Computational predictions of mass spectra from molecules have enabled the discovery of clinically relevant metabolites.

In this paper, we introduce the neural empirical interpolation method (NEIM), a neural network-based alternative to the discrete empirical interpolation method for reducing the time complexity of computing the nonlinear term in a reduced order model (ROM) for a parameterized nonlinear partial differential equation. NEIM is a greedy algorithm which accomplishes this reduction by approximating an affine decomposition of the nonlinear term of the ROM, where the vector terms of the expansion are given by neural networks depending on the ROM solution, and the coefficients are given by an interpolation of some "optimal" coefficients. Because NEIM is based on a greedy strategy, we are able to provide a basic error analysis to investigate its performance. NEIM has the advantages of being easy to implement in models with automatic differentiation, of being a nonlinear projection of the ROM nonlinearity, of being efficient for both nonlocal and local nonlinearities, and of relying solely on data and not the explicit form of the ROM nonlinearity. We demonstrate the effectiveness of the methodology on solution-dependent and solution-independent nonlinearities, a nonlinear elliptic problem, and a nonlinear parabolic model of liquid crystals.

Computational predictions of mass spectra from molecules have enabled the discovery of clinically relevant metabolites. However, such predictive tools are still limited as they occupy one of two extremes, either operating (a) by fragmenting molecules combinatorially with overly rigid constraints on potential rearrangements and poor time complexity or (b) by decoding lossy and nonphysical discretized spectra vectors. In this work, we use a new intermediate strategy for predicting mass spectra from molecules by treating mass spectra as sets of molecular formulae, which are themselves multisets of atoms. After first encoding an input molecular graph, we decode a set of molecular subformulae, each of which specify a predicted peak in the mass spectrum, the intensities of which are predicted by a second model. Our key insight is to overcome the combinatorial possibilities for molecular subformulae by decoding the formula set using a prefix tree structure, atom-type by atom-type, representing a general method for ordered multiset decoding. We show promising empirical results on mass spectra prediction tasks.

When confronted with a substance of unknown identity, researchers often perform mass spectrometry on the sample and compare the observed spectrum to a library of previously-collected spectra to identify the molecule. While popular, this approach will fail to identify molecules that are not in the existing library. In response, we propose to improve the library's coverage by augmenting it with synthetic spectra that are predicted using machine learning. We contribute a lightweight neural network model that quickly predicts mass spectra for small molecules. Achieving high accuracy predictions requires a novel neural network architecture that is designed to capture typical fragmentation patterns from electron ionization. We analyze the effects of our modeling innovations on library matching performance and compare our models to prior machine learning-based work on spectrum prediction.