Reasoning-Enhanced Rare-Event Prediction with Balanced Outcome Correction
Authors: Vitaly Bulgakov, Alexander Turchin
Organizations: Mass General Brigham, Boston, MA, USA · Profiteya LLC, Boston, MA, USA
Abstract
Rare-event prediction is critical in domains such as healthcare, finance, reliability engineering, customer support, aviation safety, where positive outcomes are infrequent yet potentially catastrophic. Extreme class imbalance biases conventional models toward majority-class predictions, limiting recall, calibration, and operational usefulness. We propose LPCORP (Low-Prevalence CORrector for Prediction)*, a two-stage framework that combines reasoning-enhanced prediction with confidence-based outcome correction. A reasoning model first produces enriched predictions from narrative inputs, after which a lightweight classifier evaluates and selectively corrects these outputs to mitigate prevalence-driven bias. In this study we used Logistic-Regression (LR) and a simple Multilayer Perceptron (MLP) classifiers for this purpose. We evaluate LPCORP on real-world datasets from medical and consumer service domains. The results show that this method transforms the original rare-event prediction problem into a more balanced supervised correction task without discarding or resampling observations. Test-set evaluation demonstrates substantially improved performance, particularly in precision, which is a known weakness in low-prevalence data. We further provide a cost-reduction analysis comparing the expenses associated with rare-event damage control without preventive measures to those incurred when low-cost, prediction-based preventive interventions are applied that showed up to 40+% reduction in some cases.
Post-hoc calibration corrects reported confidence, yet a multiclass calibrator can also change the associated top-1 prediction. Accuracy captures only the net effect of these changes on correctness, not how often predictions change; the Top-1 Prediction Change Rate (TPCR) instead measures this frequency. We propose Calibrator-Output Repair for Top-1 Decision Preservation (CORD), the first post-fit adapter to impose exact prediction preservation by repairing the full calibrated probability vector. From the original and calibrated outputs alone, CORD determines the mass assigned to the original top-1. The calibrated conditional distribution allocates the remaining mass over the other classes, yielding a repaired vector whose own argmax recovers the original prediction. On the calibration split, CORD coordinates the repaired masses to retain the calibrated outputs' mean mass on original predictions whenever attainable. The adapter alters neither the fitted calibrator nor its direct output, fits no additional supervised map, and requires no user- or validation-tuned hyperparameter. Across CIFAR-10/100 and ImageNet-1K, CORD attains zero TPCR by construction and lowers mean ECE, NLL, and Brier relative to the corresponding direct outputs in every dataset; paired gains persist under distribution shift and across calibration-set sizes. CORD thus removes the preservation constraint from calibrator fitting and assigns exact recovery of the original decision to subsequent output repair. Our code is available at https://github.com/labhai/CORD.
Rare diseases represent one of the most challenging settings for clinical decision-making, where heterogeneous presentations, sparse evidence and limited expertise create persistent uncertainty throughout the care pathway. Although artificial intelligence could help, existing systems largely address isolated tasks, particularly diagnosis, and usually rely on downstream investigations rather than information available at initial presentation. Here we show that clinical AI performance under uncertainty can be improved not by scaling a single model, but by exploiting the diversity of multiple imperfect reasoning systems. Across heterogeneous large language models, we identify divergent reasoning trajectories with complementary error patterns and develop RareLens, which learns to reconcile these perspectives into actionable decisions across four stages of rare disease care: risk screening, diagnosis, treatment planning and prognosis prediction. Built on RarelensBench, a real-world dataset of 157,525 cases spanning all 33 Orphanet categories and more than 7,000 conditions, RareLens outperformed every frontier model tested, including GPT-5, DeepSeek-R1, Claude-3.7-Sonnet and Gemini-2.5-Pro, across all stages. It achieved an area under the curve of 0.917 for screening and top-1 accuracies of 65.5% and 89.8% for diagnosis and treatment. In an external evaluation involving 1,287 cases and 23 physicians, autonomous RareLens and physicians assisted by RareLens both outperformed unaided physicians, while demonstrating that effective human-AI collaboration requires more than simply providing model outputs. These findings establish divergent model reasoning as an exploitable source of information and suggest a general strategy for building AI systems that operate reliably under high clinical uncertainty.
Recent advances in uncertainty quantification for time series forecasting show that conformal prediction can provide reliable prediction intervals, yet standard conformal methods are often inefficient under temporal dependence, drift, and heterogeneous error behavior. Existing methods typically either update miscoverage rates over time or learn unconstrained calibration weights, without explicitly separating two central sources of nonstationarity: smoothly drifting error distributions and co-existing distinct error regimes. We introduce RareCP, a regime-aware retrieval method for adaptive conformal time series prediction. RareCP learns local calibration representations through a mixture of cosine-attention experts that each capture distinct error regimes, while a compact hypernetwork adapts the kernel parameters to track temporal drift. Given a new forecasting context, RareCP retrieves the top-k most relevant calibration examples, assigns similarity weights, and forms a weighted conformal quantile over their signed residuals, yielding asymmetric prediction intervals. The adaptive kernel is trained using a smooth interval score objective, with a parameter-space anchor to a lightweight teacher kernel to preserve stable local representations. On the GIFT-Eval benchmark, RareCP improves interval efficiency over recent conformal baselines and foundation model uncertainty estimates while maintaining empirical coverage. Ablations confirm that regime-specific experts, drift-adaptive kernels, sparse retrieval, and teacher anchoring each contribute to the final performance.