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jaybee84 / ml-in-rd

Manuscript for perspective on machine learning in rare disease
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Add snippets to references #234

Open jaybee84 opened 1 year ago

jaybee84 commented 1 year ago

Identify those references (≤ 10% of the total) that, in your opinion, represent key contributions to the field. Please add a short note (1–2 sentences) at the end of each of these references, explaining their importance.

jaybee84 commented 1 year ago

@allaway @jaclyn-taroni I forgot to mention this in the meeting today, but this is one thing that we can probably work on in parallel. Would you both like to select 2 references of your choice each from our ref list and add a couple of sentences to explain the key contributions?

jaybee84 commented 1 year ago

@jaclyn-taroni and @allaway would you like to list here which publications you would like to add snippet to? Just so that we can avoid working on the same ones.

allaway commented 1 year ago

I am thinking

A Literature-Based Knowledge Graph Embedding Method for Identifying Drug Repurposing Opportunities in Rare Diseases Daniel N. Sosa, Alexander Derry, Margaret Guo, Eric Wei, Connor Brinton, Russ B. Altman Biocomputing 2020 (2019-12) >https://doi.org/gmpgs7 DOI: 10.1142/9789811215636_0041 · ISBN: 9789811215629

and

Improving rare disease classication using imperfect knowledge graph Xuedong Li, Yue Wang, Dongwu Wang, Walter Yuan, Dezhong Peng, Qiaozhu Mei BMC Medical Informatics and Decision Making (2019-12) https://doi.org/gg5j65 DOI: 10.1186/s12911-019-0938-1 · PMID: 31801534 · PMCID: PMC6894101

What do you all think?

jaybee84 commented 1 year ago

@allaway My suggestion would be to pick one paper to represent KGs. We can add snippets to <10 papers from our ref list, so I was hoping we can touch upon one paper from each of the main concepts. What do you think?

allaway commented 1 year ago

Makes sense. How about substituting Li et al for

Quellec G, Lamard M, Conze PH, Massin P, Cochener B. Automatic detection of rare pathologies in fundus photographs using few-shot learning. Med Image Anal. 2020 Apr;61:101660. doi: 10.1016/j.media.2020.101660. Epub 2020 Jan 28. PMID: 32028213.

jaybee84 commented 1 year ago

Sounds good to me

jaybee84 commented 1 year ago

I have added three refs + snippets in #247.

Also thinking of adding:

Mao, W., Zaslavsky, E., Hartmann, B.M. et al. Pathway-level information extractor (PLIER) for gene expression data. Nat Methods 16, 607–610 (2019). https://doi.org/10.1038/s41592-019-0456-1