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Céline Marquet

dblp:344/7145 · DBLP profile ↗
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1ranked-venue papers
1as first author
1since 2021 · last 2024
—ORCID · unresolved

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

Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author · 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%

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

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › protein function prediction
protein variant effect prediction
0.812024
Expert-guided protein language models enable accurate and blazingly fast fitness prediction · Bioinform. 2024
Bioinformatics and computational biology › protein sequence analysis › protein sequence representation
protein language model
0.212024
Expert-guided protein language models enable accurate and blazingly fast fitness prediction · Bioinform. 2024
Bioinformatics and computational biology › statistical genetics
variant effect prediction
0.212024
Expert-guided protein language models enable accurate and blazingly fast fitness prediction · Bioinform. 2024

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

protein language model embeddings · 0.8multiple sequence alignment · 0.8deep learning · 0.8
YearPublicationVenuePosition
2024 Expert-guided protein language models enable accurate and blazingly fast fitness prediction
abstract
MOTIVATION: Exhaustive experimental annotation of the effect of all known protein variants remains daunting and expensive, stressing the need for scalable effect predictions. We introduce VespaG, a blazingly fast missense amino acid variant effect predictor, leveraging protein language model (pLM) embeddings as input to a minimal deep learning model. RESULTS: To overcome the sparsity of experimental training data, we created a dataset of 39 million single amino acid variants from the human proteome applying the multiple sequence alignment-based effect predictor GEMME as a pseudo standard-of-truth. This setup increases interpretability compared to the baseline pLM and is easily retrainable with novel or updated pLMs. Assessed against the ProteinGym benchmark (217 multiplex assays of variant effect-MAVE-with 2.5 million variants), VespaG achieved a mean Spearman correlation of 0.48 ± 0.02, matching top-performing methods evaluated on the same data. VespaG has the advantage of being orders of magnitude faster, predicting all mutational landscapes of all proteins in proteomes such as Homo sapiens or Drosophila melanogaster in under 30 min on a consumer laptop (12-core CPU, 16 GB RAM). AVAILABILITY AND IMPLEMENTATION: VespaG is available freely at https://github.com/jschlensok/vespag. The associated training data and predictions are available at https://doi.org/10.5281/zenodo.11085958.
Céline Marquet, Julius Schlensok, Marina Abakarova, Burkhard Rost, Elodie Laine
Bioinform.1