crypticbio 0.3.0

CrypticBio: A Large Multimodal Dataset for Visually Confusing Biodiversity

CrypticBio: A Large Multimodal Dataset for Visually Confusing Biodiversity

We present CrypticBio, the largest publicly available multimodal dataset of visually confusing species groups, specifically curated to support the development of AI models in the context of biodiversity identification applications. Visually confusing or cryptic species are groups of two or more taxa that are nearly indistinguishable based on visual characteristics alone. We open source-data the data pipeline, CrypticBio-Curate, which allows for custom subsets curation.

Data Preprocessing

Before using this script, download the metadata from the Hugging Face repo.

Models

We evaluate state-of-the-art CLIP-style models trained on biodiversity data using the scientific and vernacular terminology of species. We use BioCLIP; BioTrove-CLIP's BioCLIP ViT-B-16 and OpenAI ViT-B-16 fine-tuned variants; and TaxaBind as image-only baseline models. For multimodal learning, we add embeddings obtained from the image encoders to those obtained from TaxaBind location and environmental features encoders, which are then used for zero-shot classification. We collect from WorldClim-2.1 environmental features for each observation based on the location metadata, which are then passed through TaxaBind's environmental encoder. We benchmark on all English available vernacular terminology, and we use species scientific term when the vernacular terminology is missing.

Name	Model URL
BioCLIP	https://github.com/kim2429/AmazonParrots/tree/main/Images
BioTrove-CLIP	https://huggingface.co/BGLab/BioTrove-CLIP
TaxaBind	https://huggingface.co/MVRL/taxabind-vit-b-16

Existing Benchmarks

We report results on the following established benchmarks from prior scientific literature: Amazon Parrots, Chiroptera Rhinolophidae Rhinolophus, and Squamata Lacertidae Podarcis. We also introduce four new benchmarks: CrytpitcBio-Common, CrypticBio-CommonUnseen, CrytpicBio-Endangered, and CrytpicBio-Invasive, avaiable in the Hugging Face repo.

Our package expects a valid path to each image to exist in its corresponding metadata file; therefore, metadata CSV paths must be updated before running each benchmark.

Name	Original Source	Metadata	Images
Amazon Parrots	https://github.com/kim2429/AmazonParrots/tree/main/Images	exisitng_benchmarks/AmazonParrots.csv
Chiroptera Rhinolophidae Rhinolophus	https://zenodo.org/records/10613387	exisitng_benchmarks/ChiropteraRhinolophidaeRhinolophus.csv
Squamata Lacertidae Podarcis	https://tinyurl.com/ Podarcis-images	exisitng_benchmarks/SquamataLacertidaePodarcis.csv
Bumble Bees	not publicly available	-	-
Confounding Species	not publicly available	-	-
Sea Turtles	not publicly available	-	-

Acknowledgments

Parts of this project page were adopted from the Nerfies page.

Website License

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.