Demo Data from VLDB 2026 / reviewers in the wild / expert
Cade W. Gordon
dblp:404/7772
· DBLP profile ↗
1ranked-venue papers
1as first author
1since 2021 · last 2025
—ORCID · none
Domains — the database's venue-derived domains; a paper can count in several
Artificial intelligence and machine learning · 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% | |
| Artificial intelligence
1 paper |
Language models and text generation · 77% Representation and self-supervised learning · 23% |
Topics — the 4 heaviest of 4, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Natural language and speech › Language models and text generation › neural language model
protein language model |
0.9 | 1 | 2025 | Protein Language Model Fitness is a Matter of Preference · ICLR 2025 |
Bioinformatics and computational biology › molecular evolution
fitness prediction |
0.9 | 1 | 2025 | Protein Language Model Fitness is a Matter of Preference · ICLR 2025 |
Bioinformatics and computational biology › protein sequence analysis › protein sequence representation
protein language model |
0.9 | 1 | 2025 | Protein Language Model Fitness is a Matter of Preference · ICLR 2025 |
Machine learning › Representation and self-supervised learning
pre-training |
0.3 | 1 | 2025 | Protein Language Model Fitness is a Matter of Preference · ICLR 2025 |
Methods — techniques the papers use, named apart from their topics
protein language model · 1.7unsupervised finetuning · 0.9unsupervised fine-tuning · 0.9
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2025 | Protein Language Model Fitness is a Matter of PreferenceabstractLeveraging billions of years of evolution, scientists have trained protein language models (pLMs) to understand the sequence and structure space of proteins aiding in the design of more functional proteins. Although they have shown ability to improve efficiency in engineering, it remains unclear under what conditions they will succeed or fail. We aim to predict the circumstances in which pLMs can successfully perform zero-shot fitness estimation. Our work demonstrates the trends observed over hundreds of deep mutational scans across multiple different fitness objectives. We find that the likelihood, or abstractly, implicit preference of a certain protein sequence imbued during pretraining is predictive fitness prediction capabilities. Both over-preferred and under-preferred wild type sequences harm performance. Generating a causal link between training data and likelihood, we show a power law tail over what data increases protein likelihood which is tied to training sequence homology. Lastly, proteins of low likelihood can be remedied by unsupervised finetuning. In sum, the zero-shot fitness estimation abilities of pLMs can be predicted by the likelihood of the engineered sequence, thus suggesting when pLMs should be deployed in protein maturation campaigns and a way to improve their performance under circumstances of low likelihood. Cade W. Gordon, Amy X. Lu, Pieter Abbeel |
ICLR | 1 |