TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling
Fuente:
arXiv
Saved in:
| Main Authors: | Yang, Qirong, Guo, Yucheng, Liu, Zicheng, Yang, Yujie, Yin, Qijin, Li, Siyuan, Ji, Shaomin, Chao, Linlin, Zhang, Xiaoming, Li, Stan Z. |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification
by: Liu, Zicheng, et al.
Published: (2025)
by: Liu, Zicheng, et al.
Published: (2025)
MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging
by: Li, Siyuan, et al.
Published: (2025)
by: Li, Siyuan, et al.
Published: (2025)
EnTao-GPM: DNA Foundation Model for Predicting the Germline Pathogenic Mutations
by: Lin, Zekai, et al.
Published: (2025)
by: Lin, Zekai, et al.
Published: (2025)
GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models
by: Liu, Zicheng, et al.
Published: (2024)
by: Liu, Zicheng, et al.
Published: (2024)
VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling
by: Li, Siyuan, et al.
Published: (2024)
by: Li, Siyuan, et al.
Published: (2024)
DiscDiff: Latent Diffusion Model for DNA Sequence Generation
by: Li, Zehui, et al.
Published: (2024)
by: Li, Zehui, et al.
Published: (2024)
eccDNAMamba: A Pre-Trained Model for Ultra-Long eccDNA Sequence Analysis
by: Liu, Zhenke, et al.
Published: (2025)
by: Liu, Zhenke, et al.
Published: (2025)
Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling
by: Schiff, Yair, et al.
Published: (2024)
by: Schiff, Yair, et al.
Published: (2024)
Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning
by: Li, Zehui, et al.
Published: (2025)
by: Li, Zehui, et al.
Published: (2025)
Poisoning the Genome: Targeted Backdoor Attacks on DNA Foundation Models
by: Koilakos, Charalampos, et al.
Published: (2026)
by: Koilakos, Charalampos, et al.
Published: (2026)
Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA
by: Qiao, Lifeng, et al.
Published: (2024)
by: Qiao, Lifeng, et al.
Published: (2024)
SPACE: Your Genomic Profile Predictor is a Powerful DNA Foundation Model
by: Yang, Zhao, et al.
Published: (2025)
by: Yang, Zhao, et al.
Published: (2025)
JanusDNA: A Powerful Bi-directional Hybrid DNA Foundation Model
by: Duan, Qihao, et al.
Published: (2025)
by: Duan, Qihao, et al.
Published: (2025)
Bridging Sequence-Structure Alignment in RNA Foundation Models
by: Yang, Heng, et al.
Published: (2024)
by: Yang, Heng, et al.
Published: (2024)
How Private Are DNA Embeddings? Inverting Foundation Model Representations of Genomic Sequences
by: Ouaari, Sofiane, et al.
Published: (2026)
by: Ouaari, Sofiane, et al.
Published: (2026)
DNA Sequence Classification with Compressors
by: Ozan, Şükrü
Published: (2024)
by: Ozan, Şükrü
Published: (2024)
Embed-Search-Align: DNA Sequence Alignment using Transformer Models
by: Holur, Pavan, et al.
Published: (2023)
by: Holur, Pavan, et al.
Published: (2023)
D3LM: A Discrete DNA Diffusion Language Model for Bidirectional DNA Understanding and Generation
by: Yang, Zhao, et al.
Published: (2026)
by: Yang, Zhao, et al.
Published: (2026)
HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model
by: Ma, Mingqian, et al.
Published: (2025)
by: Ma, Mingqian, et al.
Published: (2025)
EvoLen: Evolution-Guided Tokenization for DNA Language Model
by: Huang, Nan, et al.
Published: (2026)
by: Huang, Nan, et al.
Published: (2026)
Finding low-complexity DNA sequences with longdust
by: Li, Heng, et al.
Published: (2025)
by: Li, Heng, et al.
Published: (2025)
Dy-mer: An Explainable DNA Sequence Representation Scheme using Dictionary Learning
by: Peng, Zhiyuan, et al.
Published: (2024)
by: Peng, Zhiyuan, et al.
Published: (2024)
Emerging Challenges in Molecular Paleontology: Misapplication of Environmental DNA Fragments and Misconception of Deamination as a Key Criterion for In Situ DNA Identification
by: Zhao, Wan-Qian, et al.
Published: (2024)
by: Zhao, Wan-Qian, et al.
Published: (2024)
JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures
by: Larey, Ariel, et al.
Published: (2026)
by: Larey, Ariel, et al.
Published: (2026)
Understanding the Natural Language of DNA using Encoder-Decoder Foundation Models with Byte-level Precision
by: Malusare, Aditya, et al.
Published: (2023)
by: Malusare, Aditya, et al.
Published: (2023)
A DNA Methylation Classification Model Predicts Organ and Disease Site
by: Lee, Keng-Jung, et al.
Published: (2025)
by: Lee, Keng-Jung, et al.
Published: (2025)
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA
by: Patel, Aman, et al.
Published: (2024)
by: Patel, Aman, et al.
Published: (2024)
CodonMoE: DNA Language Models for mRNA Analyses
by: Du, Shiyi, et al.
Published: (2025)
by: Du, Shiyi, et al.
Published: (2025)
DNA Fragments in Crude Oil Reveals Earth's Hidden History
by: Zhao, Wan-Qian, et al.
Published: (2024)
by: Zhao, Wan-Qian, et al.
Published: (2024)
Securing the Language of Life: Inheritable Watermarks from DNA Language Models to Proteins
by: Zhang, Zaixi, et al.
Published: (2025)
by: Zhang, Zaixi, et al.
Published: (2025)
Range-Limited Heaps' Law for Functional DNA Words in the Human Genome
by: Li, Wentian, et al.
Published: (2024)
by: Li, Wentian, et al.
Published: (2024)
GENERator: A Long-Context Generative Genomic Foundation Model
by: Wu, Wei, et al.
Published: (2025)
by: Wu, Wei, et al.
Published: (2025)
DNACHUNKER: Learnable Tokenization for DNA Language Models
by: Kim, Taewon, et al.
Published: (2026)
by: Kim, Taewon, et al.
Published: (2026)
Reverse-Complement Consistency for DNA Language Models
by: Ma, Mingqian
Published: (2025)
by: Ma, Mingqian
Published: (2025)
Probing 3D Chromatin Structure Awareness in Evo2 DNA Language Model
by: Lee, UkJin
Published: (2026)
by: Lee, UkJin
Published: (2026)
GeneZip: Region-Aware Compression for Long Context DNA Modeling
by: Zhao, Jianan, et al.
Published: (2026)
by: Zhao, Jianan, et al.
Published: (2026)
Motif Caller: Sequence Reconstruction for Motif-Based DNA Storage
by: Agarwal, Parv, et al.
Published: (2024)
by: Agarwal, Parv, et al.
Published: (2024)
PathoLM: Identifying pathogenicity from the DNA sequence through the Genome Foundation Model
by: Dip, Sajib Acharjee, et al.
Published: (2024)
by: Dip, Sajib Acharjee, et al.
Published: (2024)
Regulatory DNA sequence Design with Reinforcement Learning
by: Yang, Zhao, et al.
Published: (2025)
by: Yang, Zhao, et al.
Published: (2025)
BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects
by: Li, Hongyang, et al.
Published: (2025)
by: Li, Hongyang, et al.
Published: (2025)
Similar Items
-
Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification
by: Liu, Zicheng, et al.
Published: (2025) -
MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging
by: Li, Siyuan, et al.
Published: (2025) -
EnTao-GPM: DNA Foundation Model for Predicting the Germline Pathogenic Mutations
by: Lin, Zekai, et al.
Published: (2025) -
GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models
by: Liu, Zicheng, et al.
Published: (2024) -
VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling
by: Li, Siyuan, et al.
Published: (2024)