Machine learning (ML) models have achieved strikingly high accuracies in spectroscopic classification tasks, often without a clear proof that those models used chemically meaningful features. Existing studies have linked these results to data preprocessing choices, noise sensitivity, and model complexity, but no unifying explanation is available so far. In this work, we show that these phenomena arise naturally from the intrinsic high dimensionality of spectral data. Using a theoretical analysis grounded in the Feldman-Hajek theorem and the concentration of measure, we show that even infinitesimal distributional differences, caused by noise, normalisation, or instrumental artefacts, may become perfectly separable in high-dimensional spaces. Through a series of specific experiments on synthetic and real fluorescence spectra, we illustrate how models can achieve near-perfect accuracy even when chemical distinctions are absent, and why feature-importance maps may highlight spectrally irrelevant regions. We provide a rigorous theoretical framework, confirm the effect experimentally, and conclude with practical recommendations for building and interpreting ML models in spectroscopy.

Tandem mass spectrometry (MS/MS) is a high-throughput technology used to identify the proteins in a complex biological sample, such as a drop of blood. A collection of spectra is generated at the output of the process, each spectrum of which is representative of a peptide (protein subsequence) present in the original complex sample. In this work, we leverage the log-likelihood gradients of generative models to improve the identification of such spectra. In particular, we show that the gradient of a recently proposed dynamic Bayesian network (DBN) may be naturally employed by a kernel-based discriminative classifier. The resulting Fisher kernel substantially improves upon recent attempts to combine generative and discriminative models for post-processing analysis, outperforming all other methods on the evaluated datasets. We extend the improved accuracy offered by the Fisher kernel framework to other search algorithms by introducing Theseus, a DBN representating a large number of widely used MS/MS scoring functions. Furthermore, with gradient ascent and max-product inference at hand, we use Theseus to learn model parameters without any supervision.

Scaling laws for neural networks, in which the loss decays as a power-law in the number of parameters, data, and compute, depend fundamentally on the spectral structure of the data covariance, with power-law eigenvalue decay appearing ubiquitously in vision and language tasks. A central question is whether this spectral structure is preserved or destroyed when data passes through the basic building block of a neural network: a random linear projection followed by a nonlinear activation. We study this question for the random feature model: given data $x \sim N(0,H)\in \mathbb{R}^v$ where $H$ has $α$-power-law spectrum ($λ_j(H ) \asymp j^{-α}$, $α> 1$), a Gaussian sketch matrix $W \in \mathbb{R}^{v\times d}$, and an entrywise monomial $f(y) = y^{p}$, we characterize the eigenvalues of the population random-feature covariance $\mathbb{E}_{x }[\frac{1}{d}f(W^\top x )^{\otimes 2}]$. We prove matching upper and lower bounds: for all $1 \leq j \leq c_1 d \log^{-(p+1)}(d)$, the $j$-th eigenvalue is of order $\left(\log^{p-1}(j+1)/j\right)^α$. For $ c_1 d \log^{-(p+1)}(d)\leq j\leq d$, the $j$-th eigenvalue is of order $j^{-α}$ up to a polylog factor. That is, the power-law exponent $α$ is inherited exactly from the input covariance, modified only by a logarithmic correction that depends on the monomial degree $p$. The proof combines a dyadic head-tail decomposition with Wick chaos expansions for higher-order monomials and random matrix concentration inequalities.

LLMs with improved chemical reasoning capabilities in the other two sub-tasks.

CNNs, MLPs, and quadratic problems, and find that SGD can perform on par with Adam on problems without block heterogeneity, but performs worse than Adam when the heterogeneity exists.

Spectroscopic techniques are essential tools for determining the structure of molecules.

Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym - the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data.