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Hunter Elliott

dblp:190/7185 · DBLP profile ↗
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1ranked-venue papers
0as 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 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.

Artificial intelligence
1 paper
Optimization for machine learning · 77% Generative modeling · 23%
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
Machine learning › Optimization for machine learning › model-based optimization
bayesian optimization
0.912025
Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences · ICLR 2025
Bioinformatics and computational biology › protein design
antibody design
0.912025
Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences · ICLR 2025
Machine learning › Generative modeling › generative model
generative sequence model
0.312025
Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences · ICLR 2025

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

twisted sequential monte carlo · 1.7sequential monte carlo · 1.7large language model · 1.7
YearPublicationVenuePosition
2025 Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences
abstract
To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a *clonal family*. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic *in silico* experiments and designs stronger and more stable binders in *in vitro* wet lab experiments.
Alan Nawzad Amin, Nate Gruver, Yilun Kuang, Yucen Lily Li, Hunter Elliott, Calvin McCarter, Aniruddh Raghu, Peyton Greenside, Andrew Gordon Wilson
ICLR5