4 citations · 4 across the 2 of their papers we have counts for
3 papers
BarcodeMAE+: Rethinking Masked Pretraining and Global Representations for DNA Barcode Foundation Models
Monireh Safari, Pablo Millan Arias, Scott C. Lowe +3
Many DNA foundation models are pretrained by masking parts of a sequence and asking the model to reconstruct them. Standard masked pretraining exposes the encoder to special [MASK]…
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…
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…