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README.md
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# Model Card for DuoduoCLIP
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In this model repo we provide the official pretrained models used in the paper **CLIBD: Bridging Vision and Genomics for Biodiversity Monitoring at Scale.**
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The model usage and code can be found in the [github repo](https://github.com/bioscan-ml/clibd).
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***Note: We provide the main model in the initial release, we will soon upload the other models used in the paper.***
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## Model Details
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### Model Description
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- **Finetuned from model:**
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-image: timm model (["vit_base_patch16_224"](https://huggingface.co/3dlg-hcvc/DuoduoCLIP))
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-DNA barcode: BarcodeBERT ["bioscanr/barcodeBERT pre-trained on CANADA-1.5M"](https://huggingface.co/bioscan-ml/bioscan-clibd/tree/main/ckpt/BarcodeBERT/5_mer)
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-text: Pre-trained BERT model (["prajjwal1/bert-small"](https://huggingface.co/prajjwal1/bert-small))
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### Model Sources
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- **Repository:** https://github.com/bioscan-ml/clibd
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- **Paper:** https://arxiv.org/abs/2405.17537
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### Model Checkpoints
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- **ckpt/bioscan_clip/final_experiments/image_dna_4gpu_50epoch/best.pth:** The model trained on the BIOSCAN-1M dataset by aligning images and DNA.
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- **ckpt/bioscan_clip/final_experiments/image_dna_text_4gpu_50epoch/best.pth:** The model trained on the BIOSCAN-1M dataset by aligning images, DNA, and taxonomy labels.
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- **ckpt/bioscan_clip/new_5M_training/image_dna_4gpu_50epoch/best.pth:** The model trained on the BIOSCAN-5M dataset by aligning images and DNA.
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- **ckpt/bioscan_clip/new_5M_training/image_dna_text_4gpu_50epoch/best.pth:** The model trained on the BIOSCAN-5M dataset by aligning images, DNA, and taxonomy labels.
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## Training Data
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-[BIOSCAN-1M](https://huggingface.co/datasets/bioscan-ml/BIOSCAN-1M).
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-[BIOSCAN-5M](https://huggingface.co/datasets/bioscan-ml/BIOSCAN-5M).
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You can also find the processed data from [here](https://huggingface.co/datasets/bioscan-ml/bioscan-clibd)
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**BibTeX:**
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```bibtex
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@article{gong2024clibd,
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title={{CLIBD}: Bridging Vision and Genomics for Biodiversity Monitoring at Scale},
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author={Gong, ZeMing and Wang, Austin T. and Huo, Xiaoliang and Haurum, Joakim Bruslund and Lowe, Scott C. and Taylor, Graham W. and Chang, Angel X.},
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journal={arXiv preprint arXiv:2405.17537},
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year={2024},
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eprint={2405.17537},
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archivePrefix={arXiv},
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primaryClass={cs.AI},
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doi={10.48550/arxiv.2405.17537},
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}
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```
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We would like to express our gratitude for the use of the INSECT dataset, which played a pivotal role in the completion of our experiments. Additionally, we acknowledge the use and modification of code from the [Fine-Grained-ZSL-with-DNA](https://github.com/sbadirli/Fine-Grained-ZSL-with-DNA) repository, which facilitated part of our experimental work. The contributions of these resources have been invaluable to our project, and we appreciate the efforts of all developers and researchers involved.
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This reseach was supported by the Government of Canada’s New Frontiers in Research Fund (NFRF) [NFRFT-2020-00073],
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Canada CIFAR AI Chair grants, and the Pioneer Centre for AI (DNRF grant number P1).
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This research was also enabled in part by support provided by the Digital Research Alliance of Canada (alliancecan.ca).
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