added readme

README.md

@@ -1,3 +1,142 @@
----
-license: mit
----
+---
+License: cc0-1.0
+language:
+- en
+pretty_name: BioTrove
+task_categories:
+- image-classification
+- zero-shot-classification
+tags:
+- biology
+- image
+- animals
+- species
+- taxonomy
+- rare species
+- endangered species
+- evolutionary biology
+- balanced
+- CV
+- multimodal
+- CLIP
+- knowledge-guided
+size_categories: 100M<n<1B
+---
+
+# BioTrove: A Large Curated Image Dataset Enabling AI for Biodiversity
+
+<!-- Banner links -->
+<div style="text-align:center;">
+  <a href="https://baskargroup.github.io/BioTrove/ target="_blank">
+    <img src="https://img.shields.io/badge/Project%20Page-Visit-blue" alt="Project Page" style="margin-right:10px;">
+  </a>
+  <a href="https://github.com/baskargroup/BioTrove" target="_blank">
+    <img src="https://img.shields.io/badge/GitHub-Visit-lightgrey" alt="GitHub" style="margin-right:10px;">
+  </a>
+  <a href="https://pypi.org/project/arbor-process/" target="_blank">
+    <img src="https://img.shields.io/badge/PyPI-arbor--process%200.1.0-orange" alt="PyPI biotrove-process 0.1.0">
+  </a>
+</div>
+
+## Description
+
+[BioTrove](https://baskargroup.github.io/BioTrove/) comprises well-processed metadata with full taxa information and URLs pointing to image files. The metadata can be used to filter specific categories, visualize data distribution, and manage imbalance effectively. We provide a collection of software tools that enable users to easily download, access, and manipulate the dataset. 
+
+
+## BioTrove Dataset
+`BioTrove` comprises over `161.9M` images across several taxonomic groups- including Reptilia (reptiles), Plantae (plants), Mollusca (mollusks), Mammalia (mammals), Insecta (insects), Fungi (fungi), Aves (birds), Arachnida (arachnids), Animalia (animals), Amphibia (amphibians), and Actinopterygii (ray-finned fish).  
+These taxonomic groups were chosen to represent the span of species — outside of charismatic megafauna. The images in BioTrove span `366.6K`species. 
+Overall, this dataset nearly matches the state-of-the-art curated dataset (TREEOFLIFE-10M) in terms of species diversity, while comfortably exceeding it in terms of scale by a factor of nearly 16.2 times.
+
+## New Benchmark Datasets
+We created three new benchmark datasets for fine-grained image classification. In addition, we provide a new benchmark dataset for species recognition across various developmental Life-stages.
+
+### BioTrove-Balanced
+For balanced species distribution across the 7 categories, we curated `BioTrove-Balanced`. Each category includes up to 500 species, with 50 images per species.
+
+### BioTrove-Unseen
+To provide a robust benchmark for evaluating the generalization capability of models on unseen species, we curated `BioTrove-Unseen`. The test dataset was constructed by identifying species with fewer than 30 instances in BioTrove, ensuring that the dataset contains species that were unseen by BioTrove-CLIP. Each species contained 10 images.
+
+### BioTrove-LifeStages
+To assess the model’s ability to recognize species across various developmental stages, we curated `BioTrove-LifeStages`. This dataset has 20 labels in total and focuses on insects, since these species often exhibit significant visual differences across their lifespan. BioTrove-LifeStages contains five insect species and utilized the observation export feature on the iNaturalist platform to collect data from 2/1/2024 to 5/20/2024 to ensure no overlap with the training dataset. For each species, life stage filters (egg, larva, pupa, or adult) were applied.
+
+## Dataset Information
+
+- **Full Taxa Information**: Detailed metadata, including taxonomic hierarchy and image URLs.
+- **Comprehensive Metadata**: Enables filtering, visualization, and effective management of data imbalance.
+- **Software Tools**: Collection of tools for easy dataset access, download, and manipulation.
+- **Balanced Species Distribution**: Up to 500 species per category with 50 images per species.
+- **Unseen Species Benchmark**: Includes species with fewer than 30 instances to evaluate generalization capability.
+- **Life Stages Dataset**: Focuses on insects across various developmental stages.
+
+
+## BioTrove-CLIP Models
+
+**See the [BioTrove-CLIP](https://huggingface.co/BGLab/BioTrove-CLIP) model card on HuggingFace to download the trained model checkpoints**
+
+We released three trained model checkpoints in the [BioTrove-CLIP](https://huggingface.co/BGLab/BioTrove-CLIP) model card on HuggingFace. These CLIP-style models were trained on [BioTrove-40M](https://baskargroup.github.io/BioTrove/) for the following configurations: 
+
+- **BioTrove-CLIP-O:** Trained a ViT-B/16 backbone initialized from the [OpenCLIP's](https://github.com/mlfoundations/open_clip) checkpoint. The training was conducted for 40 epochs.
+- **BioTrove-CLIP-B:** Trained a ViT-B/16 backbone initialized from the [BioCLIP's](https://github.com/Imageomics/BioCLIP) checkpoint. The training was conducted for 8 epochs.
+- **BioTrove-CLIP-M:** Trained a ViT-L/14 backbone initialized from the [MetaCLIP's](https://github.com/facebookresearch/MetaCLIP) checkpoint. The training was conducted for 12 epochs.
+
+
+
+## Usage
+
+**To start using the BioTrove dataset, follow the instructions provided in the [GitHub](https://github.com/baskargroup/BioTrove). Model checkpoints are shared in the [model_ckpt](#directory) directory.**
+
+**Metadata files are included in the [Directory](#directory). Please download the metadata from the [Directory](#directory)** and pre-process the data using the [arbor_process](https://pypi.org/project/arbor-process/) PyPI library. The instructions to use the library can be found in [here](https://github.com/baskargroup/BioTrove/blob/main/Arbor-preprocess/README_arbor_process.md). The Readme file contains the detailed description of data preparation steps.
+
+### Directory
+```plaintext
+main/
+├── BioTrove/
+│   ├── chunk_0.csv
+│   ├── chunk_0.parquet
+│   ├── chunk_1.parquet
+│   ├── .
+│   ├── .
+│   ├── .
+│   └── chunk_2691.parquet
+├── BioTrove-benchmark/
+│   ├── BioTrove-Balanced.csv
+│   ├── BioTrove-Balanced.parquet
+│   ├── BioTrove-Lifestages.csv
+│   ├── BioTrove-Lifestages.parquet
+│   ├── BioTrove-Unseen.csv
+│   └──BioTrove-Unseen.parquet
+├──README.md
+└──.gitignore
+```
+
+### Acknowledgements
+This work was supported by the AI Research Institutes program supported by the NSF and USDA-NIFA under [AI Institute: for Resilient Agriculture](https://aiira.iastate.edu/), Award No. 2021-67021-35329. This was also
+partly supported by the NSF under CPS Frontier grant CNS-1954556. Also, we gratefully
+acknowledge the support of NYU IT [High Performance Computing](https://www.nyu.edu/life/information-technology/research-computing-services/high-performance-computing.html) resources, services, and staff
+expertise.
+
+
+<!--BibTex citation -->
+<section class="section" id="BibTeX">
+  <div class="container is-max-widescreen content">
+      <h2 class="title">Citation</h2>
+      If you find this dataset useful in your research, please consider citing our paper:
+      <pre><code>@misc{yang2024BioTrovelargemultimodaldataset,
+        title={BioTrove: A Large Multimodal Dataset Enabling AI for Biodiversity}, 
+        author={Chih-Hsuan Yang, Benjamin Feuer, Zaki Jubery, Zi K. Deng, Andre Nakkab,
+           Md Zahid Hasan, Shivani Chiranjeevi, Kelly Marshall, Nirmal Baishnab, Asheesh K Singh,
+            Arti Singh, Soumik Sarkar, Nirav Merchant, Chinmay Hegde, Baskar Ganapathysubramanian},
+        year={2024},
+        eprint={2406.17720},
+        archivePrefix={arXiv},
+        primaryClass={cs.CV},
+        url={https://arxiv.org/abs/2406.17720}, 
+  }</code></pre>
+  </div>
+</section>
+<!--End BibTex citation -->
+
+---
+
+For more details and access to the dataset, please visit the [Project Page](https://baskargroup.github.io/BioTrove/).