8,739 research outputs found
DeepCare: A Deep Dynamic Memory Model for Predictive Medicine
Personalized predictive medicine necessitates the modeling of patient illness
and care processes, which inherently have long-term temporal dependencies.
Healthcare observations, recorded in electronic medical records, are episodic
and irregular in time. We introduce DeepCare, an end-to-end deep dynamic neural
network that reads medical records, stores previous illness history, infers
current illness states and predicts future medical outcomes. At the data level,
DeepCare represents care episodes as vectors in space, models patient health
state trajectories through explicit memory of historical records. Built on Long
Short-Term Memory (LSTM), DeepCare introduces time parameterizations to handle
irregular timed events by moderating the forgetting and consolidation of memory
cells. DeepCare also incorporates medical interventions that change the course
of illness and shape future medical risk. Moving up to the health state level,
historical and present health states are then aggregated through multiscale
temporal pooling, before passing through a neural network that estimates future
outcomes. We demonstrate the efficacy of DeepCare for disease progression
modeling, intervention recommendation, and future risk prediction. On two
important cohorts with heavy social and economic burden -- diabetes and mental
health -- the results show improved modeling and risk prediction accuracy.Comment: Accepted at JBI under the new name: "Predicting healthcare
trajectories from medical records: A deep learning approach
Benchmarking Deep Learning Architectures for Predicting Readmission to the ICU and Describing Patients-at-Risk
Objective: To compare different deep learning architectures for predicting
the risk of readmission within 30 days of discharge from the intensive care
unit (ICU). The interpretability of attention-based models is leveraged to
describe patients-at-risk. Methods: Several deep learning architectures making
use of attention mechanisms, recurrent layers, neural ordinary differential
equations (ODEs), and medical concept embeddings with time-aware attention were
trained using publicly available electronic medical record data (MIMIC-III)
associated with 45,298 ICU stays for 33,150 patients. Bayesian inference was
used to compute the posterior over weights of an attention-based model. Odds
ratios associated with an increased risk of readmission were computed for
static variables. Diagnoses, procedures, medications, and vital signs were
ranked according to the associated risk of readmission. Results: A recurrent
neural network, with time dynamics of code embeddings computed by neural ODEs,
achieved the highest average precision of 0.331 (AUROC: 0.739, F1-Score:
0.372). Predictive accuracy was comparable across neural network architectures.
Groups of patients at risk included those suffering from infectious
complications, with chronic or progressive conditions, and for whom standard
medical care was not suitable. Conclusions: Attention-based networks may be
preferable to recurrent networks if an interpretable model is required, at only
marginal cost in predictive accuracy
Improving Palliative Care with Deep Learning
Improving the quality of end-of-life care for hospitalized patients is a
priority for healthcare organizations. Studies have shown that physicians tend
to over-estimate prognoses, which in combination with treatment inertia results
in a mismatch between patients wishes and actual care at the end of life. We
describe a method to address this problem using Deep Learning and Electronic
Health Record (EHR) data, which is currently being piloted, with Institutional
Review Board approval, at an academic medical center. The EHR data of admitted
patients are automatically evaluated by an algorithm, which brings patients who
are likely to benefit from palliative care services to the attention of the
Palliative Care team. The algorithm is a Deep Neural Network trained on the EHR
data from previous years, to predict all-cause 3-12 month mortality of patients
as a proxy for patients that could benefit from palliative care. Our
predictions enable the Palliative Care team to take a proactive approach in
reaching out to such patients, rather than relying on referrals from treating
physicians, or conduct time consuming chart reviews of all patients. We also
present a novel interpretation technique which we use to provide explanations
of the model's predictions.Comment: IEEE International Conference on Bioinformatics and Biomedicine 201
Using data-driven rules to predict mortality in severe community acquired pneumonia
Prediction of patient-centered outcomes in hospitals is useful for performance benchmarking, resource allocation, and guidance regarding active treatment and withdrawal of care. Yet, their use by clinicians is limited by the complexity of available tools and amount of data required. We propose to use Disjunctive Normal Forms as a novel approach to predict hospital and 90-day mortality from instance-based patient data, comprising demographic, genetic, and physiologic information in a large cohort of patients admitted with severe community acquired pneumonia. We develop two algorithms to efficiently learn Disjunctive Normal Forms, which yield easy-to-interpret rules that explicitly map data to the outcome of interest. Disjunctive Normal Forms achieve higher prediction performance quality compared to a set of state-of-the-art machine learning models, and unveils insights unavailable with standard methods. Disjunctive Normal Forms constitute an intuitive set of prediction rules that could be easily implemented to predict outcomes and guide criteria-based clinical decision making and clinical trial execution, and thus of greater practical usefulness than currently available prediction tools. The Java implementation of the tool JavaDNF will be publicly available. © 2014 Wu et al
Saturation Effects and the Concurrency Hypothesis: Insights from an Analytic Model
Sexual partnerships that overlap in time (concurrent relationships) may play
a significant role in the HIV epidemic, but the precise effect is unclear. We
derive edge-based compartmental models of disease spread in idealized dynamic
populations with and without concurrency to allow for an investigation of its
effects. Our models assume that partnerships change in time and individuals
enter and leave the at-risk population. Infected individuals transmit at a
constant per-partnership rate to their susceptible partners. In our idealized
populations we find regions of parameter space where the existence of
concurrent partnerships leads to substantially faster growth and higher
equilibrium levels, but also regions in which the existence of concurrent
partnerships has very little impact on the growth or the equilibrium.
Additionally we find mixed regimes in which concurrency significantly increases
the early growth, but has little effect on the ultimate equilibrium level.
Guided by model predictions, we discuss general conditions under which
concurrent relationships would be expected to have large or small effects in
real-world settings. Our observation that the impact of concurrency saturates
suggests that concurrency-reducing interventions may be most effective in
populations with low to moderate concurrency
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