术寻求新的评估人体微循环的参数指标．给人体激光多普勒血流灌注信号的分析和处理提供新的思路和方法。为后续电磁场对人体微循环影响的研究奠定基础。方法：运用在低频段具有较高频率分辨率的连续小波变换将二维激光多普勒血流灌注信号转换为包含时间和频率信息的三维信号，由此可以清楚地同时观察小波变换后的小波系数在不同频段随着时间的变化情况。结果：小波变换后的小波系数在0．005Hz～2Hz频率范围内存在6个可能与微循环控制机理有关的特征峰值．峰值的幅度随着时间有所变化。结论：小波变换可作为分析人体激光多普勒血流灌注信号的一种有效工具，为后续电磁场对人体微循环影响的研究奠定基础。并且其对微弱、背景噪声强的医学信号的分析和处理提供了新的思路和方法。