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Tianbo Peng

dblp:334/1716 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2023
0009-0002-7240-9326ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 1 · 1 since 2021Databases, data management, data science and information retrieval · 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
Language models and text generation · 100%

Topics — the 4 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › protein design
antibody design
0.712023
Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design · KDD 2023
Bioinformatics and computational biology › protein design › antibody design
complementarity-determining region design
0.712023
Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design · KDD 2023
Bioinformatics and computational biology
protein design
0.712023
Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design · KDD 2023
Natural language and speech › Language models and text generation › neural language model
protein language model
0.212023
Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design · KDD 2023

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

one-shot sequence and structure generation · 1.3antibody language model pre-training · 1.3
YearPublicationVenuePosition
2023 Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design
abstract
Antibodies are proteins that effectively protect the human body by binding to pathogens. Recently, deep learning-based computational antibody design has attracted popular attention since it automatically mines the antibody patterns from data that could be complementary to human experiences. However, the computational methods heavily rely on high-quality antibody structure data, which is quite limited. Besides, the complementarity-determining region (CDR), which is the key component of an antibody that determines the specificity and binding affinity, is highly variable and hard to predict. Therefore, the limited availability of high-quality antibody structure data exacerbates the difficulty of CDR generation. Fortunately, there is a large amount of sequence data for antibodies that can help model the CDR and reduce reliance on structure data. By witnessing the success of pre-training models for protein modeling, in this paper, we develop the antibody pre-training language model and incorporate it into the antigen-specific antibody design model in a systemic way. Specifically, we first pre-train a novel antibody language model based on the sequence data, then propose a one-shot way for sequence and structure generation of CDR to mitigate the high cost and error propagation associated with autoregressive methods, and finally leverage the pre-trained antibody model for the antigen-specific antibody generation model with some carefully designed modules. Our experiments demonstrate the superiority of our method over previous baselines in tasks such as sequence and structure generation, CDR-H3 design for antigen binding, and antibody optimization1. The code is available at https://github.com/KyGao/ABGNN.
Kaiyuan Gao, Lijun Wu 0003, Jinhua Zhu 0001, Tianbo Peng, Yingce Xia, Liang He 0010, Shufang Xie 0003, Tao Qin 0001, Haiguang Liu, Kun He 0001, Tie-Yan Liu
KDD4