124 citations · 266 across the 8 of their papers we have counts for
8 papers
Generative structural elucidation from mass spectra as an iterative optimization problem
Mrunali Manjrekar, Runzhong Wang, Samuel Goldman +2
Liquid chromatography tandem mass spectrometry (LC-MS/MS) is a critical analytical technique for molecular identification across metabolomics, environmental chemistry, and chemical…
A Lindbladian for exact renormalization of density operators in QFT
Samuel Goldman, Nima Lashkari, Robert G. Leigh
In arXiv:1609.03493, the authors extended the exact renormalization group (ERG) to arbitrary wave-functionals in quantum field theory (QFT). Applying this formalism, we show that t…
MIST-CF: Chemical formula inference from tandem mass spectra
Samuel Goldman, Jiayi Xin, Joules Provenzano +1
Chemical formula annotation for tandem mass spectrometry (MS/MS) data is the first step toward structurally elucidating unknown metabolites. While great strides have been made towa…
Single-model uncertainty quantification in neural network potentials does not consistently outperform model ensembles
Aik Rui Tan, Shingo Urata, Samuel Goldman +2
Neural networks (NNs) often assign high confidence to their predictions, even for points far out-of-distribution, making uncertainty quantification (UQ) a challenge. When they are…
Generating Molecular Fragmentation Graphs with Autoregressive Neural Networks
Samuel Goldman, Janet Li, Connor W. Coley
The accurate prediction of tandem mass spectra from molecular structures has the potential to unlock new metabolomic discoveries by augmenting the community's libraries of experime…
Prefix-Tree Decoding for Predicting Mass Spectra from Molecules
Samuel Goldman, John Bradshaw, Jiayi Xin +1
Computational predictions of mass spectra from molecules have enabled the discovery of clinically relevant metabolites. However, such predictive tools are still limited as they occ…
Machine learning modeling of family wide enzyme-substrate specificity screens
Samuel Goldman, Ria Das, Kevin K. Yang +1
Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex natural products, and commodity chemicals at scale. However, the adoption of biocatalysis is…
Improved Conditional Flow Models for Molecule to Image Synthesis
Karren Yang, Samuel Goldman, Wengong Jin +4
In this paper, we aim to synthesize cell microscopy images under different molecular interventions, motivated by practical applications to drug development. Building on the recent…