CuXASNet: Rapid and Accurate Prediction of Copper L-edge X-Ray Absorption Spectra Using Machine Learning

Deyu Lu; Jim Ciston; Matthew R. Carbone; Samuel P. Gleason

REVIEW 3 major objections 4 minor 1 cited by

CuXASNet: Rapid and Accurate Prediction of Copper L-edge X-Ray Absorption Spectra Using Machine Learning

T0 review · 3 major / 4 minor · reviewed 2026-08-11 · deepseek-v4-flash

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Pith's one-line read A neural network predicts Cu L-edge X-ray absorption spectra from atomic structure at FEFF9 accuracy.

desk verdict Useful FEFF9 surrogate for Cu L-edge XAS with solid internal validation, but the 14-spectrum experimental equivalence claim is undercut by an unstated energy-alignment protocol. read the letter →

arxiv 2412.02916 v1 pith:DUZAUV7K submitted 2024-12-03 cond-mat.mtrl-sci

Samuel P. Gleason , Matthew R. Carbone , Deyu Lu , Jim Ciston This is my paper · ORCID

classification cond-mat.mtrl-sci

keywords CuL-edgeX-rayabsorptionspectroscopymachinelearningspectralpredictionM3GNetfeaturizationFEFF9multiple-scatteringsimulationdenseneuralnetworkstructure-spectrumrelationshipXANEStransitionmetal

verification ladder T0 review T1 audit T2 compute T3 formal

The pith

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The reading

CuXASNet is a machine-learning model that claims to predict the Cu L3 and L2 X-ray absorption near-edge spectra of a material directly from its atomic structure, replacing the computationally expensive multiple-scattering simulations of FEFF9. The paper argues that a 64-dimensional site embedding from M3GNet, fed through a small dense neural network, captures the local Cu environment well enough to reproduce FEFF9 spectra with a median test-set MAE of 0.0391. The decisive evidence is transfer to experiment: on fourteen spectra extracted from the literature, CuXASNet achieves an average MAE of 0.125 and Spearman correlation 0.891, essentially matching FEFF9's own averages of 0.131 and 0.898. If this holds, the model can generate large Cu L-edge spectral databases in minutes, which matters because most Cu-containing structures in the Materials Project currently lack simulated L-edge spectra.

What carries the argument

The load-bearing object is the M3GNet-derived 64-dimensional site vector: for each symmetrically unique Cu absorber, M3GNet's graph representation of the unit cell is evaluated before its readout layer, and the resulting node features are the sole input to CuXASNet. The spectral branch is a pair of fully connected networks with hidden layers of 120, 240 and 480 units and ReLU activations, a softmax output layer spanning 312 energy points, and separate weights for the L3 and L2 edges. FEFF9 provides the training signal at the multiple-scattering level of theory; the interpolated 0.2 eV grid and fixed energy windows standardize the output. What the machinery does is compress the structure-spectrum relationship into a learned map from a local-environment embedding to a normalized intensity profile.

What would settle it

A decisive test: find two distinct Cu coordination environments that receive exactly the same 64-dimensional M3GNet embedding but produce measurably different FEFF9 L3 spectra; because CuXASNet is a deterministic function of that vector, it would be unable to distinguish them, falsifying the claim that the embedding contains the spectral information. A practical approximation is to train the same network from an alternative local-environment descriptor on the same split and show a significantly lower test MAE, which would disprove the sufficiency of the M3GNet featurization.

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Extended reading notes

Core claim

The central claim of the paper is that the Cu L-edge X-ray absorption spectrum is, for practical purposes, a function of a short vector encoding the absorbing site's local atomic environment: specifically, the 64-dimensional node embedding produced by M3GNet. Trained on 4,123 of 5,497 site-specific FEFF9 multiple-scattering spectra, two dense networks (one for L3, one for L2) predict the full 312-point spectrum on a 0.2 eV grid. The paper reports median test-set MAE of 0.0391, edge-onset errors that are exact or within a grid step for most spectra, and, in the experimental validation, aggregate errors indistinguishable from FEFF9's own. The authors present this as establishing CuXASNet as a drop-in replacement for FEFF9 in screening candidate structures against measured spectra, including structures outside its crystalline training distribution.

Load-bearing premise

The claim collapses if M3GNet's 64-dimensional embedding of a Cu site does not contain enough information about the local atomic environment to determine the L-edge spectrum; the paper takes this representation as fixed and does not ablate or compare it against alternative featurizations.

Editorial extensions

If this is right

CuXASNet can generate thousands of Cu L3/L2 spectra per minute, so most Cu-containing Materials Project structures without L-edge spectra could be populated at FEFF9-equivalent quality without running FEFF9.
Experimental analysis can use CuXASNet as a fast filter: candidate structural models of an unknown Cu material are screened against a measured spectrum before expensive FEFF9 refinement, since the ML-versus-experiment error is statistically the same as FEFF9-versus-experiment.
The data-scaling result, accuracy plateauing after roughly 500 training spectra, indicates that the same architecture can be retrained on more expensive levels of theory with a computationally feasible dataset.
The successful prediction for a peroxo-Cu(II) organometallic complex implies the embedding generalizes beyond crystalline periodic structures, extending the model's use to molecular Cu sites.
Because the two worst outliers are antiperovskites with unusual FEFF9 spectra, the model's reliability is chemistry-dependent and its limits cluster around rare coordination motifs rather than being uniform.

Reading between the lines

Editorial extensions of the paper, not claims the author makes directly.

Since CuXASNet only learns to imitate FEFF9, its agreement with experiment is capped by FEFF9's own systematic errors: any level-of-theory deficiency in the multiple-scattering method will be inherited by the network, so the model cannot be expected to improve on FEFF9 for elements such as Ti or Fe where FEFF9 is known to be weaker.
The absence of a featurizer ablation leaves open that a cheaper or more physically interpretable descriptor could match or beat the M3GNet embedding; a head-to-head comparison against SOAP or atom-centered symmetry functions on the same 5,497 labels would settle where the accuracy resides.
The model's speed invites an inverse-design loop not implemented in the paper: search over structures or dopant configurations to match a target experimental spectrum, then validate the top hits with full simulation.
Extension to other 3d transition-metal L-edges will require new training labels but, if the data-scaling trend holds, would need only a few thousand spectra per element, a modest simulation budget relative to database-scale studies.

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Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, and a circularity audit.

Desk Editor's Note

read the letter

CuXASNet is a workmanlike ML surrogate for FEFF9 Cu L-edge XAS, and the internal test-set results are convincing. The experimental comparison is the weak link: the paper never explains how the simulated energy axes were aligned to the digitized spectra, and that makes the headline equivalence claim uninterpretable as written.

What is actually new: the authors train two dense networks (L3 and L2) on 5497 site-specific FEFF9 spectra, using M3GNet node features as input, and they validate the models against 14 experimental spectra extracted from the literature. The Cu-specific dataset, the two-edge models, and the experimental screening are real additions beyond the same group's earlier universal XAS framework (Ref. 10). The paper also does several things well: it filters unconverged FEFF9 calculations, removes the experimental comparison structures from training, shows PCA and chemical-trend analyses, reports edge-location error histograms, and includes a training-data-volume curve. The internal accuracy is demonstrated convincingly: median MAE around 0.039, edge onsets mostly predicted within 0.2 eV, and the worst outliers are discussed honestly.

The soft spots are real but separable. First, the experimental validation protocol is thin. Section II.D says only that spectra were cropped to the measured energy range and MAE was computed; no energy calibration or alignment is mentioned. FEFF9 spectra are not automatically on an absolute experimental energy scale, and the paper itself manually aligns the L3 peak for the molecular complex in Section III.G, which proves alignment matters. Without knowing whether the 14 spectra were aligned, the reported MAE=0.125 and Spearman=0.891 (vs FEFF9's 0.131/0.898) could reflect a shared systematic offset rather than genuine spectral accuracy. There are also no per-spectrum metrics or error bars. This is the load-bearing weakness in the external claim. Second, the code and dataset are private until publication, so the results cannot currently be checked independently. Third, the M3GNet embedding is not ablated; the test-set performance suggests it is adequate, but the paper does not test alternatives. That is minor. The novelty is incremental over Ref. 10, but that is fine.

This paper is for practitioners who want a fast FEFF9-quality surrogate for Cu L-edge screening in high-throughput studies. It deserves a serious referee. I would send it to review with a request that the authors state the energy-alignment procedure explicitly, provide per-spectrum MAE and Spearman values, and release the code and data. With those revisions, the experimental claim would be checkable and the paper would be a solid contribution.

Referee Report

3 major / 4 minor

Summary. The paper introduces CuXASNet, a dense neural network that predicts Cu L3- and L2-edge X-ray absorption spectra from a 64-dimensional M3GNet embedding of the absorbing Cu site. The model is trained on 5497 FEFF9 multiple-scattering spectra of Cu-containing materials, and the authors report median test-set MAE of 0.0391, accurate edge-onset prediction to within 0.2 eV for roughly half of the test set, and agreement with FEFF9 across oxidation states, coordination numbers, and neighbor types. The external validation uses 14 experimental spectra digitized from the literature, for which the authors report an average MAE of 0.125 and Spearman correlation of 0.891, comparable to the FEFF9 values of 0.131 and 0.898. The authors also demonstrate a molecular example outside the crystalline training distribution and analyze how model accuracy scales with training-set size.

Significance. If the claims hold, CuXASNet would be a useful, fast surrogate for FEFF9 L-edge simulations, enabling structure screening and rapid generation of reference spectra for Cu systems. The internal validation against FEFF9 is strong and clearly presented: the test-set MAE distributions, edge-location histograms, and error breakdown by chemical environment give a convincing picture of surrogate accuracy. The experimental comparison is potentially valuable evidence that the model is not systematically worse than FEFF9, but its current lack of methodological detail limits the strength of the external claim. The paper also provides useful scaling data on training-set size and an honest discussion of outlier classes such as antiperovskites.

major comments (3)

[Sections II.D and III.D] The manuscript does not state whether the simulated energy axes were aligned to the experimental axes before computing MAE and Spearman correlation. Section III.G explicitly mentions manually aligning the L3 peak for the molecular comparison, which is standard practice for FEFF9 L-edge calculations because their absolute energy scale is not directly transferable to experiment. If no such alignment was applied to the 14 literature spectra, a uniform energy offset could substantially change both metrics, and the claimed equivalence between CuXASNet and FEFF9 might reflect a shared systematic offset rather than true spectral accuracy. Please specify the alignment procedure used for all 14 spectra, report any alignment shifts, and provide metrics both with and without alignment.
[Section III.D] The external validation is summarized only by averages over 14 spectra, with no per-spectrum table and no uncertainty estimates. Figure 5(d) shows the distribution of MAE values, but the reader cannot tell which systems drive the average, whether any single spectrum is an outlier, or whether the FEFF9 and CuXASNet values are statistically distinguishable. Provide a table with per-spectrum MAE and Spearman correlation for both methods, together with the experimental energy range used for each system and the corresponding digitization source.
[Sections II.C and III.B] The train/test split is not described. The paper reports that the test set contains 1375 spectra but does not state how the split was constructed (e.g., random by spectrum, random by material, stratified by oxidation state) or whether test structures can share near-duplicate local environments with training structures. This detail is load-bearing for the central claim that CuXASNet generalizes to new atomic structures, and it should be stated explicitly.

minor comments (4)

[Throughout] Several typos should be cleaned up: 'igure S4' is missing the capital F, 'epocs' should be 'epochs', 'principle component' should be 'principal component', and 'For for biological' has a duplicated word.
[Section III.C and Figure 4] The text refers to bar plots in Figure 4(a-b) and two-dimensional histograms in Figure 4(c-d), but the figure caption and the actual panel arrangement appear to place the two-dimensional histograms in (a-b) and the bar plots in (c-d). Please correct the subplot references so the text matches the figure.
[Section V] The data and code repository is described as private and 'will be shared upon request.' For a reproducibility claim, the authors should either make the repository accessible to reviewers before publication or provide a review copy, since the paper's central results depend on the exact training and evaluation pipeline.
[Section II.D] The description of experimental data extraction is thin: the authors cite webplotdigitizer and the source references, but do not state which curve from each reference was digitized, how the smoothing broadening function was chosen, or how the intensity normalization was performed before computing MAE. A short supplementary table or paragraph would make the experimental comparison reproducible.

Circularity Check

0 steps flagged · score 2.0 of 10

No circular derivation: CuXASNet is a supervised surrogate for FEFF9, and its experimental comparison is an external benchmark; the only same-author citations are non-load-bearing.

full rationale

The paper's core claim is that a neural network trained on FEFF9 multiple-scattering spectra reproduces those spectra on held-out structures and achieves experimental agreement comparable to FEFF9. This is a regression against an external simulation code, not a quantity defined by the model inputs: the FEFF9 target spectra in the test set are not used in training (Section II.B), and the 14 experimental spectra are independent literature data (Section II.D). The M3GNet featurizer (Ref. 60) is a fixed, pretrained graph neural network representation, not fitted to XAS data, so the featurization is not constructed from the target spectra. The same-author citations (Ref. 10 for featurizer benchmarking, Ref. 45 for the simulated dataset and Ref. 61 for the Lightshow workflow) support methodological choices and data provenance, but the quantitative conclusions do not reduce to them: held-out FEFF9 MAE and external experimental MAE/Spearman values are reported and are falsifiable. The absence of an explicit energy-alignment protocol for the 14 spectra (Section II.D vs. the manual alignment in Section III.G) is a legitimate external-validity concern, but it is not a circularity, since no fitted parameter is renamed as a prediction. No equation in the paper defines the predicted spectrum as the training input, and no fitted quantity is presented as an independent first-principles result. Score 2 reflects the presence of minor same-author citations (notably Refs. 10 and 45) that are ancillary rather than load-bearing.

Assumptions & free parameters 1 free parameters · 4 assumptions · 0 invented entities

The central result depends on four domain assumptions, no invented physical entities, and one set of manually chosen hyperparameters. The FEFF9 accuracy and M3GNet featurizer sufficiency are the most consequential; the experimental comparison only partially validates the former, and the latter is not tested directly.

free parameters (1)

Neural network hyperparameters = hidden layers: 120, 240, 480; batch size: 10; epochs: 500
Chosen by hand; the paper reports that batch size and epoch count have minimal impact on the median MAE (less than 2% variation), so their influence on the central claim is low.

assumptions (4)

domain assumption FEFF9 multiple-scattering theory provides accurate Cu L-edge spectra
Training labels are FEFF9 spectra; the experimental comparison (14 spectra) gives an average MAE of 0.131, providing partial support, but accuracy is not guaranteed across all Cu environments. Invoked throughout, e.g., Section II.A.
domain assumption M3GNet 64-dim node embedding is a sufficient representation of the local Cu environment for spectral prediction
The entire method rests on this featurization sufficiency; no ablation or comparison to other featurizers is provided in this paper. Invoked in Section II.B and Figure 1.
domain assumption The training set of 5497 spectra is representative of Cu chemical environments in practice
The dataset is filtered to stable/synthesized Materials Project structures; the two antiperovskite outliers (Mn3CuN, Ni3CuN) show coverage gaps. Invoked in Section II.A and Section III.E.
domain assumption The 14 literature experimental spectra are correctly digitized and energy-aligned with the simulated spectra
Digitization used webplotdigitizer and a broadening function, but no energy alignment procedure is described for the 14 materials; the comparison assumes the FEFF9 and experimental energy scales coincide. Invoked in Section II.D.

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Cite this review

Pith. "Pith review of CuXASNet: Rapid and Accurate Prediction of Copper L-edge X-Ray Absorption Spectra Using Machine Learning." pith.science (2026). https://pith.science/paper/DUZAUV7K

@misc{pith2026241202916,
  author       = {Pith},
  title        = {Pith review of: CuXASNet: Rapid and Accurate Prediction of Copper L-edge X-Ray Absorption Spectra Using Machine Learning},
  year         = {2026},
  howpublished = {\url{https://pith.science/paper/DUZAUV7K}},
  note         = {Machine review of arXiv:2412.02916}
}

read the original abstract

In this work, we have developed CuXASNet, a dense neural network that predicts simulated Cu L-edge X-ray absorption spectra (XAS) from atomic structures. Featurization of the Cu local environment is performed using a component of M3GNet, a graph neural network developed for predicting the potential energy surface. CuXASNet is trained on simulated spectra from FEFF9 at the multiple scattering level of theory, and can predict the L3 and L2 edges for Cu sites to quantitative accuracy. To validate our approach, we compare 14 experimental spectra extracted from the literature with the predictions of CuXASNet. The agreement of CuXASNet with experiments is shown by an average MAE of 0.125 and an average Spearman's correlation coefficient of 0.891, which is comparable to FEFF9's values of 0.131 and 0.898 for the same metrics. As such, CuXASNet can rapidly generate a large number of L-edge XAS spectra at the same accuracy as FEFF9 simulations. This can be used as a drop-in replacement for multiple scattering codes for fast screening of candidate atomic structure models of a measured system. This model establishes a general framework for Cu XAS prediction, and can be extended to more computationally expensive levels of theory and to other transition metal L-edges.

Figures

Figures reproduced from arXiv: 2412.02916 by the authors.

**Figure 1.** FIG. 1. Outline of the CuXASNet model architecture. A structure object of a Cu containing material from the Materials [PITH_FULL_IMAGE:figures/full_fig_p002_1.png] view at source ↗

**Figure 2.** FIG. 2. Illustration of the data spread in our spectral dataset. Each row shows a principle component analysis (PCA) and [PITH_FULL_IMAGE:figures/full_fig_p003_2.png] view at source ↗

**Figure 3.** FIG. 3. Waterfall plots showcasing the accuracy of our model at reproducing spectra simulated with FEFF9. (a-b) show decile [PITH_FULL_IMAGE:figures/full_fig_p004_3.png] view at source ↗

Figures from the paper (5 more)

**Figure 4.** Figure 4: FIG. 4. Accuracy of CuXASNet in predicting the FEFF9 simulated edge onset location of the [PITH_FULL_IMAGE:figures/full_fig_p006_4.png]

**Figure 5.** Figure 5: FIG. 5. Performance of CuXASNet when compared to experimental spectra. Comparisons between FEFF9 simulations (blue), [PITH_FULL_IMAGE:figures/full_fig_p007_5.png]

**Figure 6.** Figure 6: FIG. 6. The accuracy of CuXASNet when predicting Cu spectra with different nearest neighbor elemental configurations. The [PITH_FULL_IMAGE:figures/full_fig_p008_6.png]

**Figure 7.** Figure 7: FIG. 7. Accuracy of the model, as determined by the median MAE, when the model is applied to the test set using different [PITH_FULL_IMAGE:figures/full_fig_p009_7.png]

**Figure 8.** Figure 8: FIG. 8. An application of our CuXASNet model to an uncommon and complicated Cu organometallic structure, extracted [PITH_FULL_IMAGE:figures/full_fig_p009_8.png]

Discussion (0). Continue with ORCID to comment.

Forward citations

Cited by 1 Pith paper

Reviewed papers in the Pith corpus that reference this work. Sorted by Pith novelty score. Full citation record

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