arXiv subjects

Nikita Makarov

Publications and source records attributed to Nikita Makarov.

3 recordsLinked to original sources

arXiv2026

OphthaDT: Generative Digital Twins for Forecasting Visual Acuity Trajectories in Ophthalmology

Precision medicine in ophthalmology requires accurate longitudinal predictions, but the fragmented nature of multimodal clinical data remains a barrier to forecasting. We introduce OphthaDT, an LLM-based digital twin for ophthalmology that serializes longitudinal patient histories from 3,220 patients across four Phase III clinical trials into structured narratives to forecast best corrected visual acuity (BCVA). In benchmarks spanning up to 100 weeks, OphthaDT demonstrated the lowest prediction error in neovascular age-related macular degeneration (nAMD), achieving an average mean absolute error (MAE) reduction of 6.0% compared to all baselines. In diabetic macular edema (DME), OphthaDT demonstrated competitive performance against all baselines while outperforming Random Forest and XGBoost by an average MAE reduction of 2.6% and 6.9%, respectively. Results reveal that OphthaDT's predictive advantage scales with trajectory complexity: whereas linear models remain effective for the more stable treatment responses of DME, OphthaDT's capacity is better suited for capturing the high longitudinal variability of nAMD. Finally, OphthaDT handles irregular sampling without imputation, positioning LLM-based clinical trajectory modeling as a methodology that could reduce patient burden and accelerate drug development.

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arXiv2026

TwinWeaver: An LLM-Based Foundation Model Framework for Pan-Cancer Digital Twins

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.

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arXiv2025

Development of a graph neural network surrogate for travel demand modelling

As urban environments grow, the modelling of transportation systems becomes increasingly complex. This paper advances the field of travel demand modelling by introducing advanced Graph Neural Network (GNN) architectures as surrogate models, addressing key limitations of previous approaches. Building on prior work with Graph Convolutional Networks (GCNs), we introduce GATv3, a new Graph Attention Network (GAT) variant that mitigates over-smoothing through residual connections, enabling deeper and more expressive architectures. Additionally, we propose a fine-grained classification framework that improves predictive stability while achieving numerical precision comparable to regression, offering a more interpretable and efficient alternative. To enhance model performance, we develop a synthetic data generation strategy, which expands the augmented training dataset without overfitting. Our experiments demonstrate that GATv3 significantly improves classification performance, while the GCN model shows unexpected dominance in fine-grained classification when supplemented with additional training data. The results highlight the advantages of fine-grained classification over regression for travel demand modelling tasks and reveal new challenges in extending GAT-based architectures to complex transport scenarios. Notably, GATv3 appears well-suited for classification-based transportation applications, such as section control and congestion warning systems, which require a higher degree of differentiation among neighboring links. These findings contribute to refining GNN-based surrogates, offering new possibilities for applying GATv3 and fine-grained classification in broader transportation challenges.

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