4 citations · 10 across the 4 of their papers we have counts for
5 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]…
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…
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…
BIOSCAN-5M: A Multimodal Dataset for Insect Biodiversity
Zahra Gharaee, Scott C. Lowe, ZeMing Gong +10
As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establ…
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…