diff --git a/README.md b/README.md index 63969248e26258e995ec48235b0e93b7b80cd375..83119bb8b4c88c6f8bc1559d94af1b954985d2db 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ size_categories: datasets: - imageomics/TreeOfLife-200M description: >- - Pre-computed image embeddings for 200M+ images from the TreeOfLife-200M + Pre-computed image embeddings for all images from the TreeOfLife-200M dataset, sorted by taxonomic hierarchy for efficient filtered access via DuckDB. Multiple embedding model configs supported. No images stored. dataset_info: @@ -68,11 +68,55 @@ dataset_info: splits: - name: train num_examples: 233055986 + - config_name: bioclip-2.5-vith14_float16 + features: + - name: uuid + dtype: string + - name: emb + sequence: float16 + length: 1024 + - name: source_dataset + dtype: string + - name: source_id + dtype: string + - name: kingdom + dtype: string + - name: phylum + dtype: string + - name: class + dtype: string + - name: order + dtype: string + - name: family + dtype: string + - name: genus + dtype: string + - name: species + dtype: string + - name: scientific_name + dtype: string + - name: common_name + dtype: string + - name: publisher + dtype: string + - name: basisOfRecord + dtype: string + - name: identifier + dtype: string + - name: img_type + dtype: string + splits: + - name: train + num_examples: 233055986 configs: - config_name: bioclip-2_float16 data_files: - split: train path: bioclip-2_float16/*.parquet + - config_name: bioclip-2.5-vith14_float16 + data_files: + - split: train + path: bioclip-2.5-vith14_float16/*.parquet - config_name: darwins_finches data_files: - split: train @@ -85,12 +129,9 @@ configs: # TreeOfLife-200M Embeddings - -> **Work in progress.** This dataset and card are under active development. +Pre-computed image embeddings for all images from the [TreeOfLife-200M](https://huggingface.co/datasets/imageomics/TreeOfLife-200M) dataset (revision [94bbc0b](https://huggingface.co/datasets/imageomics/TreeOfLife-200M/commit/94bbc0b90cd26cbb15f94d3144941026f4b41213)), sorted by taxonomic hierarchy for efficient filtered access. -Pre-computed image embeddings for 200M+ images from the [TreeOfLife-200M](https://huggingface.co/datasets/imageomics/TreeOfLife-200M) dataset, sorted by taxonomic hierarchy for efficient filtered access. - -This repository hosts embedding **configs** for TreeOfLife-200M. Each config corresponds to a different embedding model and/or precision. Currently available: [BioCLIP 2](https://huggingface.co/imageomics/bioclip-2) (float16). Additional configs (e.g., [BioCLIP 2.5 Huge](https://huggingface.co/imageomics/bioclip-2.5-vith14)) will be added as new embeddings are generated. +This repository hosts embedding **configs** for TreeOfLife-200M. Each config corresponds to a different embedding model and/or precision. Currently available: [BioCLIP 2](https://huggingface.co/imageomics/bioclip-2) (float16) and [BioCLIP 2.5 Huge](https://huggingface.co/imageomics/bioclip-2.5-vith14) (float16, L2-normalized). Additional configs will be added as new embeddings are generated. We recommend using [DuckDB](https://duckdb.org/) to access this dataset. @@ -130,11 +171,16 @@ from datasets import load_dataset ds = load_dataset("imageomics/TreeOfLife-200M-Embeddings", "bioclip-2_float16") ``` -| Config | Model | Precision | Dimensions | Files | Size | Rows | -|--------|-------|-----------|------------|-------|------|------| -| `bioclip-2_float16` | [BioCLIP 2](https://huggingface.co/imageomics/bioclip-2) (ViT-L/14) | float16 | 768 | 666 | ~346 GB | 233,055,986 | -| `darwins_finches` | [BioCLIP 2](https://huggingface.co/imageomics/bioclip-2) (ViT-L/14) | float16 | 768 | 1 | ~1 MB | 677 | -| `wolf_sample` | [BioCLIP 2](https://huggingface.co/imageomics/bioclip-2) (ViT-L/14) | float16 | 768 | 1 | ~1.5 MB | 960 | +| Config | Model | Precision | Normalized | Dimensions | Files | Size | Rows | +|--------|-------|-----------|------------|------------|-------|------|------| +| `bioclip-2_float16` | [BioCLIP 2](https://huggingface.co/imageomics/bioclip-2) (ViT-L/14) | float16 | No | 768 | 666 | ~346 GB | 233,055,986 | +| `bioclip-2.5-vith14_float16` | [BioCLIP 2.5 Huge](https://huggingface.co/imageomics/bioclip-2.5-vith14) (ViT-H/14) | float16 | Yes (L2) | 1024 | 933 | ~457 GB | 233,055,986 | +| `darwins_finches` | [BioCLIP 2](https://huggingface.co/imageomics/bioclip-2) (ViT-L/14) | float16 | No | 768 | 1 | ~1 MB | 677 | +| `wolf_sample` | [BioCLIP 2](https://huggingface.co/imageomics/bioclip-2) (ViT-L/14) | float16 | No | 768 | 1 | ~1.5 MB | 960 | + +**Normalization:** +- `bioclip-2.5-vith14_float16` config stores **L2-normalized** embeddings +- `bioclip-2_float16` config stores **un-normalized** embeddings, which should be normalized before computing the cosine similarity. The `demo_subset/` directory contains small **curated subsets** of the full `bioclip-2_float16` TreeOfLife-200M embeddings, such as `darwins_finches` and @@ -182,6 +228,9 @@ TreeOfLife-200M-Embeddings/ ├── bioclip-2_float16/ # full dataset — 666 shards │ ├── train-00000-of-00666.parquet │ └── ... +├── bioclip-2.5-vith14_float16/ # full dataset — 933 shards +│ ├── train-00000-of-00933.parquet +│ └── ... └── demo_subset/ # curated subsets for quick experiments / demos ├── darwins_finches/ │ └── bioclip-2_float16/ @@ -208,7 +257,7 @@ We recommend using [DuckDB](https://duckdb.org/) to access this dataset. All exa The fastest and most reliable workflow is to download the config once, then run DuckDB queries against the local files. All filtered slices return in seconds thanks to ZSTD decompression and page-index predicate pushdown. -**Benchmark** ([Cardinal](https://www.osc.edu/resources/technical_support/supercomputers/cardinal) login node, single session): full download ~6 min at ~1 GB/s. Once local, a Felidae slice (152,867 rows, 466 MB) is extracted in ~6 s. +**Benchmark** ([Cardinal](https://www.osc.edu/resources/technical_support/supercomputers/cardinal) login node, single session, `bioclip-2_float16`): full download ~6 min at ~1 GB/s. Once local, a Felidae slice (152,867 rows, 466 MB) is extracted in ~6 s. #### 1. Download the config @@ -334,7 +383,7 @@ The [TreeOfLife-200M](https://huggingface.co/datasets/imageomics/TreeOfLife-200M 1. **Embedding generation.** All images in [TreeOfLife-200M](https://huggingface.co/datasets/imageomics/TreeOfLife-200M) are embedded using a vision foundation model (see [Configs](#configs) for model details). Each image produces a fixed-dimensional vector. 2. **Global sort.** All rows are sorted by `source_dataset > kingdom > phylum > class > order > family > genus > species > common_name`, so taxonomically similar rows are adjacent. This enables page-index predicate pushdown for fast filtered access. -3. **Precision.** Embedding precision is config-dependent (e.g., float16 for `bioclip-2_float16`). +3. **Precision & Normalization** Embedding precision is config-dependent (e.g., float16 for `bioclip-2_float16`, `bioclip-2.5-vith14_float16`). The `bioclip-2.5-vith14_float16` config is L2-normalized; `bioclip-2_float16` is not. 4. **Parquet write.** PyArrow writes files targeting ~500 MB each, with ZSTD level 3 compression, [page indexes](https://huggingface.co/docs/hub/en/datasets-data-files-configuration#dataset-viewer-size-limit-errors-toobigcontenterror), and 50,000-row row groups for optimal streaming and query performance. #### Source Data Producers @@ -431,6 +480,21 @@ Please also cite the source dataset and embedding model (include data sources as +**BioCLIP 2.5 Huge Model:** +```bibtex +@software{Gu_BioCLIP_2.5_Huge_model, + author = {Jianyang Gu and Samuel Stevens and Elizabeth G Campolongo and Matthew J Thompson and Net Zhang and Jiaman Wu and Andrei Kopanev and Zheda Mai and Alexander E. White and James Balhoff and Wasila M Dahdul and Daniel Rubenstein and Hilmar Lapp and Tanya Berger-Wolf and Wei-Lun Chao and Yu Su}, + license = {MIT}, + title = {{BioCLIP 2.5 Huge}}, + url = {https://huggingface.co/imageomics/bioclip-2.5-vith14}, + version = {1.0.0}, + doi = {10.57967/hf/10131}, + publisher = {Hugging Face}, + year = {2026} +} +``` + + ## Acknowledgements diff --git a/bioclip-2.5-vith14_float16/train-00000-of-00933.parquet b/bioclip-2.5-vith14_float16/train-00000-of-00933.parquet new file mode 100644 index 0000000000000000000000000000000000000000..ce8cd64c1a5220b34b8a2a924942d4c3c6a06982 --- /dev/null +++ b/bioclip-2.5-vith14_float16/train-00000-of-00933.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:96de57da612c2e3e513d1cde32e4edec534fb14556b917c2db41d366fbae04b5 +size 488162203 diff --git a/bioclip-2.5-vith14_float16/train-00001-of-00933.parquet b/bioclip-2.5-vith14_float16/train-00001-of-00933.parquet new file mode 100644 index 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