EDBT 2026 Demo / reviewers in the wild / expert
Andrew B. Waight
dblp:337/6397
· DBLP profile ↗
1ranked-venue papers
0as 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 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 2 heaviest of 2, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology › molecular property prediction
protein property prediction |
0.8 | 1 | 2024 | AbLEF: antibody language ensemble fusion for thermodynamically empowered property predictions · Bioinform. 2024 |
Bioinformatics and computational biology
protein structure prediction |
0.8 | 1 | 2024 | AbLEF: antibody language ensemble fusion for thermodynamically empowered property predictions · Bioinform. 2024 |
Methods — techniques the papers use, named apart from their topics
transformer · 0.8protein language model · 0.8molecular simulation · 0.8
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2024 | AbLEF: antibody language ensemble fusion for thermodynamically empowered property predictionsabstractMOTIVATION: Pre-trained protein language and/or structural models are often fine-tuned on drug development properties (i.e. developability properties) to accelerate drug discovery initiatives. However, these models generally rely on a single structural conformation and/or a single sequence as a molecular representation. We present a physics-based model, whereby 3D conformational ensemble representations are fused by a transformer-based architecture and concatenated to a language representation to predict antibody protein properties. Antibody language ensemble fusion enables the direct infusion of thermodynamic information into latent space and this enhances property prediction by explicitly infusing dynamic molecular behavior that occurs during experimental measurement. RESULTS: We showcase the antibody language ensemble fusion model on two developability properties: hydrophobic interaction chromatography retention time and temperature of aggregation (Tagg). We find that (i) 3D conformational ensembles that are generated from molecular simulation can further improve antibody property prediction for small datasets, (ii) the performance benefit from 3D conformational ensembles matches shallow machine learning methods in the small data regime, and (iii) fine-tuned large protein language models can match smaller antibody-specific language models at predicting antibody properties. AVAILABILITY AND IMPLEMENTATION: AbLEF codebase is available at https://github.com/merck/AbLEF. Zachary A. Rollins, Talal Widatalla, Andrew B. Waight, Alan C. Cheng, Essam Metwally |
Bioinform. | 3 |