MENSA: A Multi-Event Network for Survival Analysis under Informative Censoring

Given an instance, a multi-event survival model predicts the time until that instance experiences each of several different events. These events are not mutually exclusive and there are often statistical dependencies between them. There are relatively few multi-event survival results, most focusing on producing a simple risk score, rather than the time-to-event itself. To overcome these issues, we introduce MENSA, a novel, deep learning approach for multi-event survival analysis that can jointly learn representations of the input covariates and the dependence structure between events. As a practical motivation for multi-event survival analysis, we consider the problem of predicting the time until a patient with amyotrophic lateral sclerosis (ALS) loses various physical functions, i.e., the ability to speak, swallow, write, or walk. When estimating when a patient is no longer able to swallow, our approach achieves an L1-Margin loss of 278.8 days, compared to 355.2 days when modeling each event separately. In addition, we also evaluate our approach in single-event and competing risk scenarios by modeling the censoring and event distributions as equal contributing factors in the optimization process, and show that our approach performs well across multiple benchmark datasets. The source code is available at: https://github.com/thecml/mensa

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.

Improving ECG-based COVID-19 diagnosis and mortality predictions using pre-pandemic medical records at population-scale

Pandemic outbreaks such as COVID-19 occur unexpectedly, and need immediate action due to their potential devastating consequences on global health. Point-of-care routine assessments such as electrocardiogram (ECG), can be used to develop prediction models for identifying individuals at risk. However, there is often too little clinically-annotated medical data, especially in early phases of a pandemic, to develop accurate prediction models. In such situations, historical pre-pandemic health records can be utilized to estimate a preliminary model, which can then be fine-tuned based on limited available pandemic data. This study shows this approach -- pre-train deep learning models with pre-pandemic data -- can work effectively, by demonstrating substantial performance improvement over three different COVID-19 related diagnostic and prognostic prediction tasks. Similar transfer learning strategies can be useful for developing timely artificial intelligence solutions in future pandemic outbreaks.

ECG for high-throughput screening of multiple diseases: Proof-of-concept using multi-diagnosis deep learning from population-based datasets

Electrocardiogram (ECG) abnormalities are linked to cardiovascular diseases, but may also occur in other non-cardiovascular conditions such as mental, neurological, metabolic and infectious conditions. However, most of the recent success of deep learning (DL) based diagnostic predictions in selected patient cohorts have been limited to a small set of cardiac diseases. In this study, we use a population-based dataset of >250,000 patients with >1000 medical conditions and >2 million ECGs to identify a wide range of diseases that could be accurately diagnosed from the patient's first in-hospital ECG. Our DL models uncovered 128 diseases and 68 disease categories with strong discriminative performance.

Multilabel 12-Lead Electrocardiogram Classification Using Gradient Boosting Tree Ensemble

The 12-lead electrocardiogram (ECG) is a commonly used tool for detecting cardiac abnormalities such as atrial fibrillation, blocks, and irregular complexes. For the PhysioNet/CinC 2020 Challenge, we built an algorithm using gradient boosted tree ensembles fitted on morphology and signal processing features to classify ECG diagnosis. For each lead, we derive features from heart rate variability, PQRST template shape, and the full signal waveform. We join the features of all 12 leads to fit an ensemble of gradient boosting decision trees to predict probabilities of ECG instances belonging to each class. We train a phase one set of feature importance determining models to isolate the top 1,000 most important features to use in our phase two diagnosis prediction models. We use repeated random sub-sampling by splitting our dataset of 43,101 records into 100 independent runs of 85:15 training/validation splits for our internal evaluation results. Our methodology generates us an official phase validation set score of 0.476 and test set score of -0.080 under the team name, CVC, placing us 36 out of 41 in the rankings.