REVIEW 3 major objections 4 minor 38 references
Revisiting the Question of Information Content of EXAFS Spectra through a Bayesian Approach
T0 review · 3 major / 4 minor · reviewed 2026-08-04 · deepseek-v4-flash
Pith's one-line read This paper claims that the Bayes Factor Integral, not the Shannon-Nyquist criterion, gives the true information content of EXAFS spectra, and that for liquid gallium the BFI peaks at 10 free parameters even though the conventional limit all
desk verdict Applies the authors' own prior-sensitive BFI to EXAFS information content; the l-Ga result is plausible, but the prior-range dependence undercuts the 'superior measure' claim. read the letter →
The pith
A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.
The reading
What carries the argument
The Bayes Factor Integral (BFI), defined as BFI = (2π)^(m/2) Lmax √det(Covp) / ∏Δp_i, is the central object. It is a Laplace-approximated marginal likelihood that combines the maximum likelihood of a fit with an Occam factor built from the parameter covariance matrix and the prior ranges. The covariance matrix injects parameter correlations into the criterion, while the prior ranges encode structural knowledge and penalize models whose parameters are allowed to roam too widely. Comparing ln(BFI) between models yields a Bayes factor with a standard evidence scale, giving a quantitative rule for when an added parameter is justified.
What would settle it
Recompute the BFI for the same liquid-gallium spectrum using numerical (non-Laplace) integration of the marginal likelihood, or repeat the analysis with the prior ranges scaled by a factor of two in either direction; if the ln(BFI) maximum moves away from 10 parameters or the favored three-path model changes, the claimed information-content limit is an artifact of the prior and approximation choices rather than a fixed feature of the spectrum.
Extended reading notes
Core claim
The central claim is that the information content of an EXAFS spectrum is not fixed by the Shannon-Nyquist count Nind = 2ΔkΔR/π + 2, but should be determined by a Bayesian model-comparison quantity, the Bayes Factor Integral BFI = (2π)^(m/2) Lmax √det(Covp) / ∏Δp_i, where m is the number of fitted parameters, Lmax is the maximum likelihood, Covp is the parameter covariance matrix, and Δp_i are the user-chosen prior ranges on each parameter. Because Covp is not assumed diagonal, the BFI lifts the independence assumption and includes an Occam factor that penalizes models with broader priors or stronger correlations. Applied to the liquid gallium EXAFS spectrum, the BFI-determined parameter lim
Load-bearing premise
The result depends on the user-chosen uniform prior ranges (Δp_i) and on the Laplace approximation of the marginal likelihood computed from a single fit; if those ranges or the approximation are inappropriate, the BFI-determined parameter limit is not a property of the data itself.
Editorial extensions
If this is right
- Analysts can stop adding parameters when ln(BFI) peaks, rather than trusting the Shannon-Nyquist count alone.
- BFI can rank competing fitting strategies on the same data, such as whether to describe a peak with more scattering paths or with higher-order cumulants.
- The criterion responds to data quality: with intentionally poor background subtraction, the BFI maximum shifts toward the Shannon-Nyquist limit and favors different models.
- Reducing the k-range lowers the BFI-determined parameter limit, showing that the measure tracks the information actually available in the data.
- Because BFI is computed from a single fit's covariance and likelihood, it lends itself to automated testing of many structural models.
Reading between the lines
- The BFI's dependence on user-chosen prior ranges means the 'information content' it reports is conditional on prior knowledge; two labs using different reasonable priors could obtain different parameter limits from the same spectrum.
- Since the paper shows the BFI ranking changes when the ΔR range is tightened, the method's power to distinguish models is partly a statement about how well the analyst knows the structure in advance, not solely about the data.
- If applied to other spectroscopies, the BFI might reveal when an extra model component is merely absorbing systematic errors (such as imperfect background removal) rather than capturing real physical signal.
- A natural next test is whether the BFI peak converges to a stable parameter count as prior ranges are varied continuously, or whether the peak itself moves—this would separate a property of the data from a property of the prior.
Signed reviews
Editorial analysis
A structured set of objections, weighed in public.
Referee Report
Summary. The manuscript proposes a new figure of merit, the Bayes Factor Integral (BFI, Eq. 5), as a measure of the information content of EXAFS spectra. The authors argue that the traditional Shannon–Nyquist criterion (Eq. 4) assumes independent fitting parameters, which is rarely true in EXAFS, and that BFI lifts this assumption by using the parameter covariance matrix and prior ranges. They test BFI on a liquid-gallium EXAFS spectrum by fitting a ladder of models with 1–4 scattering paths and cumulant terms, under three k-ranges and two background-subtraction conditions. They report that ln(BFI) peaks at 10 parameters, corresponding to a 3-path model, below the Shannon–Nyquist limit Nind = 11, and that the ranking changes when the data range or background quality is altered. The paper concludes that BFI provides a superior measure of EXAFS information content and can guide model selection.
Significance. If substantiated, the BFI would offer EXAFS practitioners a principled, correlation-aware criterion for deciding when to stop adding parameters and for comparing fitting strategies, going beyond the heuristic 'happiness' parameter currently used. The experimental test is well designed in several respects: real l-Ga data, a systematic sequence of 1-, 2-, 3-, and 4-path models, a cumulant-based alternative strategy, variation of the k-range, and a deliberately poor-background control. The authors also provide transparent fit descriptions and full result tables in the supplementary material. However, the central claim that BFI is a superior measure of data information content is not yet supported, because the BFI explicitly depends on user-chosen prior ranges and the reported conclusions change with those ranges.
major comments (3)
- [§III, Eq. (5)] The BFI formula contains ∏Δp_i in the denominator, so any change in a user-set prior range rescales every model's BFI and can reorder models with different numbers of parameters. The authors themselves changed the ΔR range from ±0.25 Å to ±0.025 Å after initial fits, stating the initial range was 'later found to be too large' and reduced 'to give a more meaningful comparison of models.' This is consequential: with default ranges and poor background, the maximum moves to Nind = 11 (model 4a), while with restricted ranges the 10-parameter model 3b is preferred (Fig. 5). No sensitivity analysis over ΔR, ΔN, Δσ², or ΔE0 is reported, and no uncertainties on ln(BFI) are given. The claimed '10-parameter limit' is therefore not established as a property of the data; it is a property of the selected priors. The authors should quantify how the ranking changes as the priors are varied within physic
- [§III.A, §III.B, Appendix B] The BFI is computed via a Laplace approximation to the marginal likelihood using a covariance matrix from a single Larch fit (Eq. B14–B15). The paper does not validate that the posterior is adequately Gaussian, that the Larch covariance is a reliable estimate of the Hessian, or that the uniform prior is appropriate. This matters because the covariance enters the Occam factor directly. Furthermore, the paper states in §III.A that 'in Larch covariance is no longer calculated once Nvar > Nind (and hence BFI cannot be calculated).' Thus the method cannot even evaluate models above the Shannon–Nyquist limit, so the claim that BFI lifts the independence assumption and provides a new information-content limit is only partial. The authors should test the Laplace approximation against direct numerical marginal-likelihood integration for at least a few models, and discuss whether the Nvar ≤ Nind r
- [Abstract; §IV] The claim that BFI is a 'superior measure of the data information content' is not backed by any comparison with existing information criteria. The manuscript presents ln(BFI) curves showing a peak below Nind, but does not compare with AIC, BIC, χ²ν, or the Shannon–Nyquist value on the same fits, nor with any synthetic-data benchmark where the true number of independent parameters is known. A model-selection criterion that favors a 3-path model is not the same as a measure of the information content of the spectrum. The authors should either benchmark BFI against these established FoMs or soften the claim to 'a model-selection criterion that correlates with information content' unless additional evidence is provided.
minor comments (4)
- [§II] The definition of the Bayes factor is mistyped: 'ln BF = lnBFI1 / lnBFI2 = ln(BFI1−BFI2)' should read ln BF = ln(BFI1 / BFI2) = ln BFI1 − ln BFI2. The current expression is dimensionally and logically incorrect.
- [§III.A] The R-space range used to compute Nind = 11 is not specified in the text. To reproduce Eq. (4), the reader needs ΔR; please state the R range explicitly (e.g., the FT window used for the first-shell peak).
- [Fig. 2] The caption refers to 'the legend indicating choice of colour for the bars,' but no legend is visible in the figure as presented. Please add the legend or describe the color coding in the caption.
- [Appendix B] Equation (B7) writes the prior as P({Aα}|D,I), which should presumably be P({Aα}|M,I) or the prior density for the parameters; the notation is confusing as written.
Circularity Check
No significant circularity: BFI is a self-contained Bayesian model evidence, and the 10-parameter peak for l-Ga is robust to the reported prior-range change.
full rationale
The claimed derivation chain is not circular. BFI (Eq. 5) is derived in Appendix B from the standard Laplace approximation to the marginal likelihood (Gregory [20]; Knuth [34]) with a uniform prior, giving P(D|M_i,I) ≈ Ω_m Lmax. The non-diagonal covariance enters naturally from the information matrix; the citation to the authors' ref. 14 is for the name and prior use, not for an unproved ansatz. The central empirical claim — that the BFI peaks at 10 parameters for l-Ga — is a data-dependent outcome: Lmax and det(Covp) come from Larch fits, and the number of parameters is varied across models. The reported adjustment of ΔR from ±0.25 Å to ±0.025 Å is a prior-sensitivity issue, and it is disclosed; importantly, for the good-background full-range data the maximum remains at 10 parameters under both ranges (model 3c vs 3b), so the main 'information content' number is not manufactured by the prior change. The poor-background test shows a range-dependent shift, which the paper interprets as sensitivity to data quality/priors rather than as a hidden fit. The 'superior measure' claim is arguably under-validated, and the Bayes-factor algebra around ln BF is sloppy, but these are correctness risks, not circularity. No step reduces by construction to its own input.
Assumptions & free parameters
free parameters (6)
- ΔE0 prior range =
±10 eV
- ΔR prior range =
±0.25 Å, later ±0.025 Å
- ΔN prior range =
±3.5
- Δσ² prior range =
±0.02 Ų
- ΔC3 prior range =
±0.1 ų
- noise scale εk =
0.00996 Å⁻¹ (approx)
assumptions (5)
- standard math Laplace approximation to the marginal likelihood (Bayesian evidence)
- ad hoc to paper Uniform prior over user-set parameter ranges Δp_i
- domain assumption White-noise model for k- and R-space fluctuations
- domain assumption EXAFS sum-over-paths model (Eq. 1) with FEFF-computed amplitudes and phases
- domain assumption Larch parameter covariance matrix approximates the inverse information matrix
Cite this review
Pith. "Pith review of Revisiting the Question of Information Content of EXAFS Spectra through a Bayesian Approach." pith.science (2026). https://pith.science/paper/3Q54BUEE
@misc{pith2026250907950,
author = {Pith},
title = {Pith review of: Revisiting the Question of Information Content of EXAFS Spectra through a Bayesian Approach},
year = {2026},
howpublished = {\url{https://pith.science/paper/3Q54BUEE}},
note = {Machine review of arXiv:2509.07950}
}
read the original abstract
Over the last several decades the Shannon-Nyquist criterion has been widely used as a measure of the maximum information content in EXAFS spectra and provided an upper limit on the number of parameters used in fitting data. However, the criterion implicitly assumes independent parameters which is never the case in EXAFS analysis. Here we introduce a new criterion to measure the information content in EXAFS based on Bayesian approach that lifts the above condition. We test the new criterion by fitting the EXAFS spectrum of liquid gallium and demonstrate that not only it does constitute a superior measure of the data information content, but can also provide guidance in data analysis to differentiate between various fitting strategies.
Figures
Reference graph
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