BEADS jointly addresses the problem of simultaneous baseline/trend/drift correction and (Gaussian, Poisson) noise reduction for 1D signals. It was designed for positive and sparse signals arising in analytical chemistry: chromatography, Raman spectroscopy, infrared, XRD, mass spectrometry, etc.). The baseline corresponds to slow-varying trends, instrumental drifts or background offset. The proposed BEADS baseline filtering algorithm is based on modeling of a series of (chromatogram) peaks as mostly positive, sparse with sparse derivatives, and on modeling the baseline as a low-pass signal. A convex optimization problems formulated so as to encapsulate these non-parametric models. To account for the positivity of chromatogram peaks, an asymmetric penalty function, similar to a regularized l1 norm is utilized. A robust, computationally efficient, iterative algorithm is developed that is guaranteed to converge to the unique optimal solution. It implements the method published in the paper "Chromatogram baseline estimation and denoising using sparsity (BEADS)", by Xiaoran Ning, Ivan W. Selesnick, Laurent Duval, in Chemometrics and Intelligent Laboratory Systems, December 2014, http://dx.doi.org/10.1016/j.chemolab.2014.09.014
The ZIP file contains two Matlab functions:
* a demonstration script (example.m);
* the main function (beads.m),
and an html readme help.
BEADS has since been used in 1D and 2D (GCxGC) chromatography, Raman spectroscopy, high-resolution mass spectrometry for astronomical hyperspectral data, electroencephalogram (EEG), electrocardiogram (ECG), arabic script analysis, power signal detrending for monitoring. Other uses, implementations in Python, R and C++ are provided at the BEADS page:
Laurent Duval (2021). BEADS Baseline Estimation And Denoising with Sparsity (https://www.mathworks.com/matlabcentral/fileexchange/49974-beads-baseline-estimation-and-denoising-with-sparsity), MATLAB Central File Exchange. Retrieved .
@Junelle Rey. Thank you for the kind interaction. I cannot be sure without looking at signals. If you can share them, that could be great. However, I suspect a side effect of the filtering. I have been thinking about a totally generic workaround for a while. I only got partial solutions so far, don't hesitate to contribute why your examples
Great work! I just noticed that the solution to f begins to approach to zero at the latter portion of the signal y. As as result, there seems to be an extraneous or artificial peak at the end of the corrected signal x (x = y - f). What could be the explanation and a possible solution for this? Is this a limitation to the optimization of the cost function at the boundaries of the signal?
To recent contributions (eg Jane Yi, MR Yang, Yi Liu) : thank you for your feedback. I shall say that I do not know of magic parameters. Regarding not zero ends, removing the line between the start and end points can be a useful preprocessing. To Yi Liu : I am happy of this use away from the origjnal application. Don't hesitate to share more details
This is perfect, but the algorithm seems to think my baseline at the start and end of my vector are at 0. How do I correct this? This creates an exaggerated "U" shape for my baseline.
It's a great deal tool.I want to denoise the fault machines components by this tool.However, the parameters fc, d and r, lam0, lam1, lam2 cannot input right. If you have a principle to sure these parameters, please email this address:email@example.com.
Thanks a lot
@DavidŠkandera I deeply appreciate your feedback, and especially glad it works on background-baseline-trend removal for biomedical ECG or EEG data. We have been working on parameter heuristics for a while, with first details in Section 5 of the paper. A good starting point is a lambda inversely proportional to the l_1 norm of each derivative, and a global scale factor proportional to the noise energy. I am working on an ancillary program to provide those estimate.However, we lack feedback on 1) how sparse signals are 2) how stationary noise is 3) how one estimates the baseline is well-extracted (often, visually). So, any contribution is welcome on such matters
Hi, first very thanks for this tool, it works very good. I have the same question as the users below. Can you tell me pls, how can I correct settings for fECG signals? Mainly parameters r and lam0-2?
@LazarosMichailidis https://fr.mathworks.com/matlabcentral/profile/authors/13406043-lazaros-michailidis We appreciate your contribution. This question is quick, the answer by be longer: what kind of peak width distorsion did you experience? That might really depend on signal morphology.
Very nice tool, thank you very much. A quick question, how to prevent the distortion of the peaks' width, please? Thank you in advance.
Dear Junpeng Yang https://www.mathworks.com/matlabcentral/profile/authors/14576206-junpeng-yang We truly appreciate your comment. As we are working on updates, do not hesitate to provide us with hints of your use, your data, for further improvements. Best
It is an excellent tool - works very well ones you figure out parameters. Would be much better with more extensive documentation.
how can I choose fc,d,r,amp,lam0,lam1.lam2 values for NIRS data in BEADS TOOLBOX?can u upload a video about BEADS TOOLBOX?
@Yigal Barkan thank you very much for sharing the data and the parameters, it will help me provide more hints
@Mariam Alharthi I do appreciate our exchange and the nice and original use of BEADS
Regarding my X-ray diffraction pattern back removal, I thought I'd share the parameters I used:
beads_parm.fc = 0.01;
beads_parm.d = 1;
beads_parm.r = 6;
beads_parm.amp = 0.5;
beads_parm.lam0 = 0.5* beads_parm.amp;
beads_parm.lam1 = 5* beads_parm.amp;
beads_parm.lam2 = 4* beads_parm.amp;
Here are links to two diffractograms I used this parameterization for:
Thanks a lot for this code! Let me know when you write the documentation.
amazing code, it helps me lots.
thank you so much.
@Yigal Barkan Thanks for the questions. They provide me with directions for parameter choice prediction
I agree with Ole, I just looked at the documentation and came here for answers.
here are my initial Qs:
d: How do I choose d? is 1 or 2 the polynomial order? please give examples when to use what.
fc: what do you mean by cycles/sample? how should I choose it?
r,lam0, lam1, lam2: don't know where to start with these.
I am about to use the toolbox for background removal of X-ray diffraction patterns. Then do a peak based quantitative analysis of a mixture.
Thanks for the toolbox, I Bet you'll get the documentation ready in no time.
@Ole Kjos This is an issue I would like to improve on in the coming weeks, with a few rules of thumb. Could you share the type of signals you are dealing with?
Great tool, but a bit under documented for regular use. I really struggle to adjust parameters and tune the toolbox to optimal performance on my data. The published paper is to advanced for me to understand and relate to the actual toolbox parameters, and in the example the user input parameters (lam0,lam1,lam2, rc, r and d) is poorly explained.
Google have given me some vague idea, but I would have preferred that the authors wrote 2-3 lines for each parameter giving me some indication on which effect the parameters will have (filtering high frequency noise, adjusting baseline shape, effecting peak identification etc.) as that would make it easier to use the toolbox without understanding every detail about the mathematics behind it.
Thank you a lot for your nice feedback. I am very glad it is helpful for your research. The frequency is typically easy to fix in my application. How do your signals look like?
Thank you for sharing. I am very glad to obtian this toolbox. It's very helpful to my current research. But I have a problem with this script that I have no idea how to set value for fc. Could you please tell me in detail. I will very appreciate if you send email to my Email address: firstname.lastname@example.org
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