4 citations · 9 across the 7 of their papers we have counts for
5 papers · 1 filter
BarcodeMamba+: Advancing State-Space Models for Fungal Biodiversity Research
Tiancheng Gao, Scott C. Lowe, Brendan Furneaux +2
Accurate taxonomic classification from DNA barcodes is a cornerstone of global biodiversity monitoring, yet fungi present extreme challenges due to sparse labelling and long-tailed…
Hyperbolic Multimodal Representation Learning for Biological Taxonomies
ZeMing Gong, Chuanqi Tang, Xiaoliang Huo +6
Taxonomic classification in biodiversity research involves organizing biological specimens into structured hierarchies based on evidence, which can come from multiple modalities su…
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…
An Empirical Study into Clustering of Unseen Datasets with Self-Supervised Encoders
Scott C. Lowe, Joakim Bruslund Haurum, Sageev Oore +2
Can pretrained models generalize to new datasets without any retraining? We deploy pretrained image models on datasets they were not trained for, and investigate whether their embe…
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…