Raul Rodriguez-Esteban

Nikita Makarov, Maria Bordukova, Lena Voith von Voithenberg et al.

Precision oncology requires forecasting clinical events and trajectories, yet modeling sparse, multi-modal clinical time series remains a critical challenge. We introduce TwinWeaver, an open-source framework that serializes longitudinal patient histories into text, enabling unified event prediction as well as forecasting with large language models, and use it to build Genie Digital Twin (GDT) on 93,054 patients across 20 cancer types. In benchmarks, GDT significantly reduces forecasting error, achieving a median Mean Absolute Scaled Error (MASE) of 0.87 compared to 0.97 for the strongest time-series baseline (p<0.001). Furthermore, GDT improves risk stratification, achieving an average concordance index (C-index) of 0.703 across survival, progression, and therapy switching tasks, surpassing the best baseline of 0.662. GDT also generalizes to out-of-distribution clinical trials, matching trained baselines at zero-shot and surpassing them with fine-tuning, achieving a median MASE of 0.75-0.88 and outperforming the strongest baseline in event prediction with an average C-index of 0.672 versus 0.648. Finally, TwinWeaver enables an interpretable clinical reasoning extension, providing a scalable and transparent foundation for longitudinal clinical modeling.

Igor Kulev, Berkay Köprü, Raul Rodriguez-Esteban et al.

The BioCreative VII Track 3 challenge focused on the identification of medication names in Twitter user timelines. For our submission to this challenge, we expanded the available training data by using several data augmentation techniques. The augmented data was then used to fine-tune an ensemble of language models that had been pre-trained on general-domain Twitter content. The proposed approach outperformed the prior state-of-the-art algorithm Kusuri and ranked high in the competition for our selected objective function, overlapping F1 score.