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Cited by 12Spectroscopy and Chemometric AnalysesSpectroscopy Techniques in Biomedical and Chemical ResearchMachine Learning in Materials Science

The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.

Infrared spectrum analysis of organic molecules with neural networks using standard reference data sets in combination with real-world data

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Published version of a preprint

Abstract

In this study, we propose a neural network- based approach to analyze IR spectra and detect the presence of functional groups. Our neural network architecture is based on the concept of learning split representations. We demonstrate that our method achieves favorable validation performance using the NIST dataset. Furthermore, by incorporating additional data from the open-access research data repository Chemotion, we show that our model improves the classification performance for nitriles and amides. Scientific contribution : Our method exclusively uses IR data as input for a neural network, making its performance, unlike other well-performing models, independent of additional data types obtained from analytical measurements. Furthermore, our proposed method leverages a deep learning model that outperforms previous approaches, achieving F1 scores above 0.7 to identify 17 functional groups. By incorporating real-world data from various laboratories, we demonstrate how open-access, specialized research data repositories can serve as yet unexplored, valuable benchmark datasets for future machine learning research.

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Registry

Crossref · 10.1186/s13321-025-00960-2

Cites

25 of 25 references verified0 citation errors · 0 not checkable

Statistics

Figures

Fig. 1 Functional group distribution in the NIST dataset. The figure shows the percentages of functional groups present in the NIST and Chemotion dataset. As there are multiple functional groups per molecule, the cumulative percentage is not 100
Fig. 1 Functional group distribution in the NIST dataset. The figure shows the percentages of functional groups present in the NIST and Chemotion dataset. As there are multiple functional groups per molecule, the cumulative percentage is not 100CC BY · PubMed Central
Fig. 2 Functional groups present per sample on an average in a NIST, b Chemotion, and c NIST + Chemotion subset
Fig. 2 Functional groups present per sample on an average in a NIST, b Chemotion, and c NIST + Chemotion subsetCC BY · PubMed Central
Fig. 3 The figure presents a scatter plot depicting the projection of datasets onto the principal components derived from the NIST dataset. Both the Chemotion and Chemotion subset datasets are included in this analysis, allowing for an examination of similarities or differences between Chemotion datasets and the NIST dataset
Fig. 3 The figure presents a scatter plot depicting the projection of datasets onto the principal components derived from the NIST dataset. Both the Chemotion and Chemotion subset datasets are included in this analysis, allowing for an examination of similarities or differences between Chemotion datasets and the NIST datasetCC BY · PubMed Central
Fig. 4 Data preprocessing pipeline
Fig. 4 Data preprocessing pipelineCC BY · PubMed Central
Fig. 5 Our network architecture consists of two input heads. Each input head consists of one input layer and one hidden layer. The learned feature vectors are concatenated and passed to another fully connected layer. The output of the last layer is a multilabel prediction, 1 if the respective functional group is present and 0 if the functional group is not present
Fig. 5 Our network architecture consists of two input heads. Each input head consists of one input layer and one hidden layer. The learned feature vectors are concatenated and passed to another fully connected layer. The output of the last layer is a multilabel prediction, 1 if the respective functional group is present and 0 if the functional group is not presentCC BY · PubMed Central
Fig. 6 Figure shows the mean F1 scores of the validation set for each functional group. The bars are grouped by different datasets and models
Fig. 6 Figure shows the mean F1 scores of the validation set for each functional group. The bars are grouped by different datasets and modelsCC BY · PubMed Central
Fig. 7 Figure shows the mean F1 scores of the validation set for each functional group. The methods compared in this plot are our model ’Own NIST + Chemotion’ and the retraining of Fine et al.’s “IR spectra only” model with our NIST + Chemotion dataset
Fig. 7 Figure shows the mean F1 scores of the validation set for each functional group. The methods compared in this plot are our model ’Own NIST + Chemotion’ and the retraining of Fine et al.’s “IR spectra only” model with our NIST + Chemotion datasetCC BY · PubMed Central
Fig. 8 Illustration of the perfect match results for the validation sets across five iterations of a five-fold cross-validation for our ’Own NIST’ model. a Count of molecules grouped by the number of functional groups present in them; b Mean perfect match ratio of a number of perfect match molecules to the number of total molecules grouped by the number of functional groups present
Fig. 8 Illustration of the perfect match results for the validation sets across five iterations of a five-fold cross-validation for our ’Own NIST’ model. a Count of molecules grouped by the number of functional groups present in them; b Mean perfect match ratio of a number of perfect match molecules to the number of total molecules grouped by the number of functional groups presentCC BY · PubMed Central
Fig. 9 The figure shows the false positive rate and the false negative rate for validation sets of a 5-fold cross-validation of the ’Own NIST’ model. The plot is grouped by the number of functional groups present in molecules depicted by x-axis and the mean false positive and false negative rate depicted by y-axis
Fig. 9 The figure shows the false positive rate and the false negative rate for validation sets of a 5-fold cross-validation of the ’Own NIST’ model. The plot is grouped by the number of functional groups present in molecules depicted by x-axis and the mean false positive and false negative rate depicted by y-axisCC BY · PubMed Central
Fig. 10 Figure shows SHAP analysis plots for predictions for the input spectrum of the molecule 4-Fluoroanisole COc1ccc(F)cc1 for ’Own NIST’ model. Each plot provides SHAP values for every individual class. Blue regions of the spectrum are influencing the prediction of the model toward predicting the absence of a functional group, while red regions indicates the presence of a given functional group
Fig. 10 Figure shows SHAP analysis plots for predictions for the input spectrum of the molecule 4-Fluoroanisole COc1ccc(F)cc1 for ’Own NIST’ model. Each plot provides SHAP values for every individual class. Blue regions of the spectrum are influencing the prediction of the model toward predicting the absence of a functional group, while red regions indicates the presence of a given functional groupCC BY · PubMed Central
Fig. 11 The figure displays the mean F1 scores of our split model across five models from a 5-fold cross-validation, evaluated for each functional group. These scores were calculated using a holdout test set
Fig. 11 The figure displays the mean F1 scores of our split model across five models from a 5-fold cross-validation, evaluated for each functional group. These scores were calculated using a holdout test setCC BY · PubMed Central

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Citations

Cites

Show all 25 references

Research works printed but not linked: 4

  1. Jung N, Tremouilhac P, Punjabi D et. al. (2024) Chemotion repository - data collection: FT-IR spectroscopy data. Karlsruhe Institute of Technology, Karlsruhe
  2. Lundberg SM, Lee SI (2017) A unified approach to interpreting model predictions. In: NIPS'17: Proceedings of the 31st international conference on neural information processing systems, pp 4768–4777
  3. Sigma-Aldrich Library (2024) Sigma-aldrich library of FT-IR spectra. https://sciencesolutions.wiley.com/solutions/technique/ir/sigma-aldrich-library-of-ft-ir-spectra/. Accessed 5 Feb 2025
  4. Szymanski HA, Erickson RE (1970) Infrared, vol 2. Plenum Press, New York

Metadata

Authors
Punjabi, D., Huang, Y.-C., Holzhauer, L., Tremouilhac, P., Friederich, P., Jung, N., & Bräse, S.
Affiliations
Karlsruhe Institute of Technology (DE)
Corresponding author
  • Friederich, Pascal
  • Jung, Nicole
  • Bräse, Stefan
Venue
Journal of Cheminformatics
Published
2025-02-26
Volume
17
Issue
1
Pages
24-24
ISSN
1758-2946 (ISSN-L)
OpenAlex
W4407977858
Cited by
12
References
25
Citations by year
2026: 7 · 2025: 5
FWCI
4.50
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Cheminformatics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Helmholtz - Research Field Information (VirtMat)
  • Karlsruher Institut für Technologie (KIT)
Topics
  • Physical Sciences › Chemistry › Analytical Chemistry › Spectroscopy and Chemometric Analyses
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Spectroscopy Techniques in Biomedical and Chemical Research
  • Physical Sciences › Materials Science › Materials Chemistry › Machine Learning in Materials Science
Keywords
infrared spectroscopy, functional group identification, artificial neural networks, nitriles, amides, benchmark dataset, organic compounds, spectral classification

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CoChat. (2026). Citation check: Infrared spectrum analysis of organic molecules with neural networks using standard reference data sets in combination with real-world data. https://app.cochat.ai/papers/10.1186/s13321-025-00960-2
The paper
Punjabi, D., Huang, Y.-C., Holzhauer, L., Tremouilhac, P., Friederich, P., Jung, N., & Bräse, S. (2025). Infrared spectrum analysis of organic molecules with neural networks using standard reference data sets in combination with real-world data. Journal of Cheminformatics. https://doi.org/10.1186/s13321-025-00960-2

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