Clinical trial matching is the task of identifying trials for which patients may be eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process also results in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic, datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present an end-to-end large-scale empirical evaluation of a clinical trial matching system and validate it using real-world EHRs. We perform comprehensive experiments with proprietary LLMs and our custom fine-tuned model called OncoLLM and show that OncoLLM outperforms GPT-3.5 and matches the performance of qualified medical doctors for clinical trial matching.

High-quality, openly accessible clinical datasets remain a significant bottleneck in advancing both research and clinical applications within medical artificial intelligence. Case reports, often rich in multimodal clinical data, represent an underutilized resource for developing medical AI applications. We present an enhanced version of MultiCaRe, a dataset derived from open-access case reports on PubMed Central. This new version addresses the limitations identified in the previous release and incorporates newly added clinical cases and images (totaling 93,816 and 130,791, respectively), along with a refined hierarchical taxonomy featuring over 140 categories. Image labels have been meticulously curated using a combination of manual and machine learning-based label generation and validation, ensuring a higher quality for image classification tasks and the fine-tuning of multimodal models. To facilitate its use, we also provide a Python package for dataset manipulation, pretrained models for medical image classification, and two dedicated websites. The updated MultiCaRe dataset expands the resources available for multimodal AI research in medicine. Its scale, quality, and accessibility make it a valuable tool for developing medical AI systems, as well as for educational purposes in clinical and computational fields.

This paper details the acquisition, structure and preprocessing of the MultiCaRe Dataset, a multimodal case report dataset which contains data from 75,382 open access PubMed Central articles spanning the period from 1990 to 2023. The dataset includes 96,428 clinical cases, 135,596 images, and their corresponding labels and captions. Data extraction was performed using different APIs and packages such as Biopython, requests, Beautifulsoup, BioC API for PMC and EuropePMC RESTful API. Image labels were created based on the contents of their corresponding captions, by using Spark NLP for Healthcare and manual annotations. Images were preprocessed with OpenCV in order to remove borders and split figures containing multiple images, data were analyzed and described, and a subset was randomly selected for quality assessment. The dataset's structure allows for seamless integration of different types of data, making it a valuable resource for training or fine-tuning medical language, computer vision or multi-modal models.

Classification is a fundamental task in machine learning. While conventional methods—such as binary, multiclass, and multi-label classification—are effective for simpler problems, they may not adequately address the complexities of some real-world scenarios. This article introduces the Multiplex Classification Framework, a novel approach developed to tackle these and similar challenges through the integration of problem transformation, ontology engineering, and model ensembling. The framework offers several advantages, including adaptability to any number of classes and logical constraints, an innovative method for managing class imbalance, the elimination of confidence threshold selection, and a modular structure. Two experiments were conducted to compare the performance of conventional classification models with the multiplex approach. Our results demonstrate that the multiplex approach can improve classification performance significantly (up to 10% gain in overall F1 score), particularly in classification problems with a large number of classes and pronounced class imbalances. However, it also has limitations, as it requires a thorough understanding of the problem domain and some experience with ontology engineering, and it involves training multiple models, which can make the whole process more intricate. Overall, this methodology provides a valuable tool for researchers and practitioners dealing with complex classification problems in machine learning.

Classification is a fundamental task in machine learning. While conventional methods-such as binary, multiclass, and multi-label classification-are effective for simpler problems, they may not adequately address the complexities of some real-world scenarios. This paper introduces the Multiplex Classification Framework, a novel approach developed to tackle these and similar challenges through the integration of problem transformation, ontology engineering, and model ensembling. The framework offers several advantages, including adaptability to any number of classes and logical constraints, an innovative method for managing class imbalance, the elimination of confidence threshold selection, and a modular structure. Two experiments were conducted to compare the performance of conventional classification models with the Multiplex approach. Our results demonstrate that the Multiplex approach can improve classification performance significantly (up to 10% gain in overall F1 score), particularly in classification problems with a large number of classes and pronounced class imbalances. However, it also has limitations, as it requires a thorough understanding of the problem domain and some experience with ontology engineering, and it involves training multiple models, which can make the whole process more intricate. Overall, this methodology provides a valuable tool for researchers and practitioners dealing with complex classification problems in machine learning.