The generative capabilities of LLM models present opportunities in accelerating tasks and concerns with the authenticity of the knowledge it produces. To address the concerns, we present a computational approach that systematically evaluates the factual accuracy of biomedical knowledge that an LLM model has been prompted to generate. Our approach encompasses two processes: the generation of disease-centric associations and the verification of them using the semantic knowledge of the biomedical ontologies. Using ChatGPT as the select LLM model, we designed a set of prompt-engineering processes to generate linkages between diseases, drugs, symptoms, and genes to establish grounds for assessments. Experimental results demonstrate high accuracy in identifying disease terms (88%-97%), drug names (90%-91%), and genetic information (88%-98%). The symptom term identification accuracy was notably lower (49%-61%), as verified against the DOID, ChEBI, SYMPTOM, and GO ontologies accordingly. The verification of associations reveals literature coverage rates of (89%-91%) among disease-drug and disease-gene associations. The low identification accuracy for symptom terms also contributed to the verification of symptom-related associations (49%-62%).

The objective of this research is to introduce a network specialized in predicting drugs that can be repurposed by investigating real-world evidence sources, such as clinical trials and biomedical literature. Specifically, it aims to generate drug combination therapies for complex diseases (e.g., cancer, Alzheimer's). We present a multilayered network medicine approach, empowered by a highly configured ChatGPT prompt engineering system, which is constructed on the fly to extract drug mentions in clinical trials. Additionally, we introduce a novel algorithm that connects real-world evidence with disease-specific signaling pathways (e.g., KEGG database). This sheds light on the repurposability of drugs if they are found to bind with one or more protein constituents of a signaling pathway. To demonstrate, we instantiated the framework for breast cancer and found that, out of 46 breast cancer signaling pathways, the framework identified 38 pathways that were covered by at least two drugs. This evidence signals the potential for combining those drugs. Specifically, the most covered signaling pathway, ID hsa:2064, was covered by 108 drugs, some of which can be combined. Conversely, the signaling pathway ID hsa:1499 was covered by only two drugs, indicating a significant gap for further research. Our network medicine framework, empowered by GenAI, shows promise in identifying drug combinations with a high degree of specificity, knowing the exact signaling pathways and proteins that serve as targets. It is noteworthy that ChatGPT successfully accelerated the process of identifying drug mentions in clinical trials, though further investigations are required to determine the relationships among the drug mentions.

This serves the purpose A. Structured Use Case Analysis of making sure we have control over the input to the engine vs using the default behavior The results in Figure 2 reveal that, for the of the main ChatGPT engine; (2)Supervisedprompt 50 structured use cases, there were a total where we encode the rules one at a of 47 cases where only 1 rule was triggered, time, to train the ChatGPT engine to process while 3 cases had zero rules triggered (seen and made a decision based on a given use case in the N-Rule(s) Triggered). Regarding the to also be entered; (3) the expectation of this recommendations, 47 cases produced correct supervised prompt is to force explanation of recommendations, while 3 cases received incorrect the recommendations made by the rules upon recommendations as shown in Table I. firing which is the premise of this work; (4) It is noteworthy to mention that the 3 cases the actual encoding of the prompt performing with incorrect recommendations does not correlate the task of supervised prompt-engineering can at all with the 3 cases that had 0 rules be captured algorithmically in Algorithm 3: triggered.

Background: The emergence of generative AI tools, empowered by Large Language Models (LLMs), has shown powerful capabilities in generating content. To date, the assessment of the usefulness of such content, generated by what is known as prompt engineering, has become an interesting research question. Objectives Using the mean of prompt engineering, we assess the similarity and closeness of such contents to real literature produced by scientists. Methods In this exploratory analysis, (1) we prompt-engineer ChatGPT and Google Bard to generate clinical content to be compared with literature counterparts, (2) we assess the similarities of the contents generated by comparing them with counterparts from biomedical literature. Our approach is to use text-mining approaches to compare documents and associated bigrams and to use network analysis to assess the terms' centrality. Results The experiments demonstrated that ChatGPT outperformed Google Bard in cosine document similarity (38% to 34%), Jaccard document similarity (23% to 19%), TF-IDF bigram similarity (47% to 41%), and term network centrality (degree and closeness). We also found new links that emerged in ChatGPT bigram networks that did not exist in literature bigram networks. Conclusions: The obtained similarity results show that ChatGPT outperformed Google Bard in document similarity, bigrams, and degree and closeness centrality. We also observed that ChatGPT offers linkage to terms that are connected in the literature. Such connections could inspire asking interesting questions and generate new hypotheses.

Background: Since the launch of various generative AI tools, scientists have been striving to evaluate their capabilities and contents, in the hope of establishing trust in their generative abilities. Regulations and guidelines are emerging to verify generated contents and identify novel uses. Objective: we aspire to demonstrate how ChatGPT claims are checked computationally using the rigor of network models. We aim to achieve fact-checking of the knowledge embedded in biological graphs that were contrived from ChatGPT contents at the aggregate level. Methods: We adopted a biological networks approach that enables the systematic interrogation of ChatGPT's linked entities. We designed an ontology-driven fact-checking algorithm that compares biological graphs constructed from approximately 200,000 PubMed abstracts with counterparts constructed from a dataset generated using the ChatGPT-3.5 Turbo model. Results: in 10-samples of 250 randomly selected records a ChatGPT dataset of 1000 "simulated" articles, the fact-checking link accuracy ranged from 70% to 86%. The computational process was followed by a manual process using IntAct Interaction database and the Gene regulatory network database (GRNdb) to confirm the validity of the links identified computationally. We also found that the proximity of the edges of ChatGPT graphs were significantly shorter (90 -- 153) while literature distances were (236 -- 765). This pattern held true in all 10-samples. Conclusion: This study demonstrated high accuracy of aggregate disease-gene links relationships found in ChatGPT-generated texts. The strikingly consistent pattern offers an illuminate new biological pathways that may open the door for new research opportunities.

ChatGPT is becoming a new reality. In this paper, we show how to distinguish ChatGPT-generated publications from counterparts produced by scientists. Using a newly designed supervised Machine Learning algorithm, we demonstrate how to detect machine-generated publications from those produced by scientists. The algorithm was trained using 100 real publication abstracts, followed by a 10-fold calibration approach to establish a lower-upper bound range of acceptance. In the comparison with ChatGPT content, it was evident that ChatGPT contributed merely 23\% of the bigram content, which is less than 50\% of any of the other 10 calibrating folds. This analysis highlights a significant disparity in technical terms where ChatGPT fell short of matching real science. When categorizing the individual articles, the xFakeBibs algorithm accurately identified 98 out of 100 publications as fake, with 2 articles incorrectly classified as real publications. Though this work introduced an algorithmic approach that detected the ChatGPT-generated fake science with a high degree of accuracy, it remains challenging to detect all fake records. This work is indeed a step in the right direction to counter fake science and misinformation.