Identifying Critical Phases for Disease Onset with Sparse Haematological Biomarkers

Routinely collected clinical blood tests are an emerging molecular data source for large-scale biomedical research but inherently feature irregular sampling and informative observation. Traditional approaches rely on imputation, which can distort learning signals and bias predictions while lacking biological interpretability. We propose a novel methodology using Graph Neural Additive Networks (GNAN) to model biomarker trajectories as time-weighted directed graphs, where nodes represent sampling events and edges encode the time delta between events. GNAN's additive structure enables the explicit decomposition of feature and temporal contributions, allowing the detection of critical disease-associated time points. Unlike conventional imputation-based approaches, our method preserves the temporal structure of sparse data without introducing artificial biases and provides inherently interpretable predictions by decomposing contributions from each biomarker and time interval. This makes our model clinically applicable, as well as allowing it to discover biologically meaningful disease signatures.

LaT-PFN: A Joint Embedding Predictive Architecture for In-context Time-series Forecasting

We introduce LatentTimePFN (LaT-PFN), a foundational Time Series model with a strong embedding space that enables zero-shot forecasting. To achieve this, we perform in-context learning in latent space utilizing a novel integration of the Prior-data Fitted Networks (PFN) and Joint Embedding Predictive Architecture (JEPA) frameworks. We leverage the JEPA framework to create a prediction-optimized latent representation of the underlying stochastic process that generates time series and combines it with contextual learning, using a PFN. Furthermore, we improve on preceding works by utilizing related time series as a context and introducing an abstract time axis. This drastically reduces training time and increases the versatility of the model by allowing any time granularity and forecast horizon. We show that this results in superior zero-shot predictions compared to established baselines. We also demonstrate our latent space produces informative embeddings of both individual time steps and fixed-length summaries of entire series. Finally, we observe the emergence of multi-step patch embeddings without explicit training, suggesting the model actively learns discrete tokens that encode local structures in the data, analogous to vision transformers.