arXiv subjects

Jenna Wiens

Publications and source records attributed to Jenna Wiens.

At least 37 records · Page 2Linked to original sources

arXiv2023

Leveraging Factored Action Spaces for Efficient Offline Reinforcement Learning in Healthcare

Many reinforcement learning (RL) applications have combinatorial action spaces, where each action is a composition of sub-actions. A standard RL approach ignores this inherent factorization structure, resulting in a potential failure to make meaningful inferences about rarely observed sub-action combinations; this is particularly problematic for offline settings, where data may be limited. In this work, we propose a form of linear Q-function decomposition induced by factored action spaces. We study the theoretical properties of our approach, identifying scenarios where it is guaranteed to lead to zero bias when used to approximate the Q-function. Outside the regimes with theoretical guarantees, we show that our approach can still be useful because it leads to better sample efficiency without necessarily sacrificing policy optimality, allowing us to achieve a better bias-variance trade-off. Across several offline RL problems using simulators and real-world datasets motivated by healthcare, we demonstrate that incorporating factored action spaces into value-based RL can result in better-performing policies. Our approach can help an agent make more accurate inferences within underexplored regions of the state-action space when applying RL to observational datasets.

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arXiv2023

Forecasting with Sparse but Informative Variables: A Case Study in Predicting Blood Glucose

In time-series forecasting, future target values may be affected by both intrinsic and extrinsic effects. When forecasting blood glucose, for example, intrinsic effects can be inferred from the history of the target signal alone (\textit{i.e.} blood glucose), but accurately modeling the impact of extrinsic effects requires auxiliary signals, like the amount of carbohydrates ingested. Standard forecasting techniques often assume that extrinsic and intrinsic effects vary at similar rates. However, when auxiliary signals are generated at a much lower frequency than the target variable (e.g., blood glucose measurements are made every 5 minutes, while meals occur once every few hours), even well-known extrinsic effects (e.g., carbohydrates increase blood glucose) may prove difficult to learn. To better utilize these \textit{sparse but informative variables} (SIVs), we introduce a novel encoder/decoder forecasting approach that accurately learns the per-timepoint effect of the SIV, by (i) isolating it from intrinsic effects and (ii) restricting its learned effect based on domain knowledge. On a simulated dataset pertaining to the task of blood glucose forecasting, when the SIV is accurately recorded our approach outperforms baseline approaches in terms of rMSE (13.07 [95% CI: 11.77,14.16] vs. 14.14 [12.69,15.27]). In the presence of a corrupted SIV, the proposed approach can still result in lower error compared to the baseline but the advantage is reduced as noise increases. By isolating their effects and incorporating domain knowledge, our approach makes it possible to better utilize SIVs in forecasting.

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arXiv2022

Disparate Censorship & Undertesting: A Source of Label Bias in Clinical Machine Learning

As machine learning (ML) models gain traction in clinical applications, understanding the impact of clinician and societal biases on ML models is increasingly important. While biases can arise in the labels used for model training, the many sources from which these biases arise are not yet well-studied. In this paper, we highlight disparate censorship (i.e., differences in testing rates across patient groups) as a source of label bias that clinical ML models may amplify, potentially causing harm. Many patient risk-stratification models are trained using the results of clinician-ordered diagnostic and laboratory tests of labels. Patients without test results are often assigned a negative label, which assumes that untested patients do not experience the outcome. Since orders are affected by clinical and resource considerations, testing may not be uniform in patient populations, giving rise to disparate censorship. Disparate censorship in patients of equivalent risk leads to undertesting in certain groups, and in turn, more biased labels for such groups. Using such biased labels in standard ML pipelines could contribute to gaps in model performance across patient groups. Here, we theoretically and empirically characterize conditions in which disparate censorship or undertesting affect model performance across subgroups. Our findings call attention to disparate censorship as a source of label bias in clinical ML models.

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arXiv2022

Combining chest X-rays and electronic health record (EHR) data using machine learning to diagnose acute respiratory failure

Objective: When patients develop acute respiratory failure, accurately identifying the underlying etiology is essential for determining the best treatment. However, differentiating between common medical diagnoses can be challenging in clinical practice. Machine learning models could improve medical diagnosis by aiding in the diagnostic evaluation of these patients. Materials and Methods: Machine learning models were trained to predict the common causes of acute respiratory failure (pneumonia, heart failure, and/or COPD). Models were trained using chest radiographs and clinical data from the electronic health record (EHR) and applied to an internal and external cohort. Results: The internal cohort of 1,618 patients included 508 (31%) with pneumonia, 363 (22%) with heart failure, and 137 (8%) with COPD based on physician chart review. A model combining chest radiographs and EHR data outperformed models based on each modality alone. Models had similar or better performance compared to a randomly selected physician reviewer. For pneumonia, the combined model area under the receiver operating characteristic curve (AUROC) was 0.79 (0.77-0.79), image model AUROC was 0.74 (0.72-0.75), and EHR model AUROC was 0.74 (0.70-0.76). For heart failure, combined: 0.83 (0.77-0.84), image: 0.80 (0.71-0.81), and EHR: 0.79 (0.75-0.82). For COPD, combined: AUROC = 0.88 (0.83-0.91), image: 0.83 (0.77-0.89), and EHR: 0.80 (0.76-0.84). In the external cohort, performance was consistent for heart failure and increased for COPD, but declined slightly for pneumonia. Conclusions: Machine learning models combining chest radiographs and EHR data can accurately differentiate between common causes of acute respiratory failure. Further work is needed to determine how these models could act as a diagnostic aid to clinicians in clinical settings.

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arXiv2021

Model Selection for Offline Reinforcement Learning: Practical Considerations for Healthcare Settings

Reinforcement learning (RL) can be used to learn treatment policies and aid decision making in healthcare. However, given the need for generalization over complex state/action spaces, the incorporation of function approximators (e.g., deep neural networks) requires model selection to reduce overfitting and improve policy performance at deployment. Yet a standard validation pipeline for model selection requires running a learned policy in the actual environment, which is often infeasible in a healthcare setting. In this work, we investigate a model selection pipeline for offline RL that relies on off-policy evaluation (OPE) as a proxy for validation performance. We present an in-depth analysis of popular OPE methods, highlighting the additional hyperparameters and computational requirements (fitting/inference of auxiliary models) when used to rank a set of candidate policies. We compare the utility of different OPE methods as part of the model selection pipeline in the context of learning to treat patients with sepsis. Among all the OPE methods we considered, fitted Q evaluation (FQE) consistently leads to the best validation ranking, but at a high computational cost. To balance this trade-off between accuracy of ranking and computational efficiency, we propose a simple two-stage approach to accelerate model selection by avoiding potentially unnecessary computation. Our work serves as a practical guide for offline RL model selection and can help RL practitioners select policies using real-world datasets. To facilitate reproducibility and future extensions, the code accompanying this paper is available online at https://github.com/MLD3/OfflineRL_ModelSelection.

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arXiv2021

Mind the Performance Gap: Examining Dataset Shift During Prospective Validation

Once integrated into clinical care, patient risk stratification models may perform worse compared to their retrospective performance. To date, it is widely accepted that performance will degrade over time due to changes in care processes and patient populations. However, the extent to which this occurs is poorly understood, in part because few researchers report prospective validation performance. In this study, we compare the 2020-2021 ('20-'21) prospective performance of a patient risk stratification model for predicting healthcare-associated infections to a 2019-2020 ('19-'20) retrospective validation of the same model. We define the difference in retrospective and prospective performance as the performance gap. We estimate how i) "temporal shift", i.e., changes in clinical workflows and patient populations, and ii) "infrastructure shift", i.e., changes in access, extraction and transformation of data, both contribute to the performance gap. Applied prospectively to 26,864 hospital encounters during a twelve-month period from July 2020 to June 2021, the model achieved an area under the receiver operating characteristic curve (AUROC) of 0.767 (95% confidence interval (CI): 0.737, 0.801) and a Brier score of 0.189 (95% CI: 0.186, 0.191). Prospective performance decreased slightly compared to '19-'20 retrospective performance, in which the model achieved an AUROC of 0.778 (95% CI: 0.744, 0.815) and a Brier score of 0.163 (95% CI: 0.161, 0.165). The resulting performance gap was primarily due to infrastructure shift and not temporal shift. So long as we continue to develop and validate models using data stored in large research data warehouses, we must consider differences in how and when data are accessed, measure how these differences may affect prospective performance, and work to mitigate those differences.

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arXiv2021

Shapley Flow: A Graph-based Approach to Interpreting Model Predictions

Many existing approaches for estimating feature importance are problematic because they ignore or hide dependencies among features. A causal graph, which encodes the relationships among input variables, can aid in assigning feature importance. However, current approaches that assign credit to nodes in the causal graph fail to explain the entire graph. In light of these limitations, we propose Shapley Flow, a novel approach to interpreting machine learning models. It considers the entire causal graph, and assigns credit to \textit{edges} instead of treating nodes as the fundamental unit of credit assignment. Shapley Flow is the unique solution to a generalization of the Shapley value axioms to directed acyclic graphs. We demonstrate the benefit of using Shapley Flow to reason about the impact of a model's input on its output. In addition to maintaining insights from existing approaches, Shapley Flow extends the flat, set-based, view prevalent in game theory based explanation methods to a deeper, \textit{graph-based}, view. This graph-based view enables users to understand the flow of importance through a system, and reason about potential interventions.

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arXiv2020

Deep Learning Applied to Chest X-Rays: Exploiting and Preventing Shortcuts

While deep learning has shown promise in improving the automated diagnosis of disease based on chest X-rays, deep networks may exhibit undesirable behavior related to shortcuts. This paper studies the case of spurious class skew in which patients with a particular attribute are spuriously more likely to have the outcome of interest. For instance, clinical protocols might lead to a dataset in which patients with pacemakers are disproportionately likely to have congestive heart failure. This skew can lead to models that take shortcuts by heavily relying on the biased attribute. We explore this problem across a number of attributes in the context of diagnosing the cause of acute hypoxemic respiratory failure. Applied to chest X-rays, we show that i) deep nets can accurately identify many patient attributes including sex (AUROC = 0.96) and age (AUROC >= 0.90), ii) they tend to exploit correlations between such attributes and the outcome label when learning to predict a diagnosis, leading to poor performance when such correlations do not hold in the test population (e.g., everyone in the test set is male), and iii) a simple transfer learning approach is surprisingly effective at preventing the shortcut and promoting good generalization performance. On the task of diagnosing congestive heart failure based on a set of chest X-rays skewed towards older patients (age >= 63), the proposed approach improves generalization over standard training from 0.66 (95% CI: 0.54-0.77) to 0.84 (95% CI: 0.73-0.92) AUROC. While simple, the proposed approach has the potential to improve the performance of models across populations by encouraging reliance on clinically relevant manifestations of disease, i.e., those that a clinician would use to make a diagnosis.

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arXiv2020

Deep Reinforcement Learning for Closed-Loop Blood Glucose Control

People with type 1 diabetes (T1D) lack the ability to produce the insulin their bodies need. As a result, they must continually make decisions about how much insulin to self-administer to adequately control their blood glucose levels. Longitudinal data streams captured from wearables, like continuous glucose monitors, can help these individuals manage their health, but currently the majority of the decision burden remains on the user. To relieve this burden, researchers are working on closed-loop solutions that combine a continuous glucose monitor and an insulin pump with a control algorithm in an `artificial pancreas.' Such systems aim to estimate and deliver the appropriate amount of insulin. Here, we develop reinforcement learning (RL) techniques for automated blood glucose control. Through a series of experiments, we compare the performance of different deep RL approaches to non-RL approaches. We highlight the flexibility of RL approaches, demonstrating how they can adapt to new individuals with little additional data. On over 2.1 million hours of data from 30 simulated patients, our RL approach outperforms baseline control algorithms: leading to a decrease in median glycemic risk of nearly 50% from 8.34 to 4.24 and a decrease in total time hypoglycemic of 99.8%, from 4,610 days to 6. Moreover, these approaches are able to adapt to predictable meal times (decreasing average risk by an additional 24% as meals increase in predictability). This work demonstrates the potential of deep RL to help people with T1D manage their blood glucose levels without requiring expert knowledge. All of our code is publicly available, allowing for replication and extension.

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arXiv2020

Clinician-in-the-Loop Decision Making: Reinforcement Learning with Near-Optimal Set-Valued Policies

Standard reinforcement learning (RL) aims to find an optimal policy that identifies the best action for each state. However, in healthcare settings, many actions may be near-equivalent with respect to the reward (e.g., survival). We consider an alternative objective -- learning set-valued policies to capture near-equivalent actions that lead to similar cumulative rewards. We propose a model-free algorithm based on temporal difference learning and a near-greedy heuristic for action selection. We analyze the theoretical properties of the proposed algorithm, providing optimality guarantees and demonstrate our approach on simulated environments and a real clinical task. Empirically, the proposed algorithm exhibits good convergence properties and discovers meaningful near-equivalent actions. Our work provides theoretical, as well as practical, foundations for clinician/human-in-the-loop decision making, in which humans (e.g., clinicians, patients) can incorporate additional knowledge (e.g., side effects, patient preference) when selecting among near-equivalent actions.

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arXiv2020

AdaSGD: Bridging the gap between SGD and Adam

In the context of stochastic gradient descent(SGD) and adaptive moment estimation (Adam),researchers have recently proposed optimization techniques that transition from Adam to SGD with the goal of improving both convergence and generalization performance. However, precisely how each approach trades off early progress and generalization is not well understood; thus, it is unclear when or even if, one should transition from one approach to the other. In this work, by first studying the convex setting, we identify potential contributors to observed differences in performance between SGD and Adam. In particular,we provide theoretical insights for when and why Adam outperforms SGD and vice versa. We ad-dress the performance gap by adapting a single global learning rate for SGD, which we refer to as AdaSGD. We justify this proposed approach with empirical analyses in non-convex settings. On several datasets that span three different domains,we demonstrate how AdaSGD combines the benefits of both SGD and Adam, eliminating the need for approaches that transition from Adam to SGD.

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arXiv2020

Relaxed Parameter Sharing: Effectively Modeling Time-Varying Relationships in Clinical Time-Series

Recurrent neural networks (RNNs) are commonly applied to clinical time-series data with the goal of learning patient risk stratification models. Their effectiveness is due, in part, to their use of parameter sharing over time (i.e., cells are repeated hence the name recurrent). We hypothesize, however, that this trait also contributes to the increased difficulty such models have with learning relationships that change over time. Conditional shift, i.e., changes in the relationship between the input X and the output y, arises when risk factors associated with the event of interest change over the course of a patient admission. While in theory, RNNs and gated RNNs (e.g., LSTMs) in particular should be capable of learning time-varying relationships, when training data are limited, such models often fail to accurately capture these dynamics. We illustrate the advantages and disadvantages of complete parameter sharing (RNNs) by comparing an LSTM with shared parameters to a sequential architecture with time-varying parameters on prediction tasks involving three clinically-relevant outcomes: acute respiratory failure (ARF), shock, and in-hospital mortality. In experiments using synthetic data, we demonstrate how parameter sharing in LSTMs leads to worse performance in the presence of conditional shift. To improve upon the dichotomy between complete parameter sharing and no parameter sharing, we propose a novel RNN formulation based on a mixture model in which we relax parameter sharing over time. The proposed method outperforms standard LSTMs and other state-of-the-art baselines across all tasks. In settings with limited data, relaxed parameter sharing can lead to improved patient risk stratification performance.

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arXiv2019

Advocacy Learning: Learning through Competition and Class-Conditional Representations

We introduce advocacy learning, a novel supervised training scheme for attention-based classification problems. Advocacy learning relies on a framework consisting of two connected networks: 1) $N$ Advocates (one for each class), each of which outputs an argument in the form of an attention map over the input, and 2) a Judge, which predicts the class label based on these arguments. Each Advocate produces a class-conditional representation with the goal of convincing the Judge that the input example belongs to their class, even when the input belongs to a different class. Applied to several different classification tasks, we show that advocacy learning can lead to small improvements in classification accuracy over an identical supervised baseline. Though a series of follow-up experiments, we analyze when and how such class-conditional representations improve discriminative performance. Though somewhat counter-intuitive, a framework in which subnetworks are trained to competitively provide evidence in support of their class shows promise, in many cases performing on par with standard learning approaches. This provides a foundation for further exploration into competition and class-conditional representations in supervised learning.

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arXiv2019

Automatically Evaluating Balance: A Machine Learning Approach

Compared to in-clinic balance training, in-home training is not as effective. This is, in part, due to the lack of feedback from physical therapists (PTs). Here, we analyze the feasibility of using trunk sway data and machine learning (ML) techniques to automatically evaluate balance, providing accurate assessments outside of the clinic. We recruited sixteen participants to perform standing balance exercises. For each exercise, we recorded trunk sway data and had a PT rate balance performance on a scale of 1 to 5. The rating scale was adapted from the Functional Independence Measure. From the trunk sway data, we extracted a 61-dimensional feature vector representing performance of each exercise. Given these labeled data, we trained a multi-class support vector machine (SVM) to map trunk sway features to PT ratings. Evaluated in a leave-one-participant-out scheme, the model achieved a classification accuracy of 82%. Compared to participant self-assessment ratings, the SVM outputs were significantly closer to PT ratings. The results of this pilot study suggest that in the absence of PTs, ML techniques can provide accurate assessments during standing balance exercises. Such automated assessments could reduce PT consultation time and increase user compliance outside of the clinic.

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arXiv2018

Leveraging Clinical Time-Series Data for Prediction: A Cautionary Tale

In healthcare, patient risk stratification models are often learned using time-series data extracted from electronic health records. When extracting data for a clinical prediction task, several formulations exist, depending on how one chooses the time of prediction and the prediction horizon. In this paper, we show how the formulation can greatly impact both model performance and clinical utility. Leveraging a publicly available ICU dataset, we consider two clinical prediction tasks: in-hospital mortality, and hypokalemia. Through these case studies, we demonstrate the necessity of evaluating models using an outcome-independent reference point, since choosing the time of prediction relative to the event can result in unrealistic performance. Further, an outcome-independent scheme outperforms an outcome-dependent scheme on both tasks (In-Hospital Mortality AUROC .882 vs. .831; Serum Potassium: AUROC .829 vs. .740) when evaluated on test sets that mimic real-world use.

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arXiv2018

Learning to Exploit Invariances in Clinical Time-Series Data using Sequence Transformer Networks

Recently, researchers have started applying convolutional neural networks (CNNs) with one-dimensional convolutions to clinical tasks involving time-series data. This is due, in part, to their computational efficiency, relative to recurrent neural networks and their ability to efficiently exploit certain temporal invariances, (e.g., phase invariance). However, it is well-established that clinical data may exhibit many other types of invariances (e.g., scaling). While preprocessing techniques, (e.g., dynamic time warping) may successfully transform and align inputs, their use often requires one to identify the types of invariances in advance. In contrast, we propose the use of Sequence Transformer Networks, an end-to-end trainable architecture that learns to identify and account for invariances in clinical time-series data. Applied to the task of predicting in-hospital mortality, our proposed approach achieves an improvement in the area under the receiver operating characteristic curve (AUROC) relative to a baseline CNN (AUROC=0.851 vs. AUROC=0.838). Our results suggest that a variety of valuable invariances can be learned directly from the data.

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arXiv2018

A Domain Guided CNN Architecture for Predicting Age from Structural Brain Images

Given the wide success of convolutional neural networks (CNNs) applied to natural images, researchers have begun to apply them to neuroimaging data. To date, however, exploration of novel CNN architectures tailored to neuroimaging data has been limited. Several recent works fail to leverage the 3D structure of the brain, instead treating the brain as a set of independent 2D slices. Approaches that do utilize 3D convolutions rely on architectures developed for object recognition tasks in natural 2D images. Such architectures make assumptions about the input that may not hold for neuroimaging. For example, existing architectures assume that patterns in the brain exhibit translation invariance. However, a pattern in the brain may have different meaning depending on where in the brain it is located. There is a need to explore novel architectures that are tailored to brain images. We present two simple modifications to existing CNN architectures based on brain image structure. Applied to the task of brain age prediction, our network achieves a mean absolute error (MAE) of 1.4 years and trains 30% faster than a CNN baseline that achieves a MAE of 1.6 years. Our results suggest that lessons learned from developing models on natural images may not directly transfer to neuroimaging tasks. Instead, there remains a large space of unexplored questions regarding model development in this area, whose answers may differ from conventional wisdom.

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arXiv2018

Deep Multi-Output Forecasting: Learning to Accurately Predict Blood Glucose Trajectories

In many forecasting applications, it is valuable to predict not only the value of a signal at a certain time point in the future, but also the values leading up to that point. This is especially true in clinical applications, where the future state of the patient can be less important than the patient's overall trajectory. This requires multi-step forecasting, a forecasting variant where one aims to predict multiple values in the future simultaneously. Standard methods to accomplish this can propagate error from prediction to prediction, reducing quality over the long term. In light of these challenges, we propose multi-output deep architectures for multi-step forecasting in which we explicitly model the distribution of future values of the signal over a prediction horizon. We apply these techniques to the challenging and clinically relevant task of blood glucose forecasting. Through a series of experiments on a real-world dataset consisting of 550K blood glucose measurements, we demonstrate the effectiveness of our proposed approaches in capturing the underlying signal dynamics. Compared to existing shallow and deep methods, we find that our proposed approaches improve performance individually and capture complementary information, leading to a large improvement over the baseline when combined (4.87 vs. 5.31 absolute percentage error (APE)). Overall, the results suggest the efficacy of our proposed approach in predicting blood glucose level and multi-step forecasting more generally.

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