A Phylogenetic Approach to Genomic Language Modeling
Fuente:
arXiv
Saved in:
| Main Authors: | Albors, Carlos, Li, Jianan Canal, Benegas, Gonzalo, Ye, Chengzhong, Song, Yun S. |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Genomic Language Models: Opportunities and Challenges
by: Benegas, Gonzalo, et al.
Published: (2024)
by: Benegas, Gonzalo, et al.
Published: (2024)
Genome-Factory: A Library for Tuning, Deploying, and Interpreting Genomic Foundation Models
by: Wu, Weimin, et al.
Published: (2025)
by: Wu, Weimin, 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)
Quantifying Memorization and Privacy Risks in Genomic Language Models
by: Nemecek, Alexander, et al.
Published: (2026)
by: Nemecek, Alexander, et al.
Published: (2026)
Uncertainty-Aware Genomic Classification of Alzheimer's Disease: A Transformer-Based Ensemble Approach with Monte Carlo Dropout
by: Jo, Taeho, et al.
Published: (2025)
by: Jo, Taeho, et al.
Published: (2025)
Whole-Genome Phenotype Prediction with Machine Learning: Open Problems in Bacterial Genomics
by: James, Tamsin, et al.
Published: (2025)
by: James, Tamsin, et al.
Published: (2025)
HAD: Hybrid Architecture Distillation Outperforms Teacher in Genomic Sequence Modeling
by: Yang, Hexiong, et al.
Published: (2025)
by: Yang, Hexiong, et al.
Published: (2025)
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)
PlantBiMoE: A Bidirectional Foundation Model with SparseMoE for Plant Genomes
by: Lin, Kepeng, et al.
Published: (2025)
by: Lin, Kepeng, et al.
Published: (2025)
Efficient and Scalable Fine-Tune of Language Models for Genome Understanding
by: Zhan, Huixin, et al.
Published: (2024)
by: Zhan, Huixin, et al.
Published: (2024)
Celler:A Genomic Language Model for Long-Tailed Single-Cell Annotation
by: Zhao, Huan, et al.
Published: (2025)
by: Zhao, Huan, et al.
Published: (2025)
Whole Genome Transformer for Gene Interaction Effects in Microbiome Habitat Specificity
by: Li, Zhufeng, et al.
Published: (2024)
by: Li, Zhufeng, et al.
Published: (2024)
A Misclassification Network-Based Method for Comparative Genomic Analysis
by: He, Wan, et al.
Published: (2024)
by: He, Wan, et al.
Published: (2024)
Statistical Linear Models in Virus Genomic Alignment-free Classification: Application to Hepatitis C Viruses
by: Remita, Amine M., et al.
Published: (2019)
by: Remita, Amine M., et al.
Published: (2019)
Contrastive Deep Learning for Variant Detection in Wastewater Genomic Sequencing
by: Chinda, Adele, et al.
Published: (2025)
by: Chinda, Adele, et al.
Published: (2025)
Enhancing Downstream Analysis in Genome Sequencing: Species Classification While Basecalling
by: Kodra, Riselda, et al.
Published: (2025)
by: Kodra, Riselda, et al.
Published: (2025)
AGP: A Novel Arabidopsis thaliana Genomics-Phenomics Dataset and its HyperGraph Baseline Benchmarking
by: Serna-Aguilera, Manuel, et al.
Published: (2025)
by: Serna-Aguilera, Manuel, et al.
Published: (2025)
Explainable AI in Genomics: Transcription Factor Binding Site Prediction with Mixture of Experts
by: Tripathi, Aakash, et al.
Published: (2025)
by: Tripathi, Aakash, et al.
Published: (2025)
DNABERT-2: Fine-Tuning a Genomic Language Model for Colorectal Gene Enhancer Classification
by: King, Darren, et al.
Published: (2025)
by: King, Darren, et al.
Published: (2025)
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)
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)
CodonMoE: DNA Language Models for mRNA Analyses
by: Du, Shiyi, et al.
Published: (2025)
by: Du, Shiyi, et al.
Published: (2025)
Embedding Is (Almost) All You Need: Retrieval-Augmented Inference for Generalizable Genomic Prediction Tasks
by: Datta, Nirjhor, et al.
Published: (2025)
by: Datta, Nirjhor, et al.
Published: (2025)
Entropy, Disagreement, and the Limits of Foundation Models in Genomics
by: Rochkoulets, Maxime, et al.
Published: (2026)
by: Rochkoulets, Maxime, et al.
Published: (2026)
EvoLen: Evolution-Guided Tokenization for DNA Language Model
by: Huang, Nan, et al.
Published: (2026)
by: Huang, Nan, et al.
Published: (2026)
Rare Genomic Subtype Discovery from RNA-seq via Autoencoder Embeddings and Stability-Aware Clustering
by: Mezghiche, Alaa
Published: (2025)
by: Mezghiche, Alaa
Published: (2025)
Absorb & Escape: Overcoming Single Model Limitations in Generating Genomic Sequences
by: Li, Zehui, et al.
Published: (2024)
by: Li, Zehui, et al.
Published: (2024)
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)
Reverse-Complement Consistency for DNA Language Models
by: Ma, Mingqian
Published: (2025)
by: Ma, Mingqian
Published: (2025)
scMamba: A Pre-Trained Model for Single-Nucleus RNA Sequencing Analysis in Neurodegenerative Disorders
by: Oh, Gyutaek, et al.
Published: (2025)
by: Oh, Gyutaek, et al.
Published: (2025)
Towards Applying Large Language Models to Complement Single-Cell Foundation Models
by: Palayew, Steven, et al.
Published: (2025)
by: Palayew, Steven, 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)
GenoBERT: A Language Model for Accurate Genotype Imputation
by: Huang, Lei, et al.
Published: (2026)
by: Huang, Lei, et al.
Published: (2026)
How Effectively Can Large Language Models Connect SNP Variants and ECG Phenotypes for Cardiovascular Risk Prediction?
by: Menon, Niranjana Arun, et al.
Published: (2025)
by: Menon, Niranjana Arun, et al.
Published: (2025)
BEND: Benchmarking DNA Language Models on biologically meaningful tasks
by: Marin, Frederikke Isa, et al.
Published: (2023)
by: Marin, Frederikke Isa, et al.
Published: (2023)
JanusDNA: A Powerful Bi-directional Hybrid DNA Foundation Model
by: Duan, Qihao, et al.
Published: (2025)
by: Duan, Qihao, et al.
Published: (2025)
A SARS-CoV-2 Interaction Dataset and VHH Sequence Corpus for Antibody Language Models
by: Tsuruta, Hirofumi, et al.
Published: (2024)
by: Tsuruta, Hirofumi, et al.
Published: (2024)
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)
GeneZip: Region-Aware Compression for Long Context DNA Modeling
by: Zhao, Jianan, et al.
Published: (2026)
by: Zhao, Jianan, et al.
Published: (2026)
HyperHELM: Hyperbolic Hierarchy Encoding for mRNA Language Modeling
by: van Spengler, Max, et al.
Published: (2025)
by: van Spengler, Max, et al.
Published: (2025)
Similar Items
-
Genomic Language Models: Opportunities and Challenges
by: Benegas, Gonzalo, et al.
Published: (2024) -
Genome-Factory: A Library for Tuning, Deploying, and Interpreting Genomic Foundation Models
by: Wu, Weimin, et al.
Published: (2025) -
GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models
by: Liu, Zicheng, et al.
Published: (2024) -
Quantifying Memorization and Privacy Risks in Genomic Language Models
by: Nemecek, Alexander, et al.
Published: (2026) -
Uncertainty-Aware Genomic Classification of Alzheimer's Disease: A Transformer-Based Ensemble Approach with Monte Carlo Dropout
by: Jo, Taeho, et al.
Published: (2025)