Update README.md

README.md

@@ -2,12 +2,16 @@
 license: cc-by-4.0
 ---
 # Synthetic mass spectra dataset No. 1
-This is the first variant of the GC-EI-MS synthetic dataset generated by NEIMS and RASSP models from 4.8 million structures downloaded from ZINC. 
+This is the first variant of the GC-EI-MS synthetic dataset generated by [NEIMS] and [RASSP] models from 4.8 million structures downloaded from [ZINC 20].
 The overlap with version 2 is approximately 8k structures (negligible), so it's usable as an extension to synth2. If you're choosing between synth1
-and synth2, see section Dataset choice.
+and synth2, see section Dataset choice. 
+
+
+## Spectra generators 
+For generating this dataset, we used custom-trained NEIMS and RASSP models. We did this step because RASSP model is not publicly available and we wanted to 
+have more control over potential dataleaks in the context of further models stemming from this dataset. For better reproducibility we make the NIST splits 
+used for training NEIMS and RASSP models available in our [GitHub repository] (#TODO)
 
-For generating this dataset, we used the original NEIMS model downloaded from the official [NEIMS] repository. Since the [RASSP] model is not publicly available,
-we trained our own.
 
 ## Dataset creation
 
@@ -26,16 +30,22 @@ Lastly, we split each synthetic dataset into training, validation, and test sets
 ## Size
 
 ```text
-train.jsonl    4364715
-valid.jsonl    242489
-test.jsonl     242479
-TOTAL          4849737
+rassp_custom_gen/train.jsonl    4364744
+rassp_custom_gen/valid.jsonl    242486
+rassp_custom_gen/test.jsonl     242486
+TOTAL          4849716
+
+neims_custom_gen/train.jsonl    4364748
+neims_custom_gen/valid.jsonl    242483
+neims_custom_gen/test.jsonl     242485
+TOTAL          4849716
 ```
 
 
 ## Dataset choice
-If you're choosing between synth1 and synth2 (and don't need both), choose synth2. Its origin is better documented, custom-NEIMS spectra are of better quality
-and the NIST train sets for training the NEIMS and RASSP models (that generated synth2) are identical. Plus we make the NIST splits available in our [GitHub repository] (#TODO))
+If you're choosing between synth1 and synth2 (and don't need both), choose synth2. The origin of synth2 is better documented in the 3_datapreprocessing.ipynb notebook in our [GitHub repository], 
+even though the creation process is in essence the same for both datasets. There are the same compound in the splits of both RASSP and NEIMS generated datasets but some
+duplicities emerged, so the sets are not identical (!the scale of the leak is less than 10 compounds in over 2M set, so we call it negligible!)
 
 
 ## Data format
@@ -48,10 +58,14 @@ Each line of every file is a `json` comprising three items:
 "smiles":"CCC(C)C1CCCCN1C(=O)CNc1cccc(C#N)c1"}
 ```
 
+From the nature of the NEIMS spectra predictor, all NEIMS-generated peak intensities are in 2 decimals precision. RASSP generated intensities are not restricted in this way,
+so to save storage we rounded them up to 6 decimal places which is beyond recognition for our model in the downstream task.
+
 Our [preprint] (TODO) provides more information about the task background, the final finetuned model, and the experiments.
 
 
 
 [NEIMS]: https://github.com/brain-research/deep-molecular-massspec
 [RASSP]: https://github.com/thejonaslab/rassp-public
+[ZINC 20]: https://zinc20.docking.org/
 [GitHub repository]: TODO