Ali Soroush

Seyed Amir Ahmad Safavi-Naini, Shuhaib Ali, Omer Shahab et al.

Background and Aims: This study evaluates the medical reasoning performance of large language models (LLMs) and vision language models (VLMs) in gastroenterology. Methods: We used 300 gastroenterology board exam-style multiple-choice questions, 138 of which contain images to systematically assess the impact of model configurations and parameters and prompt engineering strategies utilizing GPT-3.5. Next, we assessed the performance of proprietary and open-source LLMs (versions), including GPT (3.5, 4, 4o, 4omini), Claude (3, 3.5), Gemini (1.0), Mistral, Llama (2, 3, 3.1), Mixtral, and Phi (3), across different interfaces (web and API), computing environments (cloud and local), and model precisions (with and without quantization). Finally, we assessed accuracy using a semiautomated pipeline. Results: Among the proprietary models, GPT-4o (73.7%) and Claude3.5-Sonnet (74.0%) achieved the highest accuracy, outperforming the top open-source models: Llama3.1-405b (64%), Llama3.1-70b (58.3%), and Mixtral-8x7b (54.3%). Among the quantized open-source models, the 6-bit quantized Phi3-14b (48.7%) performed best. The scores of the quantized models were comparable to those of the full-precision models Llama2-7b, Llama2--13b, and Gemma2-9b. Notably, VLM performance on image-containing questions did not improve when the images were provided and worsened when LLM-generated captions were provided. In contrast, a 10% increase in accuracy was observed when images were accompanied by human-crafted image descriptions. Conclusion: In conclusion, while LLMs exhibit robust zero-shot performance in medical reasoning, the integration of visual data remains a challenge for VLMs. Effective deployment involves carefully determining optimal model configurations, encouraging users to consider either the high performance of proprietary models or the flexible adaptability of open-source models.

Jenna Kefeli, Ali Soroush, Courtney J. Diamond et al.

Diagnostic codes for Barrett's esophagus (BE), a precursor to esophageal cancer, lack granularity and precision for many research or clinical use cases. Laborious manual chart review is required to extract key diagnostic phenotypes from BE pathology reports. We developed a generalizable transformer-based method to automate data extraction. Using pathology reports from Columbia University Irving Medical Center with gastroenterologist-annotated targets, we performed binary dysplasia classification as well as granularized multi-class BE-related diagnosis classification. We utilized two clinically pre-trained large language models, with best model performance comparable to a highly tailored rule-based system developed using the same data. Binary dysplasia extraction achieves 0.964 F1-score, while the multi-class model achieves 0.911 F1-score. Our method is generalizable and faster to implement as compared to a tailored rule-based approach.

Mohammadreza Ghaffarzadeh-Esfahani, Mahdi Ghaffarzadeh-Esfahani, Arian Salahi-Niri et al.

This study compared the performance of classical feature-based machine learning models (CMLs) and large language models (LLMs) in predicting COVID-19 mortality using high-dimensional tabular data from 9,134 patients across four hospitals. Seven CML models, including XGBoost and random forest (RF), were evaluated alongside eight LLMs, such as GPT-4 and Mistral-7b, which performed zero-shot classification on text-converted structured data. Additionally, Mistral- 7b was fine-tuned using the QLoRA approach. XGBoost and RF demonstrated superior performance among CMLs, achieving F1 scores of 0.87 and 0.83 for internal and external validation, respectively. GPT-4 led the LLM category with an F1 score of 0.43, while fine-tuning Mistral-7b significantly improved its recall from 1% to 79%, yielding a stable F1 score of 0.74 during external validation. Although LLMs showed moderate performance in zero-shot classification, fine-tuning substantially enhanced their effectiveness, potentially bridging the gap with CML models. However, CMLs still outperformed LLMs in handling high-dimensional tabular data tasks. This study highlights the potential of both CMLs and fine-tuned LLMs in medical predictive modeling, while emphasizing the current superiority of CMLs for structured data analysis.

Akhil Vaid, Joshua Lampert, Juhee Lee et al.

Generative Large Language Models (LLMs) hold significant promise in healthcare, demonstrating capabilities such as passing medical licensing exams and providing clinical knowledge. However, their current use as information retrieval tools is limited by challenges like data staleness, resource demands, and occasional generation of incorrect information. This study assessed the potential of LLMs to function as autonomous agents in a simulated tertiary care medical center, using real-world clinical cases across multiple specialties. Both proprietary and open-source LLMs were evaluated, with Retrieval Augmented Generation (RAG) enhancing contextual relevance. Proprietary models, particularly GPT-4, generally outperformed open-source models, showing improved guideline adherence and more accurate responses with RAG. The manual evaluation by expert clinicians was crucial in validating models' outputs, underscoring the importance of human oversight in LLM operation. Further, the study emphasizes Natural Language Programming (NLP) as the appropriate paradigm for modifying model behavior, allowing for precise adjustments through tailored prompts and real-world interactions. This approach highlights the potential of LLMs to significantly enhance and supplement clinical decision-making, while also emphasizing the value of continuous expert involvement and the flexibility of NLP to ensure their reliability and effectiveness in healthcare settings.

Zahra Atf, Seyed Amir Ahmad Safavi-Naini, Peter R. Lewis et al.

This study investigates uncertainty quantification in large language models (LLMs) for medical applications, emphasizing both technical innovations and philosophical implications. As LLMs become integral to clinical decision-making, accurately communicating uncertainty is crucial for ensuring reliable, safe, and ethical AI-assisted healthcare. Our research frames uncertainty not as a barrier but as an essential part of knowledge that invites a dynamic and reflective approach to AI design. By integrating advanced probabilistic methods such as Bayesian inference, deep ensembles, and Monte Carlo dropout with linguistic analysis that computes predictive and semantic entropy, we propose a comprehensive framework that manages both epistemic and aleatoric uncertainties. The framework incorporates surrogate modeling to address limitations of proprietary APIs, multi-source data integration for better context, and dynamic calibration via continual and meta-learning. Explainability is embedded through uncertainty maps and confidence metrics to support user trust and clinical interpretability. Our approach supports transparent and ethical decision-making aligned with Responsible and Reflective AI principles. Philosophically, we advocate accepting controlled ambiguity instead of striving for absolute predictability, recognizing the inherent provisionality of medical knowledge.

Nariman Naderi, Zahra Atf, Peter R Lewis et al.

This paper investigates how prompt engineering techniques impact both accuracy and confidence elicitation in Large Language Models (LLMs) applied to medical contexts. Using a stratified dataset of Persian board exam questions across multiple specialties, we evaluated five LLMs - GPT-4o, o3-mini, Llama-3.3-70b, Llama-3.1-8b, and DeepSeek-v3 - across 156 configurations. These configurations varied in temperature settings (0.3, 0.7, 1.0), prompt styles (Chain-of-Thought, Few-Shot, Emotional, Expert Mimicry), and confidence scales (1-10, 1-100). We used AUC-ROC, Brier Score, and Expected Calibration Error (ECE) to evaluate alignment between confidence and actual performance. Chain-of-Thought prompts improved accuracy but also led to overconfidence, highlighting the need for calibration. Emotional prompting further inflated confidence, risking poor decisions. Smaller models like Llama-3.1-8b underperformed across all metrics, while proprietary models showed higher accuracy but still lacked calibrated confidence. These results suggest prompt engineering must address both accuracy and uncertainty to be effective in high-stakes medical tasks.