Related papers: One Small Step with Fingerprints, One Giant Leap f…
Molecular structure elucidation from tandem mass spectra (MS/MS) remains challenging, particularly for de novo generation beyond database coverage. A common approach decomposes the task into spectrum-to-fingerprint prediction followed by…
We propose a novel molecular fingerprint-based variational autoencoder applied for molecular generation on real-world drug molecules. We define more suitable and pharma-relevant baseline metrics and tests, focusing on the generation of…
Mass spectrometry is a powerful and widely used tool for identifying molecular structures due to its sensitivity and ability to profile complex samples. However, translating spectra into full molecular structures is a difficult,…
Molecular structure generation from mass spectrometry is fundamental for understanding cellular metabolism and discovering novel compounds. Although tandem mass spectrometry (MS/MS) enables the high-throughput acquisition of fragment…
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…
Identification of experimentally acquired mass spectra of unknown compounds presents a~particular challenge because reliable spectral databases do not cover the potential chemical space with sufficient density. Therefore machine learning…
Molecule generation is a challenging open problem in cheminformatics. Currently, deep generative approaches addressing the challenge belong to two broad categories, differing in how molecules are represented. One approach encodes molecular…
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…
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the…
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…
Molecular fingerprints, i.e. feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we…
The annotation (assigning structural chemical identities) of MS/MS spectra remains a significant challenge due to the enormous molecular diversity in biological samples and the limited scope of reference databases. Currently, the vast…
In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated…
Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism. Today, the vast majority of metabolites remain unknown, in particular for non-model organisms. Mass spectrometry is one of the predominant…
In this study, we present a novel molecular fingerprint generation method based on multiparameter persistent homology. This approach reveals the latent structures and relationships within molecular geometry, and detects topological features…
Molecular fingerprinting through absorption spectroscopy is a powerful analytical method. Wide spectral ranges are explored with Doppler-limited resolution. Fast data acquisition, accurate measurements of frequency, intensity, and line…
Mass spectrometry (MS) stands as a cornerstone analytical technique for molecular identification, yet de novo structure elucidation from spectra remains challenging due to the combinatorial complexity of chemical space and the inherent…
Fingerprint image denoising is a very important step in fingerprint identification. to improve the denoising effect of fingerprint image,we have designs a fingerprint denoising algorithm based on deep encoder-decoder network,which encoder…
Fingerprint analysis is a ubiquitous tool for pattern recognition with applications spanning from geolocation and DNA analysis to facial recognition and forensic identification. Central to its utility is the ability to provide accurate…
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…