George H. Chen

We propose an interpretable deep competing risks model called the Deep Kernel Aalen-Johansen (DKAJ) estimator, which generalizes the classical Aalen-Johansen nonparametric estimate of cumulative incidence functions (CIFs). Each data point (e.g., patient) is represented as a weighted combination of clusters. If a data point has nonzero weight only for one cluster, then its predicted CIFs correspond to those of the classical Aalen-Johansen estimator restricted to data points from that cluster. These weights come from an automatically learned kernel function that measures how similar any two data points are. On four standard competing risks datasets, we show that DKAJ is competitive with state-of-the-art baselines while being able to provide visualizations to assist model interpretation.

Understanding temporal dynamics in clinical narratives is essential for modeling patient trajectories, yet large-scale temporally annotated resources remain limited. We present PMOA–TTS, the first openly available dataset of 124,699 PubMed Open Access (PMOA) case reports, each converted into structured (event, time) timelines via a scalable LLM-based pipeline. Our approach combines heuristic filtering with Llama 3.3 to identify single-patient case reports, followed by prompt-driven extraction using Llama 3.3 and DeepSeek R1, resulting in over 5.6 million timestamped clinical events. To assess timeline quality, we evaluate against a clinician-curated reference set using three metrics: (i) event-level matching (80% match at a cosine similarity threshold of 0.1), (ii) temporal concordance (c-index > 0.90), and (iii) Area Under the Log-Time CDF (AULTC) for timestamp alignment. Corpus-level analysis shows wide diagnostic and demographic coverage. In a downstream survival prediction task, embeddings from extracted timelines achieve time-dependent concordance indices up to 0.82 ± 0.01, demonstrating the predictive value of temporally structured narratives. PMOA–TTS provides a scalable foundation for timeline extraction, temporal reasoning, and longitudinal modeling in biomedical NLP. The dataset is available at: https://huggingface.co/datasets/snoroozi/pmoa-tts .

Prognostication for comatose post-cardiac arrest patients is a critical challenge that directly impacts clinical decision-making in the ICU. Clinical information that informs prognostication is collected serially over time. Shortly after cardiac arrest, various time-invariant baseline features are collected (e.g., demographics, cardiac arrest characteristics). After ICU admission, additional features are gathered, including time-varying hemodynamic data (e.g., blood pressure, doses of vasopressor medications). We view these as two phases in which we collect new features. In this study, we propose a novel stepwise dynamic competing risks model that improves the prediction of neurological outcomes by automatically determining when to take advantage of time-invariant features (first phase) and time-varying features (second phase). Notably, our model finds patients for whom this second phase (time-varying hemodynamic) information is beneficial for prognostication and also when this information is beneficial (as we collect more hemodynamic data for a patient over time, how important these data are for prognostication varies). Our approach extends the standard Fine and Gray model to explicitly model the two phases and to incorporate neural networks to flexibly capture complex nonlinear feature relationships. Evaluated on a retrospective cohort of 2,278 comatose post-arrest patients, our model demonstrates robust discriminative performance for the competing outcomes of awakening, withdrawal of life-sustaining therapy, and death despite maximal support. Our approach generalizes to more than two phases in which new features are collected and could be used in other dynamic prediction tasks, where it may be helpful to know when and for whom newly collected features significantly improve prediction.

Many modern methods for prediction leverage nearest neighbor search to find past training examples most similar to a test example, an idea that dates back in text to at least the 11th century and has stood the test of time. This monograph aims to explain the success of these methods, both in theory, for which we cover foundational nonasymptotic statistical guarantees on nearest-neighbor-based regression and classification, and in practice, for which we gather prominent methods for approximate nearest neighbor search that have been essential to scaling prediction systems reliant on nearest neighbor analysis to handle massive datasets. Furthermore, we discuss connections to learning distances for use with nearest neighbor methods, including how random decision trees and ensemble methods learn nearest neighbor structure, as well as recent developments in crowdsourcing and graphons. In terms of theory, our focus is on nonasymptotic statistical guarantees, which we state in the form of how many training data and what algorithm parameters ensure that a nearest neighbor prediction method achieves a user-specified error tolerance. We begin with the most general of such results for nearest neighbor and related kernel regression and classification in general metric spaces. In such settings in which we assume very little structure, what enables successful prediction is smoothness in the function being estimated for regression, and a low probability of landing near the decision boundary for classification. In practice, these conditions could be difficult to verify for a real dataset. We then cover recent guarantees on nearest neighbor prediction in the three case studies of time series forecasting, recommending products to people over time, and delineating human organs in medical images by looking at image patches. In these case studies, clustering structure enables successful prediction.

Many applications involve reasoning about time durations before a critical event happens—also called time-to-event outcomes. When will a customer cancel a subscription, a coma patient wake up, or a convicted criminal reoffend? Accurate predictions of such time durations could help downstream decision-making tasks. A key challenge is censoring: commonly, when we collect training data, we do not get to observe the time-to-event outcome for every data point. For example, a coma patient has not woken up yet, so we do not know the patient’s time until awakening. However, these data points should not be excluded from analysis as they could have characteristics that explain why they have yet to or might never experience the event. Time-to-event outcomes have been studied extensively within the field of survival analysis primarily by the statistical, medical, and reliability engineering communities, with textbooks already available in the 1970s and ’80s. Recently, the machine learning community has made significant methodological advances in survival analysis that take advantage of the representation learning ability of deep neural networks. At this point, there is a proliferation of deep survival analysis models. How do these models work? Why? What are the overarching principles in how these models are generally developed? How are different models related? This monograph aims to provide a reasonably self-contained modern introduction to survival analysis. We focus on predicting time-to-event outcomes at the individual data point level with the help of neural networks. Our goal is to provide the reader with a working understanding of precisely what the basic time-to-event prediction problem is, how it differs from standard regression and classification, and how key “design patterns” have been used time after time to derive new time-to-event prediction models, from classical methods like the Cox proportional hazards model to modern deep learning approaches such as deep kernel Kaplan-Meier estimators and neural ordinary differential equation models. We further delve into two extensions of the basic time-to-event prediction setup: predicting which of several critical events will happen first along with the time until this earliest event happens (the competing risks setting), and predicting time-to-event outcomes given a time series that grows in length over time (the dynamic setting). We conclude with a discussion of a variety of topics such as fairness, causal reasoning, interpretability, and statistical guarantees. Our monograph comes with an accompanying code repository that implements every model and evaluation metric that we cover in detail: https://github.com/georgehc/survival-intro

Time series foundation models are pre-trained on large datasets and are able to achieve state-of-the-art performance in diverse tasks. However, to date, there has been limited work demonstrating how well these models perform in medical applications, where labeled data can be scarce. Further, we observe that currently, the majority of time series foundation models either are univariate in nature, or assume channel independence, meaning that they handle multivariate time series but do not model how the different variables relate. In this paper, we propose a prompt-tuning-inspired fine-tuning technique, Generalized Prompt Tuning (Gen-P-Tuning), that enables us to adapt an existing univariate time series foundation model (treated as frozen) to handle multivariate time series prediction. Our approach provides a way to combine information across channels (variables) of multivariate time series. We demonstrate the effectiveness of our fine-tuning approach against various baselines on two MIMIC classification tasks, and on influenza-like illness forecasting.

The third ML4H symposium was held in person on December 10, 2023, in New Orleans, Louisiana, USA. The symposium included research roundtable sessions to foster discussions between participants and senior researchers on timely and relevant topics for the \ac{ML4H} community. Encouraged by the successful virtual roundtables in the previous year, we organized eleven in-person roundtables and four virtual roundtables at ML4H 2022. The organization of the research roundtables at the conference involved 17 Senior Chairs and 19 Junior Chairs across 11 tables. Each roundtable session included invited senior chairs (with substantial experience in the field), junior chairs (responsible for facilitating the discussion), and attendees from diverse backgrounds with interest in the session's topic. Herein we detail the organization process and compile takeaways from these roundtable discussions, including recent advances, applications, and open challenges for each topic. We conclude with a summary and lessons learned across all roundtables. This document serves as a comprehensive review paper, summarizing the recent advancements in machine learning for healthcare as contributed by foremost researchers in the field.

Kernel survival analysis models estimate individual survival distributions with the help of a kernel function, which measures the similarity between any two data points. Such a kernel function can be learned using deep kernel survival models. In this paper, we present a new deep kernel survival model called a survival kernet, which scales to large datasets in a manner that is amenable to model interpretation and also theoretical analysis. Specifically, the training data are partitioned into clusters based on a recently developed training set compression scheme for classification and regression called kernel netting that we extend to the survival analysis setting. At test time, each data point is represented as a weighted combination of these clusters, and each such cluster can be visualized. For a special case of survival kernets, we establish a finite-sample error bound on predicted survival distributions that is, up to a log factor, optimal. Whereas scalability at test time is achieved using the aforementioned kernel netting compression strategy, scalability during training is achieved by a warm-start procedure based on tree ensembles such as XGBoost and a heuristic approach to accelerating neural architecture search. On four standard survival analysis datasets of varying sizes (up to roughly 3 million data points), we show that survival kernets are highly competitive compared to various baselines tested in terms of time-dependent concordance index. Our code is available at: https://github.com/georgehc/survival-kernets