README.md

---
license: cc-by-4.0
task_categories:
- visual-question-answering
- zero-shot-image-classification
- zero-shot-object-detection
tags:
- biology
- organism
- fish
- bird
- butterfly
- image classification
- zero-shot
- traits
- trait-detection
- vlms
- benchmarks
- CV
language:
- en
pretty_name: VLM4Bio
size_categories:
- 10K<n<100K
configs:
- config_name: Fish
  data_files:
  - split: species_classification
    path: datasets/Fish/metadata/metadata_10k.csv
  - split: species_classification_easy
    path: datasets/Fish/metadata/metadata_easy.csv
  - split: species_classification_medium
    path: datasets/Fish/metadata/metadata_medium.csv
  - split: species_classification_prompting
    path: datasets/Fish/metadata/metadata_prompting.csv
- config_name: Bird
  data_files:
  - split: species_classification
    path: datasets/Bird/metadata/metadata_10k.csv
  - split: species_classification_easy
    path: datasets/Bird/metadata/metadata_easy.csv
  - split: species_classification_medium
    path: datasets/Bird/metadata/metadata_medium.csv
  - split: species_classification_prompting
    path: datasets/Bird/metadata/metadata_prompting.csv
- config_name: Butterfly
  data_files:
  - split: species_classification
    path: datasets/Butterfly/metadata/metadata_10k.csv
  - split: species_classification_easy
    path: datasets/Butterfly/metadata/metadata_easy.csv
  - split: species_classification_medium
    path: datasets/Butterfly/metadata/metadata_medium.csv
  - split: species_classification_hard
    path: datasets/Butterfly/metadata/metadata_hard.csv
  - split: species_classification_prompting
    path: datasets/Butterfly/metadata/metadata_prompting.csv
---

# Dataset Card for VLM4Bio

![Alt text](assests/teaser.png)

## Dataset Details
VLM4Bio is a benchmark dataset of scientific question-answer pairs used to evaluate pretrained VLMs for trait discovery from biological images. VLM4Bio consists of images of three taxonomic groups of organisms: fish, birds, and butterflies, each containing around 10k images. 

- **Repository:** [VLM4Bio GitHub](https://github.com/Imageomics/VLM4Bio)
- **Paper:** [arXiv](https://arxiv.org/pdf/2408.16176)

### Dataset Description
VLM4Bio is a large, annotated dataset, consisting of 469K question-answer pairs involving around 30K images from three groups of organisms: fish, birds, and butterflies, covering five biologically relevant tasks.
The scientifically relevant tasks in organismal biology includes species classification, trait identification, trait grounding, trait referring, and trait counting.
These tasks are designed to test different facets of VLM performance in organismal biology, ranging from measuring predictive accuracy to assessing their ability to reason about their predictions using visual cues of known biological traits.
For example, the tasks of species classification test the ability of VLMs to discriminate between species, while in trait grounding and referring, we specifically test if VLMs are able to localize morphological traits (e.g., the presence of fins of fish or patterns and colors of birds) within the image.
We consider two types of questions in this dataset. First, we consider open-ended questions, where we do not provide any answer choices (or options) to the VLM in the input prompt.
The second type is multiple-choice (MC) questions, where we provide four choices of candidate answers for the VLM to choose from (out of which only one is correct while the remaining three are randomly selected from the set of all possible answers).

### Supported Tasks and Leaderboards
The following figure illustrates VLM4Bio tasks with different question types.
![Alt text](assests/tasks.png)

The following table demonstrates the leaderboard of the VLM baselines in terms of zero-shot accuracy.
![Alt text](assests/leaderboard.png)

### Languages
English, Latin

## Dataset Structure

**Instructions for downloading the dataset**

### Data Instances
<!--
Describe data files

Ex: All images are named <img_id>.png, each within a folder named for the species. They are 1024 x 1024, and the color has been standardized using <link to color standardization package>.
-->

### Data Fields

**Fish Files:**
- `identification_imagelist_10k.txt`:
- `identification_matrix.csv`:
- `imagelist_10k.txt`: List of image filenames for species classification and trait identification.
- `imagelist_500.txt`: 500 image subset of `imagelist_10k.txt` for trait detection and counting.
- `metadata_10k.csv`: Image filenames (`fileNameAsDelivered`, unique identifier) paired with their respective scientific names (`scientificName`).
- `metadata_500.csv`: 500 image subset of `metadata_10k.csv` for trait detection and counting. `ARKID` is unique identifier from Fish-AIR, links to full metadata information in `full_fish_metadata.csv`.
- `processed_identification_imagelist_10k.txt`: List of images included in the `processed_identification_matrix.csv`.
- `processed_identification_matrix.csv`: Presence/Absence indicator for 10 external (visible) traits: `eye`, `head`, `mouth`, `barbel`, `dorsal fin`, `two dorsal fins`, `adipose fin`, `pectoral fin`, `pelvic fin`, `anal fin`. Unique identifier is the `fileNameAsDelivered`, and scientific name is indicated (`scientificName`).

**Bird Files:**
- `bird_imagelist_10k.txt`: List of image filenames for species classification and trait identification.
- `bird_metadata_10k.csv`: Image filenames (`fileNameAsDelivered`, unique identifier) paired with their respective scientific names (`scientificName`).
- `identification.csv`:
- `processed_identification.csv`:
- `trait_category_map.pkl`:

**Butterfly Files:**
- `imagelist.txt`: List of image filenames for species classification.
- `metadata.csv`: Image filenames (`fileNameAsDelivered`, unique identifier) paired with their respective scientific names (`scientificName`).

VLM Prompts are determined through code available in the [GitHub Repository](https://github.com/Imageomics/VLM4Bio); they are summarized in the task diagram above.

### Data Splits

These images were all used for benchmarking current state-of-the-art VLMs on biological tasks.

### Curation Rationale
<!-- Motivation for the creation of this dataset. For instance, what you intended to study and why that required curation of a new dataset (or if it's newly collected data and why the data was collected (intended use)), etc. -->


### Source Data

We collected images of three taxonomic groups of organisms: fish, birds, and butterflies, each containing around 10k images. 

#### Fish

Images for fish (Fish-10k) were curated from the larger image collection, [Fish-AIR](https://fishair.org/), which contains images from the [Great Lakes Invasives Network (GLIN)](https://greatlakesinvasives.org/portal/index.php) and [Integrated Digitized Biocollections (iDigBio)](https://www.idigbio.org/).

These images originate from various museum collections, including the following:

- [Illinois Natural History Survey (INHS)](https://biocoll.inhs.illinois.edu/portal/index.php)
- [Minnesota Biodiversity Atlas, Bell Museum](https://bellatlas.umn.edu/index.php)
- [University of Michigan Museum of Zoology (UMMZ), Division of Fishes](https://ipt.lsa.umich.edu/resource?r=ummz\_fish)
- [University of Wisconsin-Madison Zoological Museum - Fish](http://zoology.wisc.edu/uwzm/)
- [Field Museum of Natural History (Zoology, FMNH) Fish Collection](https://fmipt.fieldmuseum.org/ipt/resource?r=fmnh_fishes)
- [The Ohio State University Fish Division, Museum of Biological Diversity (OSUM), Occurrence dataset](https://doi.org/10.15468/subsl8)

[Phenoscape](https://kb.phenoscape.org/about/phenoscape/kb) and [FishBase](https://www.fishbase.se/search.php) were used to obtain the information on traits. 

- **Data Processing:**

  We created the Fish-10k dataset by randomly sampling 10K images and preprocessing the images to crop and remove the background. For consistency, we leverage [GroundingDINO](https://arxiv.org/abs/2303.05499) to crop the fish body from the background and [Segment Anything Model (SAM)](https://arxiv.org/abs/2304.02643) to remove the background.
  This is the same processing done in [Fish-Vista](https://huggingface.co/datasets/imageomics/fish-vista), more details and the code is available [here](https://github.com/sajeedmehrab/Fish-Vista/tree/main/code/processing). 


#### Bird

We create the Bird-10k dataset from the [CUB-200-2011 dataset](https://www.vision.caltech.edu/datasets/cub_200_2011/). We obtain the scientific names from the [iNatLoc dataset](https://data.caltech.edu/records/ts54e-1jr46). 

- **Data Processing:**

  For Bird-10k, we take 190 species for which the common name to scientific name mapping is available. This results in a fairly balanced dataset. Please download the images following the directions under [Dataset Structure](#dataset-structure).


#### Butterflies

We created the Butterfly-10k dataset from the [Heliconius Collection (Cambridege Butterfly) dataset](https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly).

- **Data Processing:**

  For the Butterfly-10k, we carefully sampled 10K images from the Heliconius Collection dataset to ensure the images capture unique specimens and represent a diverse set of species. We adopt the following steps:

  - We filter out images with more than one image from the same view (i.e., dorsal or ventral).
  - We ensure each species has a minimum of 20 images and no more than 2,000 images.


### Annotations

##### Scientific Names
The scientific names for the images of **Fish-10k** and **Butterfly-10k** were obtained directly from their respective sources.

For **Bird-10k**, we obtained the scientific names from the [iNatLoc dataset](https://data.caltech.edu/records/ts54e-1jr46). 

In total, we curated around 31K question-answer pairs in both open and multiple-choice (MC) question-formats for evaluating species classification tasks. 

##### Trait information
The species-level trait presence/absence matrix for Fish-10k was manually curated with the help of biological experts co-authored in this paper. We leveraged the [Phenoscape knowledge base](https://kb.phenoscape.org/about/phenoscape/kb) and [FishBase](https://www.fishbase.se/search.php) along with manual annotations to procure the presence-absence trait information. We constructed approximately xK question-answer pairs for Fish-10k

For Bird-10k, we obtained the trait matrix from the attribute annotations provided along with CUB-200-2011. 

In total, we constructed approximately 380K question-answer pairs for trait identification tasks. 

##### Grounding and referring
For grounding and referring VQA tasks, the ground truths were manually annotated with the help of expert biologists on our team. We manually annotated bounding boxes corresponding to the traits of 500 fish specimens and 500 bird specimens, which are subsets of the larger Fish-10k and Bird-10k datasets, respectively. 
We used the CVAT tool for annotation.

### Personal and Sensitive Information

None

## Considerations for Using the Data

The fish-10 K and Butterfly-10K datasets are not balanced for the species classification task, while the bird-10 K dataset is balanced. Since the fish images are collected from different museums, they may inherit a small bias. 

## Licensing Information

This dataset (the compilation) has been licensed under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0). However, images may be licensed under different terms (as noted above). For license and citation information by image, see our [license file](https://huggingface.co/datasets/sammarfy/VLM4Bio/blob/main/licenses.csv).

 - The fish images are from [iDigBio](https://www.idigbio.org/) and [GLIN](https://greatlakesinvasives.org/portal/index.php), whose metadata and source URLs were accessed through [Fish-AIR](fishair.org). All iDigBio images are in the public domain ([CC0](https://creativecommons.org/publicdomain/zero/1.0/)). The GLIN images are all [CC BY-NC](https://creativecommons.org/licenses/by-nc/4.0/).
 - All the bird images are sourced from the [CUB-200-2011 dataset](https://www.vision.caltech.edu/datasets/cub_200_2011/); CalTech indicates that they do not own the copyrights to these images, and that their use is restricted to non-commercial research and educational purposes.
 - All butterfly images are from the Butterfly Genetics Group at University of Cambridge and are licensed under [Creative Commons Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/).

Each image in this dataset is provided under the least restrictive terms allowed by its licensing requirements as provided to us (i.e., we impose no additional restrictions past those specified by licenses in the license file).

We provide licensing information for every individual image within the fish and butterfly images in [license-metadata/fish-licenses.csv](license-metadata/fish-licenses.csv) and [license-metadata/butterfly-licenses.csv](license-metadata/butterfly-licenses.csv) respectively. The source_link and citation for each of the butterfly images can be obtained by matching the `record_number` field to the record numbers in [license-metadata/butterfly-licenses.json](license-metadata/butterfly-licenses.json). 

## Citation
Please cite our work as follows:

```
@misc{maruf2024vlm4bio,
      title={VLM4Bio: A Benchmark Dataset to Evaluate Pretrained Vision-Language Models for Trait Discovery from Biological Images}, 
      author={M. Maruf and Arka Daw and Kazi Sajeed Mehrab and Harish Babu Manogaran and Abhilash Neog and Medha Sawhney and Mridul Khurana and James P. Balhoff and Yasin Bakis and Bahadir Altintas and Matthew J. Thompson and Elizabeth G. Campolongo and Josef C. Uyeda and Hilmar Lapp and Henry L. Bart and Paula M. Mabee and Yu Su and Wei-Lun Chao and Charles Stewart and Tanya Berger-Wolf and Wasila Dahdul and Anuj Karpatne},
      year={2024},
      eprint={2408.16176},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url={https://arxiv.org/abs/2408.16176}, 
}
```

Please be sure to **also cite the original data sources** using all of the citations provided in the following:

- Sources for Fish-10k: [license-metadata/fish-data-bib.bib](license-metadata/fish-data-bib.bib).
- Sources for Bird-10k: [license-metadata/bird-data-bib.bib](license-metadata/bird-data-bib.bib)
- Sources for Butterfly-10k: [license-metadata/butterfly-data-bib.bib](license-metadata/butterfly-data-bib.bib)

## Acknowledgements

This work was supported by the Imageomics Institute, which is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under Award #2118240 (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.


## Dataset Card Authors

M. Maruf, Kazi Sajeed Mehrab and Elizabeth G. Campolongo

## Dataset Card Contact

[email protected], [email protected]