Demo Data from EDBT 2026 / reviewers in the wild / expert
Céline Marquet
dblp:344/7145
· DBLP profile ↗
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
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology › protein function prediction
protein variant effect prediction |
0.8 | 1 | 2024 | 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 |
0.2 | 1 | 2024 | Expert-guided protein language models enable accurate and blazingly fast fitness prediction · Bioinform. 2024 |
Bioinformatics and computational biology › statistical genetics
variant effect prediction |
0.2 | 1 | 2024 | 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
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2024 | Expert-guided protein language models enable accurate and blazingly fast fitness predictionabstractMOTIVATION: 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 |