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Shiyi Du

dblp:312/3627 · DBLP profile ↗
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3ranked-venue papers
2as first author
3since 2021 · last 2026
0009-0006-3445-2437ORCID · corroborated

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

Applied, interdisciplinary, general and emerging computing · 3 · 2 first-author · 3 since 2021Graphics, computer vision, multimedia, augmented reality and games · 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
Deep learning architectures and training · 100%

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

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › sequence analysis
DNA language model
1.012026
CodonMoE: DNA language models for codon-dependent mRNA prediction · Bioinform. 2026
Machine learning › Deep learning architectures and training
mixture of experts
0.312026
CodonMoE: DNA language models for codon-dependent mRNA prediction · Bioinform. 2026

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

mixture of experts · 2.0adapter · 2.0
YearPublicationVenuePosition
2026 CodonMoE: DNA language models for codon-dependent mRNA prediction
abstract
MOTIVATION: Genomic language models (gLMs) face a fundamental efficiency challenge: one must either maintain separate specialized models for each biological modality (DNA and RNA) or develop large multimodal architectures. Both approaches impose significant computational burdens-modality-specific models require redundant infrastructure despite inherent biological connections, while multi-modal architectures demand increased parameter counts and extensive cross-modality pretraining. RESULTS: To address this limitation, we introduce CodonMoE (Adaptive Mixture of Codon Reformative Experts), a lightweight adapter that transforms DNA language models into effective RNA analyzers without RNA-specific pretraining. Our theoretical analysis establishes CodonMoE as a universal approximator at the codon level, capable of mapping arbitrary functions from codon sequences to codon-dependent RNA properties given sufficient expert capacity. Across four RNA prediction tasks spanning stability, expression, and regulation, DNA models augmented with CodonMoE significantly outperform their unmodified counterparts, with the HyenaDNA+CodonMoE series achieving state-of-the-art results using 80% fewer parameters than specialized RNA models. By maintaining sub-quadratic complexity while achieving superior performance, our approach provides a principled path toward unifying genomic language modeling, leveraging more abundant DNA data and reducing computational overhead while preserving modality-specific performance advantages. AVAILABILITY AND IMPLEMENTATION: Source code for the method and to reproduce the results is available at https://github.com/Kingsford-Group/CodonMoE.
Shiyi Du, Litian Liang, Carl Kingsford
Bioinform.1
2023 Self-supervised anomaly detection, staging and segmentation for retinal images
Yiyue Li, Qicheng Lao, Qingbo Kang, Zekun Jiang, Shiyi Du, Shaoting Zhang 0001, Kang Li 0004
Medical Image Anal.5
2022 Distilling Knowledge from Topological Representations for Pathological Complete Response Prediction
Shiyi Du, Qicheng Lao, Qingbo Kang, Yiyue Li, Zekun Jiang, Kang Li 0004
MICCAI (2)1