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Lessons Learned

  • The highest risk item is generation of the structured query (Cyphrer or SPARQL) from a plain English request. Some publications estimate success rate of about 48% on the first attempt.

  • The structure of the database used for queries matters. LLMs can easier produce meaningful structured queries for databases with flat, simple structure.

  • Practically useful system requires filtering or secondary mining of output in addition to natural language narration.

  • It is extremely important to implement a reliable named entity recognition system. The same acronym can refer to completely different entities, which can be differentiated either from the context (hard) or by asking clarifying questions. Must also map synonyms. Without these measures naïve queries in a RAG environment will fail.

  • LLMs may produce different structured queries starting from the same natural language question. These queries may be semantically and structurally correct, but may include assumptions on the limit of the number of items to return, or order, or lack of these. These variations are not deterministic. As a result on different execution rounds the same natural language may result in different answers. It is necessary to explicitly formulate the limits, order restrictions, and other parameters when asking the question, or to determine the user’s intentions in a conversation with a chain of thought. A question related to this topic, is whether specifics in the implementation of usual RAG models with a vector database may introduce implicit restrictions on what data is explored by the LLM and what data is not, and thus artificially limit the answers. This may be happening without the user knowing the restrictions (and perhaps even without the system’s authors knowing that they introduced such restrictions embedded in the specifics of the system architecture).

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  1. https://www.sciencedirect.com/science/article/pii/S1359644613001542

  2. https://www.nature.com/articles/s41573-020-0087-3

  3. https://www.epam.com/about/newsroom/press-releases/2023/epam-launches-dial-a-unified-generative-ai-orchestration-platform

  4. https://epam-rail.com/open-source

  5. Open LLM Leaderboard: https://huggingface.co/spaces/HuggingFaceH4/open_llm_leaderboard

  6. Chatbot Arena: https://chat.lmsys.org/?arena

  7. Reasoning on Graphs: Faithful and Interpretable Large Language Model Reasoning

    https://arxiv.org/abs/2310.01061

  8. Knowledge-Consistent Dialogue Generation with Language Models and Knowledge Graphs

    https://openreview.net/forum?id=WhWlYzUTJfP&source=post_page-----97a4cf96eb69--------------------------------

  9. BioChatter Benchmark Results: https://biochatter.org/benchmark-results/#biochatter-query-generation

  10. MBET Benchmark (embeddings) https://huggingface.co/spaces/mteb/leaderboard

  11. Lora-Land and Lorax: https://predibase.com/lora-land

  12. A Benchmark to Understand the Role of Knowledge Graphs on Large Language Model's Accuracy for Question Answering on Enterprise SQL Databases. Summary: queries over a KG with GPT 4 are much more accurate than queries over a SQL database with GPT 4. https://arxiv.org/abs/2311.07509

  13. https://towardsdatascience.com/evaluating-llms-in-cypher-statement-generation-c570884089b3

  14. https://medium.com/neo4j/enhancing-the-accuracy-of-rag-applications-with-knowledge-graphs-ad5e2ffab663

  15. linkedlifedata.com

  16. Kazu - Biomedical NLP Framework: https://github.com/AstraZeneca/KAZU

  17. https://github.com/f/awesome-chatgpt-prompts/tree/main

  18. Zhou, L., Schellaert, W., Martínez-Plumed, F. et al. Larger and more instructable language models become less reliable. Nature 634, 61–68 (2024). https://doi.org/10.1038/s41586-024-07930-y

  19. Karthik Soman, Peter W Rose, John H Morris, Rabia E Akbas, Brett Smith, Braian Peetoom, Catalina Villouta-Reyes, Gabriel Cerono, Yongmei Shi, Angela Rizk-Jackson, Sharat Israni, Charlotte A Nelson, Sui Huang, Sergio E Baranzini, Biomedical knowledge graph-optimized prompt generation for large language models, Bioinformatics, Volume 40, Issue 9, September 2024, btae560, https://doi.org/10.1093/bioinformatics/btae560

  20. https://www.promptingguide.ai/

  21. References on Named Entity Recognition in biological sciences: Pubmed

  22. Incremental Knowledge Graphs Constructor Using Large Language Models