arXiv:2407.04055v2 Announce Type: replace-cross Abstract: The prediction modeling of drug-target interactions is crucial to drug discovery and design, which has seen rapid advancements owing to deep learning technologies. Recently developed methods, such as those based on graph neural networks (GNNs) and Transformers, demonstrate exceptional performance across various datasets by effectively extracting structural information. However, the benchmarking of these novel methods often varies significantly in terms of hyperparameter settings and datasets, which limits algorithmic progress. In view of these, we conducted a comprehensive survey and benchmark for drug-target interaction modeling from a structural perspective via integrating tens of explicit (i.e., GNN-based) and implicit (i.e., Transformer-based) structure learning algorithms. We conducted a macroscopical comparison between these two classes of encoding strategies as well as the different featurization techniques that inform molecules' chemical and physical properties. We then carry out the microscopical comparison between all the integrated models across the six datasets via comprehensively benchmarking their effectiveness and efficiency. To ensure fairness, we investigate model performance under individually optimized configuration. Remarkably, the summarized insights from the benchmark studies lead to the design of model combos. We demonstrate that our combos can achieve new state-of-the-art performance on various datasets associated with cost-effective memory and computation.

Background: Chatbots based on large language models (LLMs) have shown promise in evaluating the consistency of research. Previously, researchers used LLM to assess if randomized controlled trial (RCT) abstracts adhered to the CONSORT-Abstract guidelines. However, the consistency of artificial intelligence (AI) interventional RCTs align with the CONSORT-AI standards by LLMs remains unclear. Objective: The aim of this study is to identify the consistency of randomized controlled trials on AI interventions with CONSORT-AI using chatbots based on LLMs. Methods: This cross-sectional study employed six LLM models to assess the consistency of RCTs on AI interventions. The sample selection is based on articles published in JAMA Network Open, which included a total of 41 RCTs. All queries were submitted to LLMs through an API interface with a temperature setting of 0 to ensure deterministic responses. One researcher posed the questions to each model, while another independently verified the responses for validity before recording the results. The Overall Consistency Score (OCS), recall, inter-rater reliability and consistency of contents were analyzed. Results: We found gpt-4-0125-preview has the best average OCS (86.5%, 95%CI: 82.5%-90.5% and 81.6%, 95% CI: 77.6%-85.6%), followed by gpt-4-1106-preview(80.3%, 95%CI: 76.3%-84.3% and 78.0%, 95% CI: 74.0%-82.0%). The model with the worst average OCS is gpt-3.5-turbo-0125 (61.9%, 95%CI: 57.9%-65.9% and 63.0%, 95% CI: 59.0%-67.0%). Among the 11 unique items of CONSORT-AI, Item 2 (“State the inclusion and exclusion criteria at the level of the input data”) received the poorest overall evaluation across six models, with an average OCS of 48.8%. For other items, those with an average OCS greater than 80% across the six models included Items 1, 5, 8, and 9. Conclusions: GPT-4 variants demonstrate strong performance in assessing the consistency of RCTs with CONSORT-AI. Nonetheless, refining the prompts could enhance the precision and consistency of the outcomes. While AI tools like GPT-4 variants are valuable, they are not yet fully autonomous in addressing complex and nuanced tasks such as adherence to CONSORT-AI standards. Therefore, integrating AI with higher levels of human supervision and expertise will be crucial to ensuring more reliable and efficient evaluations, ultimately advancing the quality of medical research.