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Cade W. Gordon

dblp:404/7772 · DBLP profile ↗
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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

TopicWeightPapersLastEvidence papers
Natural language and speech › Language models and text generation › neural language model
protein language model
0.912025
Protein Language Model Fitness is a Matter of Preference · ICLR 2025
Bioinformatics and computational biology › molecular evolution
fitness prediction
0.912025
Protein Language Model Fitness is a Matter of Preference · ICLR 2025
Bioinformatics and computational biology › protein sequence analysis › protein sequence representation
protein language model
0.912025
Protein Language Model Fitness is a Matter of Preference · ICLR 2025
Machine learning › Representation and self-supervised learning
pre-training
0.312025
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
YearPublicationVenuePosition
2025 Protein Language Model Fitness is a Matter of Preference
abstract
Leveraging 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
ICLR1