The scientific literature is growing rapidly, making it hard to keep track of the state-of-the-art. Systematic literature reviews (SLRs) aim to identify and evaluate all relevant papers on a topic. After retrieving a set of candidate papers, the abstract screening phase determines initial relevance. To date, abstract screening methods using large language models (LLMs) focus on binary classification settings; existing question answering (QA) based ranking approaches suffer from error propagation. LLMs offer a unique opportunity to evaluate the SLR's inclusion and exclusion criteria, yet, existing benchmarks do not provide them exhaustively. We manually extract these criteria as well as research questions for 57 SLRs, mostly in the medical domain, enabling principled comparisons between approaches. Moreover, we propose LGAR, a zero-shot LLM Guided Abstract Ranker composed of an LLM based graded relevance scorer and a dense re-ranker. Our extensive experiments show that LGAR outperforms existing QA-based methods by 5-10 pp. in mean average precision. Our code and data is publicly available.

Clinical cohort definition is crucial for patient recruitment and observational studies, yet translating inclusion/exclusion criteria into SQL queries remains challenging and manual. We present an automated system utilizing large language models that combines criteria parsing, two-level retrieval augmented generation with specialized knowledge bases, medical concept standardization, and SQL generation to retrieve patient cohorts with patient funnels. The system achieves 0.75 F1-score in cohort identification on EHR data, effectively capturing complex temporal and logical relationships. These results demonstrate the feasibility of automated cohort generation for epidemiological research.

Glaucomatous optic neuropathy (GON) is a prevalent ocular disease that can lead to irreversible vision loss if not detected early and treated. The traditional diagnostic approach for GON involves a set of ophthalmic examinations, which are time-consuming and require a visit to an ophthalmologist. Recent deep learning models for automating GON detection from digital fundus images (DFI) have shown promise but often suffer from limited generalizability across different ethnicities, disease groups and examination settings. To address these limitations, we introduce GONet, a robust deep learning model developed using seven independent datasets, including over 119,000 DFIs with gold-standard annotations and from patients of diverse geographic backgrounds. GONet consists of a DINOv2 pre-trained self-supervised vision transformers fine-tuned using a multisource domain strategy. GONet demonstrated high out-of-distribution generalizability, with an AUC of 0.85-0.99 in target domains. GONet performance was similar or superior to state-of-the-art works and was significantly superior to the cup-to-disc ratio, by up to 21.6%. GONet is available at [URL provided on publication]. We also contribute a new dataset consisting of 768 DFI with GON labels as open access.

Artificial intelligence (AI) methodologies hold great promise for the rapid and accurate diagnosis of coronary artery disease (CAD) from intravascular optical coherent tomography (IVOCT) images. Numerous papers have been published describing AI-based models for different diagnostic tasks, yet it remains unclear which models have potential clinical utility and have been properly validated. This systematic review considered published literature between January 2015 and February 2023 describing AI-based diagnosis of CAD using IVOCT. Our search identified 5,576 studies, with 513 included after initial screening and 35 studies included in the final systematic review after quality screening. Our findings indicate that most of the identified models are not currently suitable for clinical use, primarily due to methodological flaws and underlying biases. To address these issues, we provide recommendations to improve model quality and research practices to enhance the development of clinically useful AI products.

Clinical trials are the gold standard for assessing the effectiveness and safety of drugs for treating diseases. Given the vast design space of drug molecules, elevated financial cost, and multi-year timeline of these trials, research on clinical trial outcome prediction has gained immense traction. Accurate predictions must leverage data of diverse modes such as drug molecules, target diseases, and eligibility criteria to infer successes and failures. Previous Deep Learning approaches for this task, such as HINT, often require wet lab data from synthesized molecules and/or rely on prior knowledge to encode interactions as part of the model architecture. To address these limitations, we propose a light-weight attention-based model, MEXA-CTP, to integrate readily-available multi-modal data and generate effective representations via specialized modules dubbed "mode experts", while avoiding human biases in model design. We optimize MEXA-CTP with the Cauchy loss to capture relevant interactions across modes. Our experiments on the Trial Outcome Prediction (TOP) benchmark demonstrate that MEXA-CTP improves upon existing approaches by, respectively, up to 11.3% in F1 score, 12.2% in PR-AUC, and 2.5% in ROC-AUC, compared to HINT. Ablation studies are provided to quantify the effectiveness of each component in our proposed method.

Systematic literature reviews and meta-analyses are essential for synthesizing research insights, but they remain time-intensive and labor-intensive due to the iterative processes of screening, evaluation, and data extraction. This paper introduces and evaluates LatteReview, a Python-based framework that leverages large language models (LLMs) and multi-agent systems to automate key elements of the systematic review process. Designed to streamline workflows while maintaining rigor, LatteReview utilizes modular agents for tasks such as title and abstract screening, relevance scoring, and structured data extraction. These agents operate within orchestrated workflows, supporting sequential and parallel review rounds, dynamic decision-making, and iterative refinement based on user feedback. LatteReview's architecture integrates LLM providers, enabling compatibility with both cloud-based and locally hosted models. The framework supports features such as Retrieval-Augmented Generation (RAG) for incorporating external context, multimodal reviews, Pydantic-based validation for structured inputs and outputs, and asynchronous programming for handling large-scale datasets. The framework is available on the GitHub repository, with detailed documentation and an installable package.

Matching patients to clinical trials demands a systematic and reasoned interpretation of documents which require significant expert-level background knowledge, over a complex set of well-defined eligibility criteria. Moreover, this interpretation process needs to operate at scale, over vast knowledge bases of trials. In this paper, we propose a scalable method that extends the capabilities of LLMs in the direction of systematizing the reasoning over sets of medical eligibility criteria, evaluating it in the context of real-world cases. The proposed method overlays a Set-guided reasoning method for LLMs. The proposed framework is evaluated on TREC 2022 Clinical Trials, achieving results superior to the state-of-the-art: NDCG@10 of 0.693 and Precision@10 of 0.73.

Foundational Large Language Models (LLMs) have changed the way we perceive technology. They have been shown to excel in tasks ranging from poem writing and coding to essay generation and puzzle solving. With the incorporation of image generation capability, they have become more comprehensive and versatile AI tools. At the same time, researchers are striving to identify the limitations of these tools to improve them further. Currently identified flaws include hallucination, biases, and bypassing restricted commands to generate harmful content. In the present work, we have identified a fundamental limitation related to the image generation ability of LLMs, and termed it The NO Syndrome. This negation blindness refers to LLMs inability to correctly comprehend NO related natural language prompts to generate the desired images. Interestingly, all tested LLMs including GPT-4, Gemini, and Copilot were found to be suffering from this syndrome. To demonstrate the generalization of this limitation, we carried out simulation experiments and conducted entropy-based and benchmark statistical analysis tests on various LLMs in multiple languages, including English, Hindi, and French. We conclude that the NO syndrome is a significant flaw in current LLMs that needs to be addressed. A related finding of this study showed a consistent discrepancy between image and textual responses as a result of this NO syndrome. We posit that the introduction of a negation context-aware reinforcement learning based feedback loop between the LLMs textual response and generated image could help ensure the generated text is based on both the LLMs correct contextual understanding of the negation query and the generated visual output.

This paper describes Toronto Metropolitan University's participation in the TREC Clinical Trials Track for 2023. As part of the tasks, we utilize advanced natural language processing techniques and neural language models in our experiments to retrieve the most relevant clinical trials. We illustrate the overall methodology, experimental settings, and results of our implementation for the run submission as part of (Team - V-TorontoMU).

Medical applications of machine learning (ML) have experienced a surge in popularity in recent years. The intensive care unit (ICU) is a natural habitat for ML given the abundance of available data from electronic health records. Models have been proposed to address numerous ICU prediction tasks like the early detection of complications. While authors frequently report state-of-the-art performance, it is challenging to verify claims of superiority. Datasets and code are not always published, and cohort definitions, preprocessing pipelines, and training setups are difficult to reproduce. This work introduces Yet Another ICU Benchmark (YAIB), a modular framework that allows researchers to define reproducible and comparable clinical ML experiments; we offer an end-to-end solution from cohort definition to model evaluation. The framework natively supports most open-access ICU datasets (MIMIC III/IV, eICU, HiRID, AUMCdb) and is easily adaptable to future ICU datasets. Combined with a transparent preprocessing pipeline and extensible training code for multiple ML and deep learning models, YAIB enables unified model development. Our benchmark comes with five predefined established prediction tasks (mortality, acute kidney injury, sepsis, kidney function, and length of stay) developed in collaboration with clinicians. Adding further tasks is straightforward by design. Using YAIB, we demonstrate that the choice of dataset, cohort definition, and preprocessing have a major impact on the prediction performance - often more so than model class - indicating an urgent need for YAIB as a holistic benchmarking tool. We provide our work to the clinical ML community to accelerate method development and enable real-world clinical implementations. Software Repository: https://github.com/rvandewater/YAIB.