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https://docs.google.com/presentation/d/1kpBzQXeyEREhfHOOFRhzpUXGdjx_p6CtCMv_QPADPHU/edit?usp=sharing
Our software is designed for the validation of knowledge graphs and the relationships between each node.
Our architecture extracts node-to-node relationships from open-source models for computational validation.
The large language model we utilized is called Vicuna.
Query data was obtained both from pubmed using edirect in conjunction with DisGeNET, where snp variant data was downloaded as tsv and used to create triplicate data in subject predicate subject form. The csv of the SPO objects can be found in SPO.csv. The DisGeNET SPO table can be found below and the literature used for prompting the LLM can be found in prompt.txt.
Table of SNPs Evaluated
| SNP | Diseases |
|---|---|
| rs113993960 | BRONCHIECTASIS |
| rs113993960 | Stenosis of duodenum |
| rs113993960 | Congenital bilateral aplasia of vas deferens |
| rs113993960 | Hereditary pancreatitis |
| rs113993960 | Recurrent pancreatitis |
| rs113993960 | Cystic Fibrosis |
| rs199473282 | LONG QT SYNDROME 3 |
| rs199473282 | Brugada Syndrome (disorder) |
| rs199473282 | Brugada Syndrome 1 |
| rs199473282 | Long QT Syndrome |
| rs199473282 | Hereditary bundle branch system defect |
| rs121909211 | Plaque, Amyloid |
| rs121909211 | Familial Amyloid Polyneuropathy, Type V |
| rs121909211 | Corneal dystrophy |
| rs121909211 | Corneal deposit |
| rs121909211 | Corneal Dystrophy, Lattice Type IIIA |
| rs121909211 | Dystrophy, granular |
| rs121909211 | Reis-Bucklers' corneal dystrophy |
| rs121909211 | Corneal guttata |
| rs121909211 | Lattice corneal dystrophy Type I |
| rs121909211 | Amyloidosis |
| rs121909211 | Neoplasms |
| rs121909211 | Granular Dystrophy, Corneal |
| rs121909211 | Thiel-Behnke corneal dystrophy |
| rs121909211 | Stromal Dystrophies, Corneal |
| rs121909211 | Avellino corneal dystrophy |
As an optional step we attempted to compress the abstracts into summaries to decrease the context window. We found that when the context was pushed past its recommended context window size it failed to write out accurate SPO objects. Therefore using GPT3.5 or 4 to summarize key abstracts could be instrumental in reconstructing knowledge graph SPO objects.
Asking a LLM to write out relationships as an RDF file typically fails across most models. We found that almost all models, with simple examples, can write out triplicate form SPO's. Below is table of models and their ability to write out different SPO's given the following prompts.
Prompt1: “User: Create subject predicate subject logic triplets using some motor vehicles and output it as a subject predicate subject logic triplet. An example subject predicate subject triplet could be Biliary Atresia - results in - biliary obstruction. Create 10 of these triplets. "
Prompt2: "User: Create subject predicate subject logic triplets using some genes and their disease associations and output it as a subject predicate subject logic triplet. An example subject predicate subject triplet could be Biliary Atresia - results in - biliary obstruction. Create 10 of these triplets.”
Prompt3: Found in prompt.txt
Table of RDF Evaluations of LLMs
| LLM | Prompt Type | Can write out SPO |
|---|---|---|
| Vicuna-7b | 1 | Yes |
| Vicuna-7b | 2 | Yes |
| Vicuna-7b | 3 | N/A |
| Vicuna-13b | 1 | Yes |
| Vicuna-13b | 2 | Yes |
| Vicuna-13b | 3 | N/A |
| llama2-7b | 1 | Yes |
| llama2-7b | 2 | No |
| llama2-7b | 3 | N/A |
| codellama2-7b | 1 | No |
| codellama2-7b | 2 | No |
| codellama2-7b | 3 | N/A |
| GPT | 1 | Yes |
| GPT | 2 | Yes |
| GPT | 3 | N/A |
It should be noted that the reason why we might need to use a summarizer module to decrease the context window size is that abstracts require too many especially given that ideally we would like to feed our large language model both the subjects that we are generating the KG for as well as the literature. This is demonstrable from two different results using a larger and smaller context size. In one, it produces gibbberish, and in the other it reliably produces SPO objects.
#Dependencies Entrez-Direct ncbiutils.edirect
#Github one line install source. git clone https://github.com/fredi-python/llama.cpp.git && cd llama.cpp && make -j && cd models && wget -c https://huggingface.co/TheBloke/vicuna-7B-v1.5-GGUF/resolve/main/vicuna-7b-v1.5.Q4_K_M.gguf