AutoForest: Automatically Generating Forest Plots from Biomedical Studies with End-to-End Evidence Extraction and Synthesis

Systematic reviews rely on forest plots to synthesise quantitative evidence across biomedical studies, but generating them remains a fragmented and labour-intensive process. Researchers must interpret complex clinical texts, manually extract outcome data from trials, define appropriate interventions and comparators, harmonise inconsistent study designs, and carry out meta-analytic computations-typically using specialised software that demands structured inputs and domain expertise. While recent work has demonstrated that large language models can extract study-level data from unstructured text, no existing system automates the complete pipeline from raw documents to synthesised forest plots. To address this gap, we introduce AutoForest, the first end-to-end system that generates publication-ready forest plots directly from biomedical papers. Given one or more study papers, AutoForest automatically suggests ICO (Intervention, Comparator, Outcome) elements, extracts outcome data, performs statistical synthesis, and renders the final forest plot. We describe the system architecture, user interface and demonstrate its effectiveness on real-world examples through a user study involving clinicians, showing how AutoForest can accelerate evidence synthesis and substantially lower the barrier to conducting meta-analyses.

Diffsurv: Differentiable sorting for censored time-to-event data

Survival analysis is a crucial semi-supervised task in machine learning with numerous real-world applications, particularly in healthcare. Currently, the most common approach to survival analysis is based on Cox's partial likelihood, which can be interpreted as a ranking model optimized on a lower bound of the concordance index. This relation between ranking models and Cox's partial likelihood considers only pairwise comparisons. Recent work has developed differentiable sorting methods which relax this pairwise independence assumption, enabling the ranking of sets of samples. However, current differentiable sorting methods cannot account for censoring, a key factor in many real-world datasets. To address this limitation, we propose a novel method called Diffsurv. We extend differentiable sorting methods to handle censored tasks by predicting matrices of possible permutations that take into account the label uncertainty introduced by censored samples. We contrast this approach with methods derived from partial likelihood and ranking losses. Our experiments show that Diffsurv outperforms established baselines in various simulated and real-world risk prediction scenarios. Additionally, we demonstrate the benefits of the algorithmic supervision enabled by Diffsurv by presenting a novel method for top-k risk prediction that outperforms current methods.

Application of Clinical Concept Embeddings for Heart Failure Prediction in UK EHR data

Electronic health records (EHR) are increasingly being used for constructing disease risk prediction models. Feature engineering in EHR data however is challenging due to their highly dimensional and heterogeneous nature. Low-dimensional representations of EHR data can potentially mitigate these challenges. In this paper, we use global vectors (GloVe) to learn word embeddings for diagnoses and procedures recorded using 13 million ontology terms across 2.7 million hospitalisations in national UK EHR. We demonstrate the utility of these embeddings by evaluating their performance in identifying patients which are at higher risk of being hospitalised for congestive heart failure. Our findings indicate that embeddings can enable the creation of robust EHR-derived disease risk prediction models and address some the limitations associated with manual clinical feature engineering.

Evaluation of Semantic Web Technologies for Storing Computable Definitions of Electronic Health Records Phenotyping Algorithms

Electronic Health Records are electronic data generated during or as a byproduct of routine patient care. Structured, semi-structured and unstructured EHR offer researchers unprecedented phenotypic breadth and depth and have the potential to accelerate the development of precision medicine approaches at scale. A main EHR use-case is defining phenotyping algorithms that identify disease status, onset and severity. Phenotyping algorithms utilize diagnoses, prescriptions, laboratory tests, symptoms and other elements in order to identify patients with or without a specific trait. No common standardized, structured, computable format exists for storing phenotyping algorithms. The majority of algorithms are stored as human-readable descriptive text documents making their translation to code challenging due to their inherent complexity and hinders their sharing and re-use across the community. In this paper, we evaluate the two key Semantic Web Technologies, the Web Ontology Language and the Resource Description Framework, for enabling computable representations of EHR-driven phenotyping algorithms.