arXiv subjects

Russell Greiner

Publications and source records attributed to Russell Greiner.

At least 19 recordsLinked to original sources

arXiv2026

Harmonized Interpretable ECG Waveform Features for Robust Cross-Dataset Clinical Prediction

Electrocardiograms (ECGs) are widely used for cardiovascular risk prediction, yet models often fail to transfer across hospitals because of protocol, population, and measurement differences. We benchmark cross-dataset generalization on three tasks - heart failure classification, 30-day all-cause mortality, and 30-day mortality among sinus-rhythm ECGs - using two large cohorts (MIMIC-IV and the Alberta Cohort). To reduce vendor-specific measurement mismatch, we build a harmonized, interpretable feature representation computed directly from raw waveforms: FeatureDB morphology/heart-rate-variability summaries plus compact time-frequency descriptors (autoregressive and wavelet features). We train XGBoost models on this unified feature space and evaluate with patient-disjoint internal and bidirectional external testing. We pre-specify two hypotheses: (H1) external AUROC retains at least 90% of source-site internal AUROC under transfer, and (H2) internal AUROC of the harmonized feature set stays within 10% of dataset-native machine-measurement models. Across tasks, internal AUROC is 0.79-0.82 and cross-dataset AUROC is 0.74-0.78, with larger and direction-dependent AUPRC shifts under transfer. As an exploratory benchmark, an end-to-end ConvNeXt model trained directly on raw ECG waveforms with age and sex achieves higher internal AUROC, while the harmonized representation remains competitive in relative cross-dataset transfer stability. These findings show that a consistent waveform-derived feature interface preserves performance, supports realistic external validation, and provides a transparent alternative for cross-site clinical prediction.

cs.LG↗

arXiv2026

SurvivalPFN: Amortizing Survival Prediction via In-Context Bayesian Inference

Survival analysis provides a powerful statistical framework for modeling time-to-event outcomes in the presence of censoring. However, selecting an appropriate estimator from the many specialized survival approaches often requires substantial methodological and domain expertise. We introduce SurvivalPFN, a prior-data fitted network that amortizes Bayesian inference for censored observations through in-context learning. SurvivalPFN is pretrained on a diverse family of synthetic, identifiable, and right-censored data-generating processes, enabling it to amortize survival analysis in a single forward pass during inference. As a result, the model adapts to the effective complexity of each dataset without task-specific training or hyperparameter tuning, avoids restrictive parametric assumptions, and produces calibrated survival distributions. In a large-scale benchmark spanning 61 datasets, 21 methods, and 5 evaluation metrics, SurvivalPFN achieves strong predictive performance and often improves upon established survival models. These results suggest that SurvivalPFN offers a principled and practical foundation model for survival analysis, with potential applications in high-impact domains such as healthcare, finance, and engineering (https://github.com/rgklab/SurvivalPFN).

cs.LG↗

arXiv2025

Budget-constrained Active Learning to Effectively De-censor Survival Data

Standard supervised learners attempt to learn a model from a labeled dataset. Given a small set of labeled instances, and a pool of unlabeled instances, a budgeted learner can use its given budget to pay to acquire the labels of some unlabeled instances, which it can then use to produce a model. Here, we explore budgeted learning in the context of survival datasets, which include (right) censored instances, where we know only a lower bound on an instance's time-to-event. Here, that learner can pay to (partially) label a censored instance -- e.g., to acquire the actual time for an instance [perhaps go from (3 yr, censored) to (7.2 yr, uncensored)], or other variants [e.g., learn about one more year, so go from (3 yr, censored) to either (4 yr, censored) or perhaps (3.2 yr, uncensored)]. This serves as a model of real world data collection, where follow-up with censored patients does not always lead to uncensoring, and how much information is given to the learner model during data collection is a function of the budget and the nature of the data itself. We provide both experimental and theoretical results for how to apply state-of-the-art budgeted learning algorithms to survival data and the respective limitations that exist in doing so. Our approach provides bounds and time complexity asymptotically equivalent to the standard active learning method BatchBALD. Moreover, empirical analysis on several survival tasks show that our model performs better than other potential approaches on several benchmarks.

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arXiv2025

Position: Stop Chasing the C-index when Evaluating Survival Analysis Models

The current state of evaluation in survival analysis is plagued by the persistent use of evaluation metrics in ways that are misaligned with the stated modeling objective. In addition, many such evaluations are based on censoring assumptions that are left implicit or unjustified. This means that the reported performance can be misleading and may fail to answer the scientific or modeling question the evaluation was intended to address. In this position paper, we critically examine evaluation practices in survival analysis and highlight how censoring makes evaluation fundamentally different from standard regression or classification. We place particular focus on concordance-based measures, such as the C-index, which we show are heavily overused in the literature. To help identify appropriate metrics, we propose a set of key desiderata and introduce a double-helix ladder, in which valid evaluation requires alignment between metric and modeling assumptions. Through controlled experiments, we show that violations of this alignment can lead to misleading model comparisons. We conclude by providing practical guidance on how to evaluate a survival model.

stat.ME↗

arXiv2025

A meaningful prediction of functional decline in amyotrophic lateral sclerosis based on multi-event survival analysis

Amyotrophic lateral sclerosis (ALS) is a degenerative disorder of the motor neurons that causes progressive paralysis in patients. Current treatment options aim to prolong survival and improve quality of life. However, due to the heterogeneity of the disease, it is often difficult to determine the optimal time for potential therapies or medical interventions. In this study, we propose a novel method to predict the time until a patient with ALS experiences significant functional impairment (ALSFRS-R <= 2) for each of five common functions: speaking, swallowing, handwriting, walking, and breathing. We formulate this task as a multi-event survival problem and validate our approach in the PRO-ACT dataset (N = 3220) by training five covariate-based survival models to estimate the probability of each event over the 500 days following the baseline visit. We then predict five event-specific individual survival distributions (ISDs) for a patient, each providing an interpretable estimate of when that event is likely to occur. The results show that covariate-based models are superior to the Kaplan-Meier estimator at predicting time-to-event outcomes in the PRO-ACT dataset. Additionally, our method enables practitioners to make individual counterfactual predictions -- where certain covariates can be changed -- to estimate their effect on the predicted outcome. In this regard, we find that Riluzole has little or no impact on predicted functional decline. However, for patients with bulbar-onset ALS, our model predicts significantly shorter time-to-event estimates for loss of speech and swallowing function compared to patients with limb-onset ALS (log-rank p<0.001, Bonferroni-adjusted alpha=0.01). The proposed method can be applied to current clinical examination data to assess the risk of functional decline and thus allow more personalized treatment planning.

q-bio.QM↗

arXiv2025

Censoring-Aware Tree-Based Reinforcement Learning for Estimating Dynamic Treatment Regimes with Censored Outcomes

Dynamic Treatment Regimes (DTRs) provide a systematic approach for making sequential treatment decisions that adapt to individual patient characteristics, particularly in clinical contexts where survival outcomes are of interest. Censoring-Aware Tree-Based Reinforcement Learning (CA-TRL) is a novel framework to address the complexities associated with censored data when estimating optimal DTRs. We explore ways to learn effective DTRs, from observational data. By enhancing traditional tree-based reinforcement learning methods with augmented inverse probability weighting (AIPW) and censoring-aware modifications, CA-TRL delivers robust and interpretable treatment strategies. We demonstrate its effectiveness through extensive simulations and real-world applications using the SANAD epilepsy dataset, where it outperformed the recently proposed ASCL method in key metrics such as restricted mean survival time (RMST) and decision-making accuracy. This work represents a step forward in advancing personalized and data-driven treatment strategies across diverse healthcare settings.

cs.LG↗

arXiv2025

Overcoming Dependent Censoring in the Evaluation of Survival Models

Dependent censoring occurs when the event time and censoring time are not conditionally independent given the observed covariates. This complicates survival model evaluation because widely used metrics, such as the Brier score, typically handle right-censoring using inverse probability of censoring weighting (IPCW). Unfortunately, IPCW is valid only when the estimated censoring distribution is independent of the event time. We propose a dependent Brier score based on an Archimedean copula and the Copula-Graphic estimator, and establish consistency and asymptotic normality of its margin-time estimator. To evaluate the metric, we introduce a semi-synthetic framework that creates realistic dependent censoring while preserving the original covariate structure and known event times. Across 12 datasets, the proposed metric reduces estimation error by 12-16\% on average relative to IPCW. Source code is available at https://github.com/thecml/DependentEVAL.

stat.ML↗

arXiv2025

Deep Learning for Disease Outbreak Prediction: A Robust Early Warning Signal for Transcritical Bifurcations

Early Warning Signals (EWSs) are vital for implementing preventive measures before a disease turns into a pandemic. While new diseases exhibit unique behaviors, they often share fundamental characteristics from a dynamical systems perspective. Moreover, measurements during disease outbreaks are often corrupted by different noise sources, posing challenges for Time Series Classification (TSC) tasks. In this study, we address the problem of having a robust EWS for disease outbreak prediction using a best-performing deep learning model in the domain of TSC. We employed two simulated datasets to train the model: one representing generated dynamical systems with randomly selected polynomial terms to model new disease behaviors, and another simulating noise-induced disease dynamics to account for noisy measurements. The model's performance was analyzed using both simulated data from different disease models and real-world data, including influenza and COVID-19. Results demonstrate that the proposed model outperforms previous models, effectively providing EWSs of impending outbreaks across various scenarios. This study bridges advancements in deep learning with the ability to provide robust early warning signals in noisy environments, making it highly applicable to real-world crises involving emerging disease outbreaks.

cs.LG↗

arXiv2024

MassSpecGym: A benchmark for the discovery and identification of molecules

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: de novo molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at https://github.com/pluskal-lab/MassSpecGym.

q-bio.QM↗

arXiv2024

Toward Conditional Distribution Calibration in Survival Prediction

Survival prediction often involves estimating the time-to-event distribution from censored datasets. Previous approaches have focused on enhancing discrimination and marginal calibration. In this paper, we highlight the significance of conditional calibration for real-world applications -- especially its role in individual decision-making. We propose a method based on conformal prediction that uses the model's predicted individual survival probability at that instance's observed time. This method effectively improves the model's marginal and conditional calibration, without compromising discrimination. We provide asymptotic theoretical guarantees for both marginal and conditional calibration and test it extensively across 15 diverse real-world datasets, demonstrating the method's practical effectiveness and versatility in various settings.

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arXiv2024

MENSA: A Multi-Event Network for Survival Analysis with Trajectory-based Likelihood Estimation

Most existing time-to-event methods focus on either single-event or competing-risks settings, leaving multi-event scenarios relatively underexplored. In many healthcare applications, for example, a patient may experience multiple clinical events, that can be non-exclusive and semi-competing. A common workaround is to train independent single-event models for such multi-event problems, but this approach fails to exploit dependencies and shared structures across events. To overcome these limitations, we propose MENSA (Multi-Event Network for Survival Analysis), a deep learning model that jointly learns flexible time-to-event distributions for multiple events, whether competing or co-occurring. In addition, we introduce a novel trajectory-based likelihood term that captures the temporal ordering between events. Across four multi-event datasets, MENSA improves predictive performance over many state-of-the-art baselines. Source code is available at https://github.com/thecml/mensa.

cs.LG↗

arXiv2024

Conformalized Survival Distributions: A Generic Post-Process to Increase Calibration

Discrimination and calibration represent two important properties of survival analysis, with the former assessing the model's ability to accurately rank subjects and the latter evaluating the alignment of predicted outcomes with actual events. With their distinct nature, it is hard for survival models to simultaneously optimize both of them especially as many previous results found improving calibration tends to diminish discrimination performance. This paper introduces a novel approach utilizing conformal regression that can improve a model's calibration without degrading discrimination. We provide theoretical guarantees for the above claim, and rigorously validate the efficiency of our approach across 11 real-world datasets, showcasing its practical applicability and robustness in diverse scenarios.

cs.LG↗

arXiv2024

Federated Learning and Differential Privacy Techniques on Multi-hospital Population-scale Electrocardiogram Data

This research paper explores ways to apply Federated Learning (FL) and Differential Privacy (DP) techniques to population-scale Electrocardiogram (ECG) data. The study learns a multi-label ECG classification model using FL and DP based on 1,565,849 ECG tracings from 7 hospitals in Alberta, Canada. The FL approach allowed collaborative model training without sharing raw data between hospitals while building robust ECG classification models for diagnosing various cardiac conditions. These accurate ECG classification models can facilitate the diagnoses while preserving patient confidentiality using FL and DP techniques. Our results show that the performance achieved using our implementation of the FL approach is comparable to that of the pooled approach, where the model is trained over the aggregating data from all hospitals. Furthermore, our findings suggest that hospitals with limited ECGs for training can benefit from adopting the FL model compared to single-site training. In addition, this study showcases the trade-off between model performance and data privacy by employing DP during model training. Our code is available at https://github.com/vikhyatt/Hospital-FL-DP.

eess.SP↗

arXiv2024

Early detection of disease outbreaks and non-outbreaks using incidence data

Forecasting the occurrence and absence of novel disease outbreaks is essential for disease management. Here, we develop a general model, with no real-world training data, that accurately forecasts outbreaks and non-outbreaks. We propose a novel framework, using a feature-based time series classification method to forecast outbreaks and non-outbreaks. We tested our methods on synthetic data from a Susceptible-Infected-Recovered model for slowly changing, noisy disease dynamics. Outbreak sequences give a transcritical bifurcation within a specified future time window, whereas non-outbreak (null bifurcation) sequences do not. We identified incipient differences in time series of infectives leading to future outbreaks and non-outbreaks. These differences are reflected in 22 statistical features and 5 early warning signal indicators. Classifier performance, given by the area under the receiver-operating curve, ranged from 0.99 for large expanding windows of training data to 0.7 for small rolling windows. Real-world performances of classifiers were tested on two empirical datasets, COVID-19 data from Singapore and SARS data from Hong Kong, with two classifiers exhibiting high accuracy. In summary, we showed that there are statistical features that distinguish outbreak and non-outbreak sequences long before outbreaks occur. We could detect these differences in synthetic and real-world data sets, well before potential outbreaks occur.

cs.LG↗

arXiv2024

FraGNNet: A Deep Probabilistic Model for Tandem Mass Spectrum Prediction

Compound identification from tandem mass spectrometry (MS/MS) data is a critical step in the analysis of complex mixtures. Typical solutions for the MS/MS spectrum to compound (MS2C) problem involve comparing the unknown spectrum against a library of known spectrum-molecule pairs, an approach that is limited by incomplete library coverage. Compound to MS/MS spectrum (C2MS) models can improve retrieval rates by augmenting real libraries with predicted MS/MS spectra. Unfortunately, many existing C2MS models suffer from problems with mass accuracy, generalization, or interpretability. We develop a new probabilistic method for C2MS prediction, FraGNNet, that can efficiently and accurately simulate MS/MS spectra with high mass accuracy. Our approach formulates the C2MS problem as learning a distribution over molecule fragments. FraGNNet achieves state-of-the-art performance in terms of prediction error and surpasses existing C2MS models as a tool for retrieval-based MS2C.

cs.LG↗

arXiv2024

An early warning indicator trained on stochastic disease-spreading models with different noises

The timely detection of disease outbreaks through reliable early warning signals (EWSs) is indispensable for effective public health mitigation strategies. Nevertheless, the intricate dynamics of real-world disease spread, often influenced by diverse sources of noise and limited data in the early stages of outbreaks, pose a significant challenge in developing reliable EWSs, as the performance of existing indicators varies with extrinsic and intrinsic noises. Here, we address the challenge of modeling disease when the measurements are corrupted by additive white noise, multiplicative environmental noise, and demographic noise into a standard epidemic mathematical model. To navigate the complexities introduced by these noise sources, we employ a deep learning algorithm that provides EWS in infectious disease outbreak by training on noise-induced disease-spreading models. The indicator's effectiveness is demonstrated through its application to real-world COVID-19 cases in Edmonton and simulated time series derived from diverse disease spread models affected by noise. Notably, the indicator captures an impending transition in a time series of disease outbreaks and outperforms existing indicators. This study contributes to advancing early warning capabilities by addressing the intricate dynamics inherent in real-world disease spread, presenting a promising avenue for enhancing public health preparedness and response efforts.

cs.LG↗

arXiv2023

Copula-Based Deep Survival Models for Dependent Censoring

A survival dataset describes a set of instances (e.g. patients) and provides, for each, either the time until an event (e.g. death), or the censoring time (e.g. when lost to follow-up - which is a lower bound on the time until the event). We consider the challenge of survival prediction: learning, from such data, a predictive model that can produce an individual survival distribution for a novel instance. Many contemporary methods of survival prediction implicitly assume that the event and censoring distributions are independent conditional on the instance's covariates - a strong assumption that is difficult to verify (as we observe only one outcome for each instance) and which can induce significant bias when it does not hold. This paper presents a parametric model of survival that extends modern non-linear survival analysis by relaxing the assumption of conditional independence. On synthetic and semi-synthetic data, our approach significantly improves estimates of survival distributions compared to the standard that assumes conditional independence in the data.

cs.LG↗

arXiv2023

An Effective Meaningful Way to Evaluate Survival Models

One straightforward metric to evaluate a survival prediction model is based on the Mean Absolute Error (MAE) -- the average of the absolute difference between the time predicted by the model and the true event time, over all subjects. Unfortunately, this is challenging because, in practice, the test set includes (right) censored individuals, meaning we do not know when a censored individual actually experienced the event. In this paper, we explore various metrics to estimate MAE for survival datasets that include (many) censored individuals. Moreover, we introduce a novel and effective approach for generating realistic semi-synthetic survival datasets to facilitate the evaluation of metrics. Our findings, based on the analysis of the semi-synthetic datasets, reveal that our proposed metric (MAE using pseudo-observations) is able to rank models accurately based on their performance, and often closely matches the true MAE -- in particular, is better than several alternative methods.

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