Journal Club [deferred]

GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information 

Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu 

National Library of Medicine, National Institutes of Health
University of Maryland, College Park

https://arxiv.org/pdf/2304.09667.pdf 

Hackathon - GPT operation

GPT 1st month review

https://episphere.github.io/gpt 

https://bard.google.com 

ChatML

Operating markup languages emerging

• https://cobusgreyling.medium.com/the-introduction-of-chat-markup-language-chatml-is-important-for-a-number-of-reasons-5061f6fe2a85 

• https://github.com/openai/openai-cookbook/blob/main/examples/How_to_format_inputs_to_ChatGPT_models.ipynb 

• ... markup languages tend to develop fast, they are driven by missing abstractions. Keep an eye on this one.

API's lacking 

OpenAI ahead:

• https://platform.openai.com/overview

• https://openai.com/product#made-for-developers

• https://platform.openai.com/docs  <-- devs start here

Contextualize documents 

Yasmmin, Jeya, ...

Jeya: https://jeyabbalas.github.io/chat-pgs/ 

Yasmmin's test:

6. Evaluation and Rationale 6.1 Cancer in humans There is inadequate evidence  in humans for  the carcinogenicity of ortho -nitroanisole. 6.2 Cancer in experimental animals There is sufficient evidence  in experimental  animals for the carcinogenicity of ortho -  nitroanisole. 6.3 Mechanistic evidence There is strong evidence  that, in view of the  metabolism of ortho -nitroanisole to the aromatic amine ortho-anisidine, ortho-nitroanisole  belongs, based on mechanistic considerations,  to a class of aromatic amines for which several  members have been classified as carcinogenic  to humans. There is also strong evidence  that  ortho-nitroanisole exhibits key characteristics of  carcinogens in experimental systems.6.4 Overall evaluation ortho -Nitroanisole is probably carcinogenic to  humans  (Group 2A) . 6.5 Rationale The Group 2A evaluation is based on strong   mechanistic evidence. In view of the metab - olism of ortho -nitroanisole to the aromatic  amine ortho -anisidine, there is strong  evidence  that ortho -nitroanisole, based on mechanistic  considerations, belongs to a class of aromatic  amines for which several members have been  classified as carcinogenic to humans. ortho-Nitroanisole exhibits concordance with aromatic  amines with respect to the formation of common  DNA-reactive moieties, genotoxicity, and target  organs of carcinogenicity in chronic animal  bioassays.  There is also sufficient evidence  of carcino - genicity in experimental animals, based on an  increased incidence of malignant neoplasms in  two species. In addition, there is strong evidence  that  ortho -nitroanisole exhibits key characteristics of  carcinogens in experimental systems. ortho -Ni- troanisole is metabolically activated to elec - trophiles, it is genotoxic, and it also alters cell  proliferation, cell death, or nutrient supply. The evidence on cancer in humans was inad ­ equate  as no data were available.ortho -Nitroanisole

• Ge, Aaron (NIH/NCI) [F]10:43 AM
  GPT-4 Chatbot Guide: Mastering Embeddings and Personalized Knowledge Bases | by Ben Selleslagh | CodeX | Mar, 2023 | Medium
  GPT-4 Chatbot Guide: Mastering Embeddings and Personalized Knowledge Bases
  A guide on how to use the OpenAI embeddings endpoint to answer questions based on information you provide, such as company documentation or…
  medium.com1 Like reaction.1

• Someone already did something similar. Here... by Ge, Aaron (NIH/NCI) [F]Ge, Aaron (NIH/NCI) [F]10:44 AM
  Someone already did something similar. Here's an article about it

• yes aaron, i am trying to replicate it at s... by yasmmin (Guest)yasmmin (Guest)10:45 AMyes aaron, i am trying to replicate it at scale in javascript

• Link https://jeyabbalas.github.io/chat-pgs/ by Balasubramanian, Jeya (NIH/NCI) [E]Balasubramanian, Jeya (NIH/NCI) [E]10:50 AM
  https://jeyabbalas.github.io/chat-pgs/

• sk-aCl7RJ0DX6yZMRWZHyGdT3BlbkFJwvUDe5Hr13Uo... by Balasubramanian, Jeya (NIH/NCI) [E]Balasubramanian, Jeya (NIH/NCI) [E]10:51 AM
  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

• Link https://pubmed.ncbi.nlm.nih.gov/305547... by Balasubramanian, Jeya (NIH/NCI) [E]Balasubramanian, Jeya (NIH/NCI) [E]10:52 AM
  https://pubmed.ncbi.nlm.nih.gov/30554720/
  Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes - PubMed
  Stratification of women according to their risk of breast cancer based on polygenic risk scores (PRSs) could improve screening and prevention strategies. Our aim was to develop PRSs, optimized for ...
  pubmed.ncbi.nlm.nih.gov

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