Update descriptions by creature data subset

README.md

@@ -10,6 +10,13 @@ tags:
 - fish
 - bird
 - butterfly
+- image classification
+- zero-shot
+- traits
+- trait-detection
+- vlms
+- benchmarks
+- CV
 language:
 - en
 pretty_name: VLM4Bio
@@ -57,6 +64,9 @@ configs:
 ## 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.
@@ -80,18 +90,51 @@ English, Latin
 **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`).
+
+**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`).
+
+**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`:
+
+
+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
+#### 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/).
 
@@ -106,28 +149,32 @@ These images originate from various museum collections, including the following:
 
 [Phenoscape](https://kb.phenoscape.org/about/phenoscape/kb) and [FishBase](https://www.fishbase.se/search.php) were used to obtain the information on traits. 
 
-##### Bird
+- **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). 
 
-##### Butterflies
+- **Data Processing:**
 
-We created the Butterfly-10k dataset from the [Heliconius Collection (Cambridege Butterfly) dataset](https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly).
+  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.
 
-#### Data Processing
 
-##### Fish
-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.
+#### Butterflies
 
-##### Bird
+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 Bird-10k, we take 190 species for which the common name to scientific name mapping is available. This results in a fairly balanced dataset.
+  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:
 
-##### Butterfly
-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.
 
-- 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
 
@@ -157,10 +204,15 @@ None
 
 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. 
 
-## <mark>Licensing Information</mark>
-The data (images) contain a variety of licensing restrictions ranging from [CC0](https://creativecommons.org/publicdomain/zero/1.0/) to [CC BY-NC](https://creativecommons.org/licenses/by-nc/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).
+## 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 <mark>[license file](https://huggingface.co/datasets/sammarfy/VLM4Bio/blob/main/licenses.csv)</mark>.
+
+ - 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 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/).
+ - All the bird images are sourced from the [CUB-200-2011 dataset](https://www.vision.caltech.edu/datasets/cub_200_2011/), and are thus licensed under [Creative Commons Attribution (CC BY)](https://creativecommons.org/licenses/by/4.0/).
 
-<mark>This dataset (the compilation) has been licensed under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0).</mark> However, images may be licensed under different terms (as noted above). For license and citation information by image, see our <mark>[license file](https://huggingface.co/datasets/sammarfy/VLM4Bio/blob/main/licenses.csv)</mark>.
+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).
 
 
 ## Citation