Dataset Information

A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images.

ABSTRACT:

Motivation

Mass Spectrometry Imaging (MSI) analyzes complex biological samples such as tissues. It simultaneously characterizes the ions present in the tissue in the form of mass spectra, and the spatial distribution of the ions across the tissue in the form of ion images. Unsupervised clustering of ion images facilitates the interpretation in the spectral domain, by identifying groups of ions with similar spatial distributions. Unfortunately, many current methods for clustering ion images ignore the spatial features of the images, and are therefore unable to learn these features for clustering purposes. Alternative methods extract spatial features using deep neural networks pre-trained on natural image tasks; however, this is often inadequate since ion images are substantially noisier than natural images.

Results

We contribute a deep clustering approach for ion images that accounts for both spatial contextual features and noise. In evaluations on a simulated dataset and on four experimental datasets of different tissue types, the proposed method grouped ions from the same source into a same cluster more frequently than existing methods. We further demonstrated that using ion image clustering as a pre-processing step facilitated the interpretation of a subsequent spatial segmentation as compared to using either all the ions or one ion at a time. As a result, the proposed approach facilitated the interpretability of MSI data in both the spectral domain and the spatial domain.

Availabilityand implementation

The data and code are available at https://github.com/DanGuo1223/mzClustering.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Guo D

PROVIDER: S-EPMC9942547 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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Publications

A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images.

Guo Dan D Föll Melanie Christine MC Bemis Kylie Ariel KA Vitek Olga O

Bioinformatics (Oxford, England) 20230201 2

<h4>Motivation</h4>Mass Spectrometry Imaging (MSI) analyzes complex biological samples such as tissues. It simultaneously characterizes the ions present in the tissue in the form of mass spectra, and the spatial distribution of the ions across the tissue in the form of ion images. Unsupervised clustering of ion images facilitates the interpretation in the spectral domain, by identifying groups of ions with similar spatial distributions. Unfortunately, many current methods for clustering ion imag ...[more]

PMID: 36744928

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Project description:BackgroundA change in the output of deep neural networks (DNNs) via the perturbation of a few pixels of an image is referred to as an adversarial attack, and these perturbed images are known as adversarial samples. This study examined strategies for compromising the integrity of DNNs under stringent conditions, specifically by inducing the misclassification of medical images of disease with minimal pixel modifications.MethodsThis study used the following three publicly available datasets: the chest radiograph of emphysema (cxr) dataset, the melanocytic lesion (derm) dataset, and the Kaggle diabetic retinopathy (dr) dataset. To attack the medical images, we proposed a method termed decrease group differential evolution (DGDE) for generating adversarial images. Under this method, a noise matrix of the same size as the input image is first used to attack the image sample several times until the initial adversarial perturbation s0 is obtained. Next, a subset s1 is randomly picked from the initial adversarial perturbation s0 that is still able to cause the samples to be misclassified by the classifier. A new subset s2 is subsequently randomly selected from the adversarial perturbation subset s1, which can still cause the adversarial samples to be misclassified by the classifier. Finally, the adversarial perturbation subset sn with the minimum number of elements is obtained by continuous reduction of the number of perturbed pixels.ResultsIn this study, the DGDE method was used to attack the images of the cxr dataset, the derm dataset, and the dr dataset; and the minimum number of pixels required to be considered a successful attack was 11, 7, and 7, respectively, while the maximum number of pixel changes was 55, 35, and 21, respectively. The average number of pixel changes was 30, 18, and 11, respectively, in the cxr dataset, the derm dataset, and the dr dataset, respectively, while the percentages of the average number of pixel changes among the total number of pixels of the image were 0.0598%, 0.0359%, and 0.0219, respectively.ConclusionsUnlike the traditional differential evolution (DE) method, the proposed DGDE method modifies fewer pixels to generate adversarial samples by introducing a variable population number and a novel crossover and selection strategy. However, the success rate of the initial attack on different image datasets varied greatly. In future studies, we intend to identify the reasons for this phenomenon and improve the success rate of the initial attack.

Dataset Information

A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images.

Motivation

Results

Availabilityand implementation

Supplementary information

Publications

A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images.

Similar Datasets

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