Search
Close
Search
Advanced Search
Search Menu
AI Discovery Assistant

Abstract

Background and Aims

The rapidly growing scientific literature poses a significant challenge for researchers seeking to distill key insights. We utilized Retrieval-Augmented Generation (RAG), a novel AI-driven approach, to efficiently process and extract meaningful information from published literature on uremic toxins. RAG is a general AI framework for improving the quality of responses generated by Large Language Models (LLMs) by supplementing the LLM's internal representation of information with curated expert knowledge.

Method

First, we collected on PubMed all abstracts related to the topic of “uremic toxins” through Metapub, a Python library designed to facilitate fetching metadata from PubMed. Second, we set up a RAG system that comprises 2 steps. In a retrieval step, the questions on topic (“uremic toxins”) and the documents (=all collected abstracts and manuscripts) are encoded into vectors (i.e., high-dimensional numerical representations). Similarity measures are used to find the best matches between documents and the questions on topic. Second, in the augmented generation step, the LLM (e.g., ChatGPT) uses these best matches of documents to generate a coherent and informed response.

Results

We collected 3497 abstracts from the PubMed and 191 expert-curated publications in PDF format related to the topic “uremic toxin”. These 191 publications were broken down to 5756 documents, each with a manageable size of text. The final vector database comprised 9253 vectors. Using RAG, we requested responses from the LLM on multiple questions related to “uremic toxins”. Some examples are shown in Table 1. The first and second responses given by the LLM are reasonable. However, the third answer shows the phenomenon of ‘hallucination’—where models generate plausible and convincingly sounding yet factually incorrect information.

Conclusion

The use of RAG improves the capability of LLMs to answer questions by leveraging the information contained within curated abstracts and publications. Despite the improvements with RAG, the phenomenon of ‘hallucination’ persists. A concerning feature of hallucinations is their eloquent and convincing language. For the time being, LLM output—even when improved with RAG—requires scrutiny and human verification.

Table 1:
Open in new tab

Examples of questions and answers.

QuestionAnswer
What are Low-Molecular-Weight Water-Soluble Uremic Toxins?Low-Molecular-Weight Water-Soluble Uremic Toxins are small molecules with a molecular weight below 500 D that are soluble in water and easily removed by any dialysis strategy. Examples of these toxins include ADMA (asymmetric dimethylarginine), creatine, creatinine, hyaluronic acid, guanidine, guanidinoacetate, guanidinosuccinate, oxalate, SDMA (symmetric dimethylarginine), urea and uric acid.
Which are the most important molecules to remove in ESKD patient among the many middle molecules that we know buildup with kidney dysfunction?It is difficult to say which are the most important molecules to remove in ESKD patients among the many middle molecules that we know buildup with kidney dysfunction. The literature suggests that cytokines, adipokines, hormones, and other proteins with a molecular mass greater than 15 kD are implicated in chronic inflammation, atherosclerosis, structural heart disease, and secondary immunodeficiency. However, larger, robustly conducted, multicenter studies are needed to assess the perceived clinical benefits of providing clearance of large middle molecules.
Is hemodialysis or hemodiafiltration better in removing p-cresol sulfate?According to the studies Martinez et al. (2005) and De Smet et al. (2003), hemodialysis is not very effective in removing p-cresol sulfate because its clearance is limited by protein binding and the ratio of its volume of distribution to its clearance is high. However, the study by Kalim et al. (2018) suggests that hemodiafiltration is more effective in reducing indoxyl sulfate and p-cresyl sulfate compared to standard high-flux hemodialysis, and this effect was extended to p-cresyl sulfate in patients achieving higher convective volumes.
QuestionAnswer
What are Low-Molecular-Weight Water-Soluble Uremic Toxins?Low-Molecular-Weight Water-Soluble Uremic Toxins are small molecules with a molecular weight below 500 D that are soluble in water and easily removed by any dialysis strategy. Examples of these toxins include ADMA (asymmetric dimethylarginine), creatine, creatinine, hyaluronic acid, guanidine, guanidinoacetate, guanidinosuccinate, oxalate, SDMA (symmetric dimethylarginine), urea and uric acid.
Which are the most important molecules to remove in ESKD patient among the many middle molecules that we know buildup with kidney dysfunction?It is difficult to say which are the most important molecules to remove in ESKD patients among the many middle molecules that we know buildup with kidney dysfunction. The literature suggests that cytokines, adipokines, hormones, and other proteins with a molecular mass greater than 15 kD are implicated in chronic inflammation, atherosclerosis, structural heart disease, and secondary immunodeficiency. However, larger, robustly conducted, multicenter studies are needed to assess the perceived clinical benefits of providing clearance of large middle molecules.
Is hemodialysis or hemodiafiltration better in removing p-cresol sulfate?According to the studies Martinez et al. (2005) and De Smet et al. (2003), hemodialysis is not very effective in removing p-cresol sulfate because its clearance is limited by protein binding and the ratio of its volume of distribution to its clearance is high. However, the study by Kalim et al. (2018) suggests that hemodiafiltration is more effective in reducing indoxyl sulfate and p-cresyl sulfate compared to standard high-flux hemodialysis, and this effect was extended to p-cresyl sulfate in patients achieving higher convective volumes.
Table 1:
Open in new tab

Examples of questions and answers.

QuestionAnswer
What are Low-Molecular-Weight Water-Soluble Uremic Toxins?Low-Molecular-Weight Water-Soluble Uremic Toxins are small molecules with a molecular weight below 500 D that are soluble in water and easily removed by any dialysis strategy. Examples of these toxins include ADMA (asymmetric dimethylarginine), creatine, creatinine, hyaluronic acid, guanidine, guanidinoacetate, guanidinosuccinate, oxalate, SDMA (symmetric dimethylarginine), urea and uric acid.
Which are the most important molecules to remove in ESKD patient among the many middle molecules that we know buildup with kidney dysfunction?It is difficult to say which are the most important molecules to remove in ESKD patients among the many middle molecules that we know buildup with kidney dysfunction. The literature suggests that cytokines, adipokines, hormones, and other proteins with a molecular mass greater than 15 kD are implicated in chronic inflammation, atherosclerosis, structural heart disease, and secondary immunodeficiency. However, larger, robustly conducted, multicenter studies are needed to assess the perceived clinical benefits of providing clearance of large middle molecules.
Is hemodialysis or hemodiafiltration better in removing p-cresol sulfate?According to the studies Martinez et al. (2005) and De Smet et al. (2003), hemodialysis is not very effective in removing p-cresol sulfate because its clearance is limited by protein binding and the ratio of its volume of distribution to its clearance is high. However, the study by Kalim et al. (2018) suggests that hemodiafiltration is more effective in reducing indoxyl sulfate and p-cresyl sulfate compared to standard high-flux hemodialysis, and this effect was extended to p-cresyl sulfate in patients achieving higher convective volumes.
QuestionAnswer
What are Low-Molecular-Weight Water-Soluble Uremic Toxins?Low-Molecular-Weight Water-Soluble Uremic Toxins are small molecules with a molecular weight below 500 D that are soluble in water and easily removed by any dialysis strategy. Examples of these toxins include ADMA (asymmetric dimethylarginine), creatine, creatinine, hyaluronic acid, guanidine, guanidinoacetate, guanidinosuccinate, oxalate, SDMA (symmetric dimethylarginine), urea and uric acid.
Which are the most important molecules to remove in ESKD patient among the many middle molecules that we know buildup with kidney dysfunction?It is difficult to say which are the most important molecules to remove in ESKD patients among the many middle molecules that we know buildup with kidney dysfunction. The literature suggests that cytokines, adipokines, hormones, and other proteins with a molecular mass greater than 15 kD are implicated in chronic inflammation, atherosclerosis, structural heart disease, and secondary immunodeficiency. However, larger, robustly conducted, multicenter studies are needed to assess the perceived clinical benefits of providing clearance of large middle molecules.
Is hemodialysis or hemodiafiltration better in removing p-cresol sulfate?According to the studies Martinez et al. (2005) and De Smet et al. (2003), hemodialysis is not very effective in removing p-cresol sulfate because its clearance is limited by protein binding and the ratio of its volume of distribution to its clearance is high. However, the study by Kalim et al. (2018) suggests that hemodiafiltration is more effective in reducing indoxyl sulfate and p-cresyl sulfate compared to standard high-flux hemodialysis, and this effect was extended to p-cresyl sulfate in patients achieving higher convective volumes.
PDF
This content is only available as a PDF.
© The Author(s) 2024. Published by Oxford University Press on behalf of the ERA.
This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://dbpia.nl.go.kr/journals/pages/open_access/funder_policies/chorus/standard_publication_model)
Topic:
Issue Section:
C4 - CO-MORBIDITIES (ANAEMIA, CARDIOVASCULAR, CKD-MBD, ETC.)
Download all slides

Comments

0 Comments
Comments (0)
Submit a comment
You have entered an invalid code
Thank you for submitting a comment on this article. Your comment will be reviewed and published at the journal's discretion. Please check for further notifications by email.