Cover Image

Genomic Next-Token Predictors are In-Context Learners

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Breslow, Nathan, Mishra, Aayush, Revsine, Mahler, Schatz, Michael C., Liu, Anqi, Khashabi, Daniel
Format:	Preprint
Published:	2025
Subjects:	Machine Learning Artificial Intelligence Genomics
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging
by: Li, Siyuan, et al.
Published: (2025)

Steered LLM Activations are Non-Surjective
by: Mishra, Aayush, et al.
Published: (2026)

IA2: Alignment with ICL Activations Improves Supervised Fine-Tuning
by: Mishra, Aayush, et al.
Published: (2025)

xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data
by: Gong, Jing, et al.
Published: (2023)

Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation
by: Wen, Hongzhi, et al.
Published: (2023)

Celler:A Genomic Language Model for Long-Tailed Single-Cell Annotation
by: Zhao, Huan, et al.
Published: (2025)

Multimodal 3D Genome Pre-training
by: Yang, Minghao, et al.
Published: (2025)

Enhanced Gene Selection in Single-Cell Genomics: Pre-Filtering Synergy and Reinforced Optimization
by: Zhang, Weiliang, et al.
Published: (2024)

Efficient and Scalable Fine-Tune of Language Models for Genome Understanding
by: Zhan, Huixin, et al.
Published: (2024)

Absorb & Escape: Overcoming Single Model Limitations in Generating Genomic Sequences
by: Li, Zehui, et al.
Published: (2024)

How Private Are DNA Embeddings? Inverting Foundation Model Representations of Genomic Sequences
by: Ouaari, Sofiane, et al.
Published: (2026)

GeneZip: Region-Aware Compression for Long Context DNA Modeling
by: Zhao, Jianan, et al.
Published: (2026)

DNABERT-2: Fine-Tuning a Genomic Language Model for Colorectal Gene Enhancer Classification
by: King, Darren, et al.
Published: (2025)

Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning
by: Li, Zehui, et al.
Published: (2025)

TEPI: Taxonomy-aware Embedding and Pseudo-Imaging for Scarcely-labeled Zero-shot Genome Classification
by: Aakur, Sathyanarayanan, et al.
Published: (2024)

Machine Learning-Based Genomic Linguistic Analysis (Gene Sequence Feature Learning): A Case Study on Predicting Heavy Metal Response Genes in Rice
by: Yang, Ruiqi, et al.
Published: (2025)

GenoBERT: A Language Model for Accurate Genotype Imputation
by: Huang, Lei, et al.
Published: (2026)

Do pretrained Transformers Learn In-Context by Gradient Descent?
by: Shen, Lingfeng, et al.
Published: (2023)

SynLeaF: A Dual-Stage Multimodal Fusion Framework for Synthetic Lethality Prediction Across Pan- and Single-Cancer Contexts
by: Xing, Zheming, et al.
Published: (2026)

Channel-Wise MLPs Improve the Generalization of Recurrent Convolutional Networks
by: Breslow, Nathan
Published: (2025)

Disentangling Genotype and Environment Specific Latent Features for Improved Trait Prediction using a Compositional Autoencoder
by: Powadi, Anirudha, et al.
Published: (2024)

Revolutionizing Genomics with Reinforcement Learning Techniques
by: Karami, Mohsen, et al.
Published: (2023)

Gene42: Long-Range Genomic Foundation Model With Dense Attention
by: Vishniakov, Kirill, et al.
Published: (2025)

F5C-finder: An Explainable and Ensemble Biological Language Model for Predicting 5-Formylcytidine Modifications on mRNA
by: Wang, Guohao, et al.
Published: (2024)

Continuous Diffusion Transformers for Designing Synthetic Regulatory Elements
by: Liu, Jonathan, et al.
Published: (2026)

Exploring the Potentials and Challenges of Using Large Language Models for the Analysis of Transcriptional Regulation of Long Non-coding RNAs
by: Wang, Wei, et al.
Published: (2024)

GenoTEX: An LLM Agent Benchmark for Automated Gene Expression Data Analysis
by: Liu, Haoyang, et al.
Published: (2024)

Identification of Prognostic Biomarkers for Stage III Non-Small Cell Lung Carcinoma in Female Nonsmokers Using Machine Learning
by: Zheng, Huili, et al.
Published: (2024)

GQVis: A Dataset of Genomics Data Questions and Visualizations for Generative AI
by: Walters, Skylar Sargent, et al.
Published: (2025)

Classification of autoimmune diseases from Peripheral blood TCR repertoires by multimodal multi-instance learning
by: Zhang, Ruihao, et al.
Published: (2025)

DP-DCAN: Differentially Private Deep Contrastive Autoencoder Network for Single-cell Clustering
by: Li, Huifa, et al.
Published: (2023)

Highly Accurate Disease Diagnosis and Highly Reproducible Biomarker Identification with PathFormer
by: Dong, Zehao, et al.
Published: (2024)

HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model
by: Ma, Mingqian, et al.
Published: (2025)

scSiameseClu: A Siamese Clustering Framework for Interpreting single-cell RNA Sequencing Data
by: Xu, Ping, et al.
Published: (2025)

Toward a Team of AI-made Scientists for Scientific Discovery from Gene Expression Data
by: Liu, Haoyang, et al.
Published: (2024)

DOGMA: Weaving Structural Information into Data-centric Single-cell Transcriptomics Analysis
by: Zhang, Ru, et al.
Published: (2026)

FGBERT: Function-Driven Pre-trained Gene Language Model for Metagenomics
by: Duan, ChenRui, et al.
Published: (2024)

DeepVRegulome: DNABERT-based deep-learning framework for predicting the functional impact of short genomic variants on the human regulome
by: Dutta, Pratik, et al.
Published: (2025)

Quantum-Boosted High-Fidelity Deep Learning
by: Wang, Feng-ao, et al.
Published: (2025)

Fusing Sequence Motifs and Pan-Genomic Features: Antimicrobial Resistance Prediction using an Explainable Lightweight 1D CNN-XGBoost Ensemble
by: Siddiqui, Md. Saiful Bari, et al.
Published: (2025)