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Chat Publications

Answer research questions based on publications from PubMed.

Introduction

You may have so many research questions about specific topics, such as:

  • What's the Long Covid?
  • Any papers mentioned relationships between TP53 gene and lung cancer?
  • More questions ...

You may find the answers from PubMed, but it is not easy to find the answers from so many publications. By using the state-of-the-art language models (LLM), such as Vicuna and ChatGPT, you can get the answers from publications easier.

But how to connect the LLM's (like Vicuna, ChatGPT) with publications from pubmed? This project provides a solution to connect the LLM's with publications from pubmed. It's based on LLM (Vicuna or ChatGPT), LLAMA index, LangChain, FastChat etc.

  • Do you want to connect your LLM's (like Vicuna, ChatGPT) with your own external data (such as publications from pubmed). You also can follow the python script as an example to build your own chatbot server.

  • If you want to know more details about LLM and LLAMA index, please access more resources

Examples

  1. What's the Long Covid? which papers mentioned it? Could you list all doi numbers of these papers?
# Vicuna
Answer: The Long Covid is a term used in several of the papers listed in the context information to refer to the long-term effects and persistence of COVID-19 symptoms and illness after acute infection. The papers that mention the Long Covid are:

1. with in/f\_lammation pro/f\_iling of \nlong-COVID and association with one-year recovery following \nhospitalisation in the UK: a prospective observational study. Preprint at \nmedRxiv <https://doi.org/10.1101/2021.12.13.21267471> (2021).
2. Taquet, M. et al. Incidence, co-occurrence, and evolution of long-COVID \nfeatures: a 6-month retrospective cohort study of 273,618 survivors of \nCOVID-19. PLoS Med. 18, e1003773 (2021).
3. Estiri, H. et al. Evolving phenotypes of non-hospitalized patients that \nindicate long COVID. BMC Med. 19, 249 (2021).
4. Caspersen, I. H., Magnus, P. & Trogstad, L. Excess risk and clusters of \nsymptoms a/f_ter COVID-19 in a large Norwegian cohort. Eur. J. Epidemiol. <https://doi.org/10.1007/s10654-022-00847-8> (2022).
5. Havervall, S. et al. Symptoms and functional impairment assessed 8 months \na/f_ter mild COVID-19 among health care workers. J. Am. Med. Assoc. 325, 2015\u20132016 (2021).
6. Blomberg, B. et al. Long COVID in a prospective cohort of home-isolated \npatients. Nat. Med. 27, 1607\u20131613 (2021).
7. Logue, J. K. et al. Sequelae in adults at 6 Months a/f_ter COVID-19 infection. \nJAMA Netw. Open 4, e210830 (2021).
8. Amin-Chowdhury, Z. et al. Characterising long COVID more than 6 \nmonths a/f_ter acute infection in adults; prospective longitudinal cohort
  1. Is ME/CFS a cause of fatigue?
# Vicuna
Yes, ME/CFS is a cause of fatigue.

No, ME/CFS is not a cause of fatigue.

I'm not sure.
  1. Which relationship is between Fatigue and ME/CFS?
# Vicuna
A. Fatigue is a symptom of ME/CFS
B. ME/CFS is a cause of fatigue
C. Fatigue is a cause of ME/CFS
D. There is no relationship between fatigue and ME/CFS

What is the answer?
  1. Which relationship is between Fatigue and Long Covid?
# Vicuna
A) Fatigue is a symptom of Long Covid
B) Long Covid is a cause of Fatigue
C) Fatigue is a symptom of Pathological Fatigue
D) Long Covid is a cause of Pathological Fatigue
E) Fatigue is a symptom of Pathological Fatigue and Long Covid is a cause of Pathological Fatigue

Answer: B) Long Covid is a cause of Fatigue

Explanation:
The text states that Long Covid can cause fatigue and that this fatigue is different from physiological fatigue, which is easily cured by rest. It also mentions that pathological fatigue may be caused by factors such as viral or bacterial infection, trauma, disease, or other cellular assault, and that the cellular metabolism changes do not always reset after providing energy for the defense/repair of the body. Therefore, Long Covid is a cause of fatigue, but it is not necessarily a cause of pathological fatigue.

Download all publication data (not full text, just title, abstract, authors, etc.) from PubMed

Please access here for more details.

How to run llm model with llama-index?

Clone the current repository

git clone https://github.com/yjcyxky/chat-publications.git
cd chat-publications

Option 1: Install dependencies for vicuna

Option 2: Install dependencies for RWKV

How to run ChatGPT with llama-index?

Assume your data is in the folder data/my-project.

How to build index for your own data?

python chatbot_chatgpt.py index -d data/my-project

How to query index for your own data?

python chatbot_chatgpt.py query -d data/my-project