update metadata format

README.md

@@ -6,4 +6,6 @@ license: pddl
  
 This dataset contains image-text pairs extracted from figures from papers in the [PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/) repository. The dataset can be used to train [CLIP](https://arxiv.org/abs/2103.00020) models.
 
-The data consists of a subset of papers from PMC stored as JSON objects in a jsonlines file. Each object contains the paper id of the paper (e.g. PMC7202302) and a list of extracted figures. For each figure, the caption (encoded in unicode) and the filename of the image is given. Note that the image files themselves are not included and have to be downloaded from the [FTP server](https://www.ncbi.nlm.nih.gov/pmc/tools/ftp/) (e.g. using the scripts provided in the [accompanying code repo](https://github.com/nopperl/clip_arxiv_pmc).
+This repo contains contains a [Parquet](https://parquet.apache.org/) file containing the metadata of a [WebDataset](https://github.com/webdataset/webdataset) in [img2dataset](https://github.com/rom1504/img2dataset) format. The images themselves are not distributed and need to be retrieved. Note that the images cannot be retrieved by an HTTP URL, so [img2dataset](https://github.com/rom1504/img2dataset) cannot be used as is to retrieve the data. Instead, the paper id (e.g. PMC7202302) and file name (e.g. gr3.jpg) are provided as identifier for each sample. The papers themselves can be downloaded from the [FTP server](https://www.ncbi.nlm.nih.gov/pmc/tools/ftp/).
+
+Furthermore, the repo contains a NumPy file which contains the uid of all samples that are not considered duplicates to the [DataComp](https://datacomp.ai) evaluation data. This file can be used to decontaminate the dataset.

ae4720b4a144e9e536c3776ebb756a31.json

@@ -0,0 +1 @@
+{"sample time (s)": 1036.3934926986694, "loader time (s)": 657.2324867248535, "number of samples": 770541}

pmc.jsonl → ae4720b4a144e9e536c3776ebb756a31.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:081ab89f5ed0970b2d299b1f0e4c6b81ae145caa265f0e94531cf0cbf95abe55
-size 416971085
+oid sha256:9dbc253686e7e2871681b5d43d5ef462f01f1c7bc0fd06deb2a420c56928ca3f
+size 209834912

decontaminated.npy

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2cbffb5cd769ffa3e0c18fb6e8d0109447076b8d66ec2657fae5e3f5e2a20dd1
+size 12269808