Related papers: MassFormer: Tandem Mass Spectrum Prediction for Sm…
Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a…
Mass spectrometry, especially so-called tandem mass spectrometry, is commonly used to assess the chemical diversity of samples. The resulting mass fragmentation spectra are representations of molecules of which the structure may have not…
The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of…
Tandem Mass Spectrometry is a cornerstone technique for identifying unknown small molecules in fields such as metabolomics, natural product discovery and environmental analysis. However, certain aspects, such as the probabilistic…
Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexity of the instrumentation and resulting data, sophisticated…
Mass spectra, which are agglomerations of ionized fragments from targeted molecules, play a crucial role across various fields for the identification of molecular structures. A prevalent analysis method involves spectral library…
Mass spectrometry plays a fundamental role in elucidating the structures of unknown molecules and subsequent scientific discoveries. One formulation of the structure elucidation task is the conditional de novo generation of molecular…
The identification and property prediction of chemical molecules is of central importance in the advancement of drug discovery and material science, where the tandem mass spectrometry technology gives valuable fragmentation cues in the form…
The discovery of new molecules based on the original chemical molecule distributions is of great importance in medicine. The graph transformer, with its advantages of high performance and scalability compared to traditional graph networks,…
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 experimental reference standards. Cheminformatic spectrum prediction…
Transformers have become methods of choice in many applications thanks to their ability to represent complex interactions between elements. However, extending the Transformer architecture to non-sequential data such as molecules and…
Compound identification from tandem mass spectrometry (MS/MS) data is a critical step in the analysis of complex mixtures. Typical solutions for the MS/MS spectrum to compound (MS2C) problem involve comparing the unknown spectrum against a…
Generative deep learning has become pivotal in molecular design for drug discovery, materials science, and chemical engineering. A widely used paradigm is to pretrain neural networks on string representations of molecules and fine-tune them…
Liquid chromatography mass spectrometry (LC-MS)-based metabolomics and exposomics aim to measure detectable small molecules in biological samples. The results facilitate hypothesis-generating discovery of metabolic changes and disease…
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…
Algorithms for the action segmentation task typically use temporal models to predict what action is occurring at each frame for a minute-long daily activity. Recent studies have shown the potential of Transformer in modeling the relations…
Establishing the relationship between 3D structures and the energy states of molecular systems has proven to be a promising approach for learning 3D molecular representations. However, existing methods are limited to modeling the molecular…
The task of radio map estimation aims to generate a dense representation of electromagnetic spectrum quantities, such as the received signal strength at each grid point within a geographic region, based on measurements from a subset of…
The CNN-based methods have achieved impressive results in medical image segmentation, but they failed to capture the long-range dependencies due to the inherent locality of the convolution operation. Transformer-based methods are recently…
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 toward solving this problem, the current state-of-the-art method…