Add offsides data from nsides by apoorvasrinivasan26 · Pull Request #110 · OpenBioML/chemnlp

apoorvasrinivasan26 · 2023-03-15T20:41:18Z

No description provided.

kjappelbaum · 2023-03-15T22:54:13Z

data/nsides/offsides/meta.yaml

+      description: Standard error of the PRR estimate
+      type: continuous
+      names:
+          - Proportional reporting ratio error


do you think this is something the model should be able to predict? (I'm just curious)

kjappelbaum · 2023-03-15T22:55:38Z

Overall, looks quite good to me. Your PR does not cause the pre-commit errors.
I'll check tomorrow more carefully, but I think we'll merge it in tomorrow. Thanks 💯

apoorvasrinivasan26 · 2023-03-15T23:03:25Z

No, I don't think the error can be predicted but it can be calculated based on other columns in the dataset like columns A, B C, and D.

apoorvasrinivasan26 · 2023-03-15T23:05:02Z

Great! Lmk if something doesn't work. I have another similar dataset in the works once that I will commit after this is merged

kjappelbaum · 2023-03-22T10:21:54Z

No, I don't think the error can be predicted but it can be calculated based on other columns in the dataset like columns A, B C, and D.

in this case, I would consider removing this column as it might add more confusion than signal to the model

kjappelbaum · 2023-03-22T10:22:36Z

Has this dataset been used in some benchmarks/papers?

Thanks again for your contribution 💯

kjappelbaum

Thanks again for your contribution; it would be great if we could address the comments/clarifications. Let me know if you want a discussion or need a hand

apoorvasrinivasan26 · 2023-03-29T17:00:16Z

@kjappelbaum I've removed those columns and yes, the dataset has been used in the following paper: https://pubmed.ncbi.nlm.nih.gov/22422992/

pls lmk if anything is unclear or if you'd like me to make further changes

kjappelbaum · 2023-03-30T05:59:26Z

Thanks a lot! Can you still remove the column from the target list in the .yml file? Thanks!

…emnlp into dataset_drugxdrug

apoorvasrinivasan26 · 2023-03-30T06:18:29Z

Done! Lmk if I missed anything else.

data/nsides/offsides/meta.yaml

kjappelbaum · 2023-04-03T08:36:19Z

data/nsides/offsides/meta.yaml

+    - id: mean_reporting_frequency
+      description: Proportion of reports for the drug that report the side effect
+      type: continuous
+      names:
+          - mean reporting frequency


is the absolute number something a model should be able to predict?

yeah, according to the paper, a model should be able to predict it

kjappelbaum · 2023-04-03T08:37:51Z

data/nsides/offsides/meta.yaml

+    - id: drug_concept_name
+      description: RxNorm name string for the drug
+      type: categorical
+    - id: condition_concept_name
+      description: MedDRA identifier for the side effect
+      type: categorical


Do we need both of them simultaneously for the ratio to be meaningful?
That is, a correct prompt would ask the model something like

"What is the proportional reporting ratio for for "

yeah, so the prompt would be "what is the PRR of <condition_concept_name> for the <drug_concept_name>?". higher PRR means higher reported side effect for that particular drug.

kjappelbaum · 2023-04-03T08:38:41Z

data/nsides/offsides/meta.yaml

+bibtex: "\n        @article{Tatonetti2012,\n        author = {Tatonetti, Nicholas P. and Ye, Peter P. and Daneshjou, Roxana and Altman, Russ B.},\n    \
+    \    title = {Data-driven prediction of drug effects and interactions},\n        journal = {Sci Transl Med},\n        volume = {4},\n        number\
+    \ = {125},\n        pages = {125ra31},\n        year = {2012},\n        doi = {10.1126/scitranslmed.3003377},\n        pmid = {22422992},\n        pmcid\
+    \ = {PMC3382018}\n        }\n        "


can we remove those newlines somehow and just have a multiline string? I can help with that

sure! i'll let you take care of it if thats ok

kjappelbaum · 2023-04-03T08:40:05Z

Sorry for being unclear with my last reviews. I have more suggestions, but I can also take care of them if you prefer. Thanks for your contribution!

Co-authored-by: Kevin M Jablonka <32935233+kjappelbaum@users.noreply.github.com>

data/offsides/meta.yaml

data/offsides/transform.py

MicPie

lgtm, I just added some minor changes to the text

kjappelbaum · 2023-05-08T21:10:22Z

data/offsides/meta.yaml

+    - id: drug_concept_name
+      description: RxNorm name string for the drug
+      type: categorical
+    - id: condition_concept_name
+      description: MedDRA identifier for the side effect
+      type: categorical


this will need to use prompt templates, I guess, because they are not independent.

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Apoorva Srinivasan and others added 2 commits March 29, 2023 09:51

updatign changes

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Merge branch 'OpenBioML:main' into dataset_drugxdrug

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Apoorva Srinivasan added 2 commits March 29, 2023 23:14

updating meta.yaml

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Merge branch 'dataset_drugxdrug' of github.com:apoorvasrinivasan26/ch…

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…emnlp into dataset_drugxdrug

apoorvasrinivasan26 requested a review from kjappelbaum April 1, 2023 19:10

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apoorvasrinivasan26 and others added 2 commits April 3, 2023 09:13

Update data/nsides/offsides/meta.yaml

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Co-authored-by: Kevin M Jablonka <32935233+kjappelbaum@users.noreply.github.com>

Update data/nsides/offsides/meta.yaml

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Co-authored-by: Kevin M Jablonka <32935233+kjappelbaum@users.noreply.github.com>

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kjappelbaum commented Apr 3, 2023

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