Embed-Search-Align: DNA Sequence Alignment using Transformer Models

Fuente: arXiv

Salvato in:

Dettagli Bibliografici
Autori principali:	Holur, Pavan, Enevoldsen, K. C., Rajesh, Shreyas, Mboning, Lajoyce, Georgiou, Thalia, Bouchard, Louis-S., Pellegrini, Matteo, Roychowdhury, Vwani
Natura:	Preprint
Pubblicazione:	2023
Soggetti:	Genomics Artificial Intelligence
Accesso online:	Acceder al recurso
Tags:	Aggiungi Tag Nessun Tag, puoi essere il primo ad aggiungerne!!

Documenti analoghi

Creating an AI Observer: Generative Semantic Workspaces
di: Holur, Pavan, et al.
Pubblicazione: (2024)

Beyond Fact Retrieval: Episodic Memory for RAG with Generative Semantic Workspaces
di: Rajesh, Shreyas, et al.
Pubblicazione: (2025)

Panini: Continual Learning in Token Space via Structured Memory
di: Rajesh, Shreyas, et al.
Pubblicazione: (2026)

Emergent invariance and scaling properties in the collective return dynamics of a stock market
di: Miyahara, Hideyuki, et al.
Pubblicazione: (2022)

DNA Sequence Classification with Compressors
di: Ozan, Şükrü
Pubblicazione: (2024)

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

Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA
di: Qiao, Lifeng, et al.
Pubblicazione: (2024)

Bridging Sequence-Structure Alignment in RNA Foundation Models
di: Yang, Heng, et al.
Pubblicazione: (2024)

Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling
di: Schiff, Yair, et al.
Pubblicazione: (2024)

Dy-mer: An Explainable DNA Sequence Representation Scheme using Dictionary Learning
di: Peng, Zhiyuan, et al.
Pubblicazione: (2024)

Motif Caller: Sequence Reconstruction for Motif-Based DNA Storage
di: Agarwal, Parv, et al.
Pubblicazione: (2024)

RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
di: Lindegger, Joël, et al.
Pubblicazione: (2023)

bDNA Medium: Secure Conversion of Raw Genomic Sequencing Data to Verifiable Cryptographic Objects
di: Lowy, Shoel
Pubblicazione: (2026)

eccDNAMamba: A Pre-Trained Model for Ultra-Long eccDNA Sequence Analysis
di: Liu, Zhenke, et al.
Pubblicazione: (2025)

A Benchmark Dataset for Multimodal Prediction of Enzymatic Function Coupling DNA Sequences and Natural Language
di: Zhang, Yuchen, et al.
Pubblicazione: (2024)

JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures
di: Larey, Ariel, et al.
Pubblicazione: (2026)

Biological Sequence Clustering: A Survey
di: Zhang, Simeng, et al.
Pubblicazione: (2026)

Murmur2Vec: A Hashing Based Solution For Embedding Generation Of COVID-19 Spike Sequences
di: Ali, Sarwan, et al.
Pubblicazione: (2025)

TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling
di: Yang, Qirong, et al.
Pubblicazione: (2025)

DiscDiff: Latent Diffusion Model for DNA Sequence Generation
di: Li, Zehui, et al.
Pubblicazione: (2024)

Finding low-complexity DNA sequences with longdust
di: Li, Heng, et al.
Pubblicazione: (2025)

Emerging Challenges in Molecular Paleontology: Misapplication of Environmental DNA Fragments and Misconception of Deamination as a Key Criterion for In Situ DNA Identification
di: Zhao, Wan-Qian, et al.
Pubblicazione: (2024)

MHASS: Microbiome HiFi Amplicon Sequencing Simulator
di: Howard-Stone, Rye, et al.
Pubblicazione: (2025)

Central Dogma Transformer III: Interpretable AI Across DNA, RNA, and Protein
di: Ota, Nobuyuki
Pubblicazione: (2026)

Investigating DNA words and their distributions across the tree of life
di: Koilakos, Charalampos, et al.
Pubblicazione: (2025)

DNAMotifTokenizer: Towards Biologically Informed Tokenization of Genomic Sequences
di: Zhou, Xiaoxiao, et al.
Pubblicazione: (2025)

DNA Fragments in Crude Oil Reveals Earth's Hidden History
di: Zhao, Wan-Qian, et al.
Pubblicazione: (2024)

DSBplot: Indels in DNA Double-strand Break Repair Experiments
di: Channagiri, Tejasvi, et al.
Pubblicazione: (2023)

Poisoning the Genome: Targeted Backdoor Attacks on DNA Foundation Models
di: Koilakos, Charalampos, et al.
Pubblicazione: (2026)

Range-Limited Heaps' Law for Functional DNA Words in the Human Genome
di: Li, Wentian, et al.
Pubblicazione: (2024)

A DNA Methylation Classification Model Predicts Organ and Disease Site
di: Lee, Keng-Jung, et al.
Pubblicazione: (2025)

ST-Align: A Multimodal Foundation Model for Image-Gene Alignment in Spatial Transcriptomics
di: Lin, Yuxiang, et al.
Pubblicazione: (2024)

A Graphical Method for Identifying Gene Clusters from RNA Sequencing Data
di: Patock, Jake R., et al.
Pubblicazione: (2025)

Interpretable DNA Sequence Classification via Dynamic Feature Generation in Decision Trees
di: Huynh, Nicolas, et al.
Pubblicazione: (2026)

The NPGS Sudan sorghum germplasm collection reveals a novel cluster of R genes associated with rust resistant
di: Hugo E. Cuevas, et al.
Pubblicazione: (2025)

In silico tool for identification of colorectal cancer from cell-free DNA biomarkers
di: Mathur, Kartavya, et al.
Pubblicazione: (2025)

Securing the Language of Life: Inheritable Watermarks from DNA Language Models to Proteins
di: Zhang, Zaixi, et al.
Pubblicazione: (2025)

Probing 3D Chromatin Structure Awareness in Evo2 DNA Language Model
di: Lee, UkJin
Pubblicazione: (2026)

Just-DNA-Seq, open-source personal genomics platform: longevity science for everyone
di: Anton, Kulaga, et al.
Pubblicazione: (2024)

SeekRBP: Leveraging Sequence-Structure Integration with Reinforcement Learning for Receptor-Binding Protein Identification
di: Luo, Xiling, et al.
Pubblicazione: (2026)