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ZaiKai He

dblp:404/6608 · 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.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Artificial intelligence
1 paper
Generative modeling · 100%

Topics — the 2 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › protein design
antibody design
0.912025
Multi-objective antibody design with constrained preference optimization · ICLR 2025
Bioinformatics and computational biology › protein design
computational protein design
0.912025
Multi-objective antibody design with constrained preference optimization · ICLR 2025

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

protein language model · 1.7primal-dual optimization · 1.7constrained preference optimization · 1.7
YearPublicationVenuePosition
2025 Multi-objective antibody design with constrained preference optimization
abstract
Antibody design is crucial for developing therapies against diseases such as cancer and viral infections. Recent deep generative models have significantly advanced computational antibody design, particularly in enhancing binding affinity to target antigens. However, beyond binding affinity, antibodies should exhibit other favorable biophysical properties such as non-antigen binding specificity and low self-association, which are important for antibody developability and clinical safety. To address this challenge, we propose AbNovo, a framework that leverages constrained preference optimization for multi-objective antibody design. First, we pre-train an antigen-conditioned generative model for antibody structure and sequence co-design. Then, we fine-tune the model using binding affinity as a reward while enforcing explicit constraints on other biophysical properties. Specifically, we model the physical binding energy with continuous rewards rather than pairwise preferences and explore a primal-and-dual approach for constrained optimization. Additionally, we incorporate a structure-aware protein language model to mitigate the issue of limited training data. Evaluated on independent test sets, AbNovo outperforms existing methods in metrics of binding affinity such as Rosetta binding energy and evolutionary plausibility, as well as in metrics for other biophysical properties like stability and specificity.
Milong Ren, ZaiKai He, Haicang Zhang
ICLR2