Circular Dichroism Spectral Similarity Plots to Extend Validation and Correction to All Measured Wavelengths

Interlaboratory comparisons of circular dichroism (CD) spectra are useful for developing confidence in the measurements associated with optically active molecules. These measurements also help define the higher-order (secondary and tertiary) structure of biopolymers. Unfortunately, the extent of the validity of these measurements has been unclear. In this work, a method is described to extend CD validation over the entire observed wavelength range using what will be called spectral similarity plots. The method involves plotting, wavelength by wavelength, all measured spectral intensities of a sample at one concentration against the intensity values of the same material at a different concentration or pathlength. These spectral similarity plots validate the instrument in terms of spectral shape and whether the shape is shifted in intensity and/or in wavelength. This comparison tests the linearity of instrument’s signal, the balance of its left and right polarizations, its wavelengths, and its spectral intensity scales. When the process is applied to materials with accepted and archived intensity values, the method can be linked to older single-wavelength and double-wavelength calibration techniques. Further, spectral similarity testing of CD spectra from samples with different concentrations run in different labs suggests that improved interlaboratory validation of CD data is possible. Since a database of archival CD measurements is available online, spectral similarity comparisons could possibly provide the ability to compare linearity, polarization balance, wavelength, and spectral intensity between all current CD instruments. If the preliminary results published here prove robust and transferable, then comparisons of full-wavelength range spectra to archived data using spectral similarity plots should become part of the standard process to validate and calibrate the performance of CD instruments.

Matlab Software for Supervised Habitat Mapping of Freshwater Systems Using Image Processing

We present a software package for the supervised classification of images useful for cover-type mapping of freshwater habitat (e.g., water surface, gravel bars, vegetation). The software allows the user to select a representative subset of pixels within a specific area of interest in the image that the user has identified as a cover-type habitat of interest. We developed a graphical user interface (GUI) that allows the user to select single pixels using a dot, line, or group of pixels within a defined polygon that appears to the user to have a spectral similarity. Histogram plots for each band of the selected ground-truth subset aid the user in determining whether to accept or reject it as input data for the classification processes. A statistical model, or classifier, is then built using this pixel subset to assign every pixel in the image to a best-fit group based on reflectance or spectral similarity. Ideally, a classifier incorporates both spectral and spatial information. In our software, we implement quadratic discriminant analysis (QDA) for spectral classification and choose three spatial methods—mode filtering, probability label relaxation, and Markov random fields—to incorporate spatial context after computation of the spectral type. This multi-step interactive process makes the software quantitatively robust, broadly applicable, and easily usable for cover-type mapping of rivers, their floodplains, wetlands often components of these functionally linked freshwater systems. Indeed, this supervised classification approach is helpful for a wide range of cover-type mapping applications in freshwater systems but also estuarine and coastal systems as well. However, it can also aid many other applications, specifically for automatic and quantitative extraction of pixels that represent the water surface area of rivers and floodplains.

An analysis of spectral similarity measures

In this paper we analyze the most used measures for the assessment of spectral similarity of reflectance and radiance signals. First of all we divide them in five groups on the basis of the type of errors they measure. We proceed analyzing their mathematical definition to identify unintended behaviors and types of errors they are blind to. Then exploiting the Munsell atlas we analyze the correlation between metrics in terms of both Pearson's Linear Correlation Coefficient (PLCC) and Spearman's Rank Order Correlation Coefficient (SROCC). Finally we analyze the behaviour of the selected metrics with respect to two different color properties: the Chroma and the Lightness computed in the CIE L* a* b* color space. The source code of the spectral measures considered is available at the following link: <ext-link ext-link-type="url" xlink:href="https://celuigi.github.io/spectral-similarity-metrics-comparison/">https://celuigi.github.io/spectral-similarity-metrics-comparison/</ext-link>.

MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra

Mass spectrometry data is one of the key sources of information in many workflows in medicine and across the life sciences. Mass fragmentation spectra are generally considered to be characteristic signatures of the chemical compound they originate from, yet the chemical structure itself usually cannot be easily deduced from the spectrum. Often, spectral similarity measures are used as a proxy for structural similarity but this approach is strongly limited by a generally poor correlation between both metrics. Here, we propose MS2DeepScore: a novel Siamese neural network to predict the structural similarity between two chemical structures solely based on their MS/MS fragmentation spectra. Using a cleaned dataset of > 100,000 mass spectra of about 15,000 unique known compounds, we trained MS2DeepScore to predict structural similarity scores for spectrum pairs with high accuracy. In addition, sampling different model varieties through Monte-Carlo Dropout is used to further improve the predictions and assess the model’s prediction uncertainty. On 3600 spectra of 500 unseen compounds, MS2DeepScore is able to identify highly-reliable structural matches and to predict Tanimoto scores for pairs of molecules based on their fragment spectra with a root mean squared error of about 0.15. Furthermore, the prediction uncertainty estimate can be used to select a subset of predictions with a root mean squared error of about 0.1. Furthermore, we demonstrate that MS2DeepScore outperforms classical spectral similarity measures in retrieving chemically related compound pairs from large mass spectral datasets, thereby illustrating its potential for spectral library matching. Finally, MS2DeepScore can also be used to create chemically meaningful mass spectral embeddings that could be used to cluster large numbers of spectra. Added to the recently introduced unsupervised Spec2Vec metric, we believe that machine learning-supported mass spectral similarity measures have great potential for a range of metabolomics data processing pipelines.

Filter feature selection for unsupervised clustering of designer drugs using DFT simulated IR spectra data

The rapid emergence of novel psychoactive substances (NPS) poses new challenges and requirements for forensic testing/analysis techniques. This paper aims to explore the application of unsupervised clustering of NPS compounds' infrared spectra. Two statistical measures, Pearson and Spearman, were used to quantify the spectral similarity and to generate the affinity matrices for hierarchical clustering. The correspondence of spectral similarity clustering trees to the commonly used structural/pharmacological categorization was evaluated and compared to the clustering generated using 2D/3D molecular fingerprints. Hybrid model feature selections were applied using different filter-based feature ranking algorithms developed for unsupervised clustering tasks. Since Spearman tends to overestimate the spectral similarity based on the overall pattern of the full spectrum, the clustering result shows the highest degree of improvement from having the non-discriminative features removed. The loading plots of the first two principal components (PCs) of the optimal feature subsets confirmed that the most important vibrational bands contributing to the clustering of NPS compounds were selected using NDFS feature selection algorithms.