Amirhossein Zare

Amirhossein Zare, Amirhessam Zare, Herlock Rahimi et al.

Longitudinal treatment decisions require predicting potential outcomes under future treatment sequences in the presence of time-varying confounding, heterogeneous patient dynamics, and limited domain-specific data. Existing longitudinal causal estimators typically train a new model for each cohort or simulator. We introduce Causal Longitudinal Prior-Fitted Networks (CausalLongPFN), a prior-fitted in-context predictor for longitudinal causal prediction. The model is pretrained entirely on synthetic episodes sampled from a broad prior over temporal structural causal models, exposing it to treatment-confounder feedback, latent heterogeneity, nonlinear state evolution, delayed effects, and cumulative treatment responses. At test time, CausalLongPFN is frozen: it conditions on support trajectories, a query history, and a proposed future treatment sequence, and returns a predictive distribution over future outcomes without gradient updates or propensity-model fitting. Multi-step predictions are obtained by recursively applying the one-step predictor under the specified treatment sequence. We evaluate on branchable cancer, HIV, and warfarin benchmarks with ground-truth counterfactual labels, and on factual-only rolling-origin prediction in MIMIC-III ICU trajectories. CausalLongPFN is competitive with domain-trained longitudinal baselines on counterfactual benchmarks and performs strongly on factual MIMIC-III prediction, suggesting that broad synthetic causal pretraining can provide a useful frozen alternative when repeated domain-specific training is costly or impractical.

Amirhossein Zare, Amirhessam Zare, Parmida Sadat Pezeshki et al.

Class imbalance remains a major challenge in machine learning, especially for high-dimensional biomedical data where nonlinear manifold structures dominate. Traditional oversampling methods such as SMOTE rely on local linear interpolation, often producing implausible synthetic samples. Deep generative models like Conditional Variational Autoencoders (CVAEs) better capture nonlinear distributions, but standard variants treat all minority samples equally, neglecting the importance of uncertain, boundary-region examples emphasized by heuristic methods like Borderline-SMOTE and ADASYN. We propose Local Entropy-Guided Oversampling with a CVAE (LEO-CVAE), a generative oversampling framework that explicitly incorporates local uncertainty into both representation learning and data generation. To quantify uncertainty, we compute Shannon entropy over the class distribution in a sample's neighborhood: high entropy indicates greater class overlap, serving as a proxy for uncertainty. LEO-CVAE leverages this signal through two mechanisms: (i) a Local Entropy-Weighted Loss (LEWL) that emphasizes robust learning in uncertain regions, and (ii) an entropy-guided sampling strategy that concentrates generation in these informative, class-overlapping areas. Applied to clinical genomics datasets (ADNI and TCGA lung cancer), LEO-CVAE consistently improves classifier performance, outperforming both traditional oversampling and generative baselines. These results highlight the value of uncertainty-aware generative oversampling for imbalanced learning in domains governed by complex nonlinear structures, such as omics data.