Cancer outcomes vary widely between individual patients, each accumulating an irregular record of treatments, diagnoses, measurements, and complications. Current prognostic models reduce this complexity into a single snapshot, focus on narrow clinical settings, and rarely generalize across hospitals. Here we introduce Chronicle, an explainable transformer that learns from entire patient trajectories, predicts diverse clinical outcomes throughout the disease course while capturing both short- and long-term temporal dependencies. Trained on 53.7 million longitudinal data points from 51,711 patients spanning 67 cancer types, Chronicle operates natively on irregular data without imputation and jointly predicts eight endpoints within a flexible framework adaptable to additional outcomes. Chronicle outperformed cross-sectional models for overall survival prediction (C-index 0.84 vs 0.76-0.79), stratified patients more accurately than established prognostic systems, including TNM stage, and predicted seven adverse event and transfusion endpoints (AUC 0.80-0.92). Applied without retraining to 69,341 patients in Germany, Switzerland, and the United States, Chronicle generalized across healthcare systems and improved further with local fine-tuning. Integrated explainability traced each risk update to patient-specific clinical factors, revealing distinct temporal persistence of prognostic information, with relevance half-lives ranging from weeks for therapies to nearly one year for baseline characteristics. These findings demonstrate that learning from hospital-wide patient trajectories enables interpretable and continuously updated predictions, providing a scalable framework to support individualized treatment decisions.
P. Keyl, N. Kiermeyer, J. Bosserhoff et al.· medRxiv· 0 citations
Background: Precision oncology relies on accurate interpretation of tumour-detected gene variants, to guide personalized treatment decisions. However, accurate interpretation of variants in context requires extensive information that is often buried within unstructured biomedical literature and obscured by inconsistent nomenclature, making manual retrieval labour-intensive and prone to omissions. Methods: To address this challenge, we developed Variantscape, a large-scale, automated pipeline and open-access web tool. It integrates traditional natural language processing methods with state-of-the-art large language models to extract, standardize, and analyze co-associations between genetic variants, cancer types, and therapeutic interventions from published biomedical abstracts. Findings: From over 3 million abstracts screened, 335,817 gene name-containing articles were eligible for downstream extraction. Among these, 7,423 (2.2%) simultaneously mentioned a variant, cancer type, and therapeutic agent, encompassing 3,902 unique variants across 98 cancer types and 388 therapeutic agents. This highlights the inefficiency of manual literature retrieval in molecular tumour board (MTB) workflows. Network analysis revealed 14,831 statistically significant co-associations, represented in a literature-derived graph with 4,388 nodes and 46,943 edges. Canonical alterations in well-studied cancers (e.g., BRAF V600E in melanoma) were strongly linked to established treatments, while several rare variants also emerged with high-confidence literature support. Interpretation: By applying large language models to biomedical literature, Variantscape enables scalable, context-aware extraction of trilateral variant-treatment-cancer relationships. This approach supports early evidence synthesis/hypothesis generation, highlights underrecognized or rare associations, and offers a practical resource for accelerating discovery and supporting precision oncology research and translation. Unlike static databases, Variantscape is continuously updatable and leverages large language model-based inference to uncover putative associations without manual curation. Variantscape has the potential to support MTB workflows and translational research by rapidly revealing signals from underlying abstracts.
M. Wosny, A. Blindu, M. Boesch et al.· medRxiv· 0 citations