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README.md

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 # Pretraining Foundation Models: Unleashing the Power of Forgotten Spectra for Advanced Geological Applications
 
-The dataset for masked autoencoder for X-ray fluorescence. For more information, please checkout https://github.com/dispink/xpt.
+The dataset for masked autoencoder for X-ray fluorescence (XRF) is a following development after the dataset [(Chao et al., 2022)](https://doi.org/10.1594/PANGAEA.949225). 
+Besides the published XRF spectra-target measurements (CaCO3 and TOC) pairs of data, we further upload the XRF spectra in that project but without alignments of the target measurements here.
+They are compiled in a machine learning ready format, which we expect for convenient implementation of other studies.
 
-TODO: Update the README.md
+The investigated cores, which form the datast, are mostly retrieved across the high- to mid-latitude Northwest Pacific (37°N-52°N) and the Pacific sector of the Southern Ocean (53°S-63°S), with a water depth coverage from 1211 to 4853 m: 
+1. Cruise SO264 in the subarctic Northwest Pacific with R/V SONNE in 2018
+2. Cruise PS97 in the central Drake Passage with RV Polarstern in 2016
+3. Cruise PS75 in the Pacific sector of the Southern Ocean in 2009/2010.
+4. Cruise KOMEX I and KOMEX II with R/V Akademik Lavrentyev in 1998 and cruise SO178 in 2004 in the Okhotsk Sea. 
+
+For more information, please checkout the published paper [(Lee et al., 2022)](https://doi.org/10.1038/s41598-022-25377-x) and previous dataset [(Chao et al., 2022)](https://doi.org/10.1594/PANGAEA.949225).
+The direct use of this dataset is documented in the GitHub [repo](https://github.com/dispink/xpt).
+
+**Data structure**
+  - **raw**: Raw spectra in the Avaatech XRF Core Scanner format. Each subfolder contains the raw data for a core series.
+  - **legacy**: Previously compiled and raw data in [(Lee et al., 2022)](https://doi.org/10.1038/s41598-022-25377-x). 
+  - **pretrain**: Data used for pre-training and is built from the previously compiled spectra data `legacy/spe_dataset_20220629.csv`. The `train` subfolder has the training and validation sets. The `test` subfolder contains the data selected during fine-tuning as the zero-shot test, i.e., case study in the published paper.
+
+  ```    
+      +- train
+          +- spe      (all spetra)
+          +- info.csv (training set spectrum list)
+          +- val.csv  (validation set spectrum list)
+      +- test
+          +- spe
+          +- info.csv (case study spectrum list)
+  ```
+  - **fine-tune**: Data used for fine-tuning. The `train` subfolder has the training and validation sets. The `test` subfolder is the data for zero-shot test, i.e., case study in the published paper.
+  ``` 
+      +- CaCO3%   
+          +- train
+              +- spe        (all spetra)
+              +- target     (all target measurements)
+              +- info.csv   (training set spectrum-target pair list)
+              +- info_#.csv (splits from the info.csv in different data amounts) 
+              +- val.csv    (validation set spectrum-target pair list)
+          +- test
+              (same as in train)
+      +- TOC%
+          (same as in CaCO3%)
+  ```
+
+The target data (CaCO3 and TOC) distribution:
+![Data distribution](https://github.com/dispink/xpt/blob/dev/files/data_hist.png)
+
+
+The case study (i.e., test set) is composed of three cores ('PS75-056-1', 'LV28-44-3', 'SO264-69-2') isolated from the beginning and not used in both the pre-training and fine-tuning process. 
+The rest of data are randomly split in to the trainging and validation sets wtih 4:2 ratio.
+The script is `src/datas/build_data.py` in the GitHub [repo](https://github.com/dispink/xpt).
+
+**Acknowledgements**
+We thank the crew and the science parties of different cruises for their contributions to core and sample acquisition on the respective expeditions.
+We are very grateful to Dr. Weng‐Si Chao, Dr. Lester Lembke‐Jene, and Dr. Frank Lamy for providing these data.
+We also sincerely thank Valéa Schumacher, Susanne Wiebe, and Rita Fröhlking and student assistants at the AWI Marine Geology Laboratory in Bremerhaven for technical assistance with XRF-scanning, CaCO3 and TOC measurements.