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William Fondrie

dblp:323/9510 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2022
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Artificial intelligence
1 paper
Deep learning architectures and training · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › proteomics › peptide sequencing
de novo peptide sequencing
0.612022
De novo mass spectrometry peptide sequencing with a transformer model · ICML 2022
Bioinformatics and computational biology
proteomics
0.612022
De novo mass spectrometry peptide sequencing with a transformer model · ICML 2022
Machine learning › Deep learning architectures and training
transformer
0.212022
De novo mass spectrometry peptide sequencing with a transformer model · ICML 2022

Methods — techniques the papers use, named apart from their topics

transformer · 1.1
YearPublicationVenuePosition
2022 De novo mass spectrometry peptide sequencing with a transformer model
abstract
Tandem mass spectrometry is the only high-throughput method for analyzing the protein content of complex biological samples and is thus the primary technology driving the growth of the field of proteomics. A key outstanding challenge in this field involves identifying the sequence of amino acids -the peptide- responsible for generating each observed spectrum, without making use of prior knowledge in the form of a peptide sequence database. Although various machine learning methods have been developed to address this de novo sequencing problem, challenges that arise when modeling tandem mass spectra have led to complex models that combine multiple neural networks and post-processing steps. We propose a simple yet powerful method for de novo peptide sequencing, Casanovo, that uses a transformer framework to map directly from a sequence of observed peaks (a mass spectrum) to a sequence of amino acids (a peptide). Our experiments show that Casanovo achieves state-of-the-art performance on a benchmark dataset using a standard cross-species evaluation framework which involves testing with spectra with never-before-seen peptide labels. Casanovo not only achieves superior performance but does so at a fraction of the model complexity and inference time required by other methods.
Melih Yilmaz, William Fondrie, Wout Bittremieux, Sewoong Oh, William Stafford Noble
ICML2