arXiv subjects

Ivana Janíčková

Publications and source records attributed to Ivana Janíčková.

3 recordsLinked to original sources

arXiv2026

SYNPRED: A Synergistic Approach to Multimodal Learning for Clinical Prediction

Multimodal medical data captures complementary aspects of disease. It provides a comprehensive basis for diagnosis and the identification of biological associations linked to progression or treatment response. Established contrastive learning approaches exploit shared information across modalities, but fall short in exploiting complementary, modality-specific signals relevant for a task. Here, we propose a synergistic multimodal variational autoencoder (VAE) framework that separates task-relevant unimodal and multimodal information from instance-specific variation task-irrelevant, allowing complementary signals across modalities to be leveraged for prediction. The method yields benefits even if modalities are missing at test time. We evaluate the method on a treatment response prediction task using medical imaging and RNA data. Empirical comparison with alignment-based and multimodal VAE state-of-the-art approaches demonstrates improved multimodal prediction performance, and consistent benefits for prediction from a single modality after multimodal training. The full code can be found here: https://github.com/cirmuw/SYNPRED.

cs.LG↗

arXiv2026

Graph Representation Learning of Longitudinal Medical Imaging Trajectories for Treatment Response Prediction

In patients with breast cancer, pathological complete response (pCR) has been established as a clinically meaningful surrogate marker for long-term outcomes. While commonly treated with neoadjuvant chemotherapy (NACT), effective treatment decision-making remains challenging, as therapeutic response can vary substantially across patients, calling for predictive models capable of accurately estimating individualized treatment response. To address this, we propose an imaging-based 3D spatio-temporal framework for treatment response prediction that integrates a state-of-the-art graph neural network with relational modeling of temporal interactions across timepoints alongside three novel complementary self-supervised treatment trajectory representation learning objectives. Experiments across a cohort of 585 patients from the public ISPY-2 dataset demonstrate that our method substantially outperforms both vision and self-supervised learning baselines across several classification metrics. Alongside establishing a breast cancer pCR prediction benchmark, we include a principled ablation of our method and further introduce and empirically assess the impact of the available number of DCE-MRI timepoints per patient trajectory and the inclusion of inter-scan time-differences. Overall, our study substantiates the utility of clinically meaningful longitudinal medical imagaging modeling for predicting NACT-induced pCR. We will publicly share our code repository and a user-friendly PyPI library for dataset curation upon publication, effectively promoting reproducible open-source research.

cs.CV↗

arXiv2025

Temporal Representation Learning of Phenotype Trajectories for pCR Prediction in Breast Cancer

Effective therapy decisions require models that predict the individual response to treatment. This is challenging since the progression of disease and response to treatment vary substantially across patients. Here, we propose to learn a representation of the early dynamics of treatment response from imaging data to predict pathological complete response (pCR) in breast cancer patients undergoing neoadjuvant chemotherapy (NACT). The longitudinal change in magnetic resonance imaging (MRI) data of the breast forms trajectories in the latent space, serving as basis for prediction of successful response. The multi-task model represents appearance, fosters temporal continuity and accounts for the comparably high heterogeneity in the non-responder cohort.In experiments on the publicly available ISPY-2 dataset, a linear classifier in the latent trajectory space achieves a balanced accuracy of 0.761 using only pre-treatment data (T0), 0.811 using early response (T0 + T1), and 0.861 using four imaging time points (T0 -> T3). The code will be made available upon paper acceptance.

cs.CV↗