3 papers
cs.LG2025
BarcodeBERT: Transformers for Biodiversity Analysis
Pablo Millan Arias, Niousha Sadjadi, Monireh Safari +9
In the global challenge of understanding and characterizing biodiversity, short species-specific genomic sequences known as DNA barcodes play a critical role, enabling fine-grained…
cs.FL2025
Bridging Chaos Game Representations and -mer Frequencies of DNA Sequences
Haoze He, Lila Kari, Pablo Millan Arias
This paper establishes formal mathematical foundations linking Chaos Game Representations (CGR) of DNA sequences to their underlying -mer frequencies. We prove that the Frequenc…
cs.LG2025
Enhancing DNA Foundation Models to Address Masking Inefficiencies
Monireh Safari, Pablo Millan Arias, Scott C. Lowe +3
Masked language modelling (MLM) as a pretraining objective has been widely adopted in genomic sequence modelling. While pretrained models can successfully serve as encoders for var…