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In our recently developed denoising method, a linear combination of five features is used to adjust the peak intensities in tandem mass spectra. Although the method shows a promise, the coefficients (weights) of the linear combination were fixed and determined empirically. In this paper, we propose an adaptive approach for estimating these weights. The proposed approach: (1) calculates the score for...
This paper proposes a dynamic-model-based method for selecting significantly expressed (SE) genes from their time-course expression profiles. A gene is considered to be SE if its time-course expression profile is more likely time-dependent than random. The proposed method describes a time-dependent gene expression profile by a nonzero-order autoregressive (AR) model, and a time-independent gene expression...
Machine learning algorithms are widely used for quality assessment of tandem mass spectra based on a number of features. However, it is still unclear which features are most relevant to the quality of tandem mass spectra. In this paper, a sparse logistical regression method is proposed for selecting the most relevant features from those features found in the literature. To investigate the performance...
In the literature, hundreds of features have been proposed to assess the quality of tandem mass spectra. However, some features may be nearly irrelevant, and thus the inclusion of these nearly irrelevant features may degenerate the performance of quality assessment. This paper introduces a two-stage support vector machine recursive feature elimination (SVM-RFE) method to select the most relevant features...
It is well known that a majority of experimental spectra are of too poor quality to be interpreted by any automatic method. It wastes time to interpret these "un-interpretable" spectra. On the other hand, some spectra with high quality also cannot be interpreted by any automatic method, but maybe by manual checking. Therefore, it is worthwhile to develop a powerful filter that could eliminate...
Tandem mass spectrometry has emerged as a cornerstone of high throughput proteomic studies owing in part to various high throughput search engines which are used to interpret these tandem mass spectra. However, majority of experimental tandem mass spectra cannot be interpreted by any existing search engines or other methods. There are many reasons why this happens. However, one of the most important...
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