Dosing models often use differential equations to model biological dynamics.

Modeling real-world multidimensional time series can be particularly challenging when these are sporadically observed ( i.e., sampling is irregular both in time

Modeling real-world multidimensional time series can be particularly challenging when these are sporadically observed (i.e., sampling is irregular both in time and across dimensions)--such as in the case of clinical patient data. To address these challenges, we propose (1) a continuous-time version of the Gated Recurrent Unit, building upon the recent Neural Ordinary Differential Equations (Chen et al., 2018), and (2) a Bayesian update network that processes the sporadic observations. We bring these two ideas together in our GRU-ODE-Bayes method. We then demonstrate that the proposed method encodes a continuity prior for the latent process and that it can exactly represent the Fokker-Planck dynamics of complex processes driven by a multidimensional stochastic differential equation. Additionally, empirical evaluation shows that our method outperforms the state of the art on both synthetic data and real-world data with applications in healthcare and climate forecast. What is more, the continuity prior is shown to be well suited for low number of samples settings.

Modeling real-world multidimensional time series can be particularly challenging when these are sporadically observed (i.e., sampling is irregular both in time and across dimensions)--such as in the case of clinical patient data. To address these challenges, we propose (1) a continuous-time version of the Gated Recurrent Unit, building upon the recent Neural Ordinary Differential Equations (Chen et al., 2018), and (2) a Bayesian update network that processes the sporadic observations. We bring these two ideas together in our GRU-ODE-Bayes method. We then demonstrate that the proposed method encodes a continuity prior for the latent process and that it can exactly represent the Fokker-Planck dynamics of complex processes driven by a multidimensional stochastic differential equation. Additionally, empirical evaluation shows that our method outperforms the state of the art on both synthetic data and real-world data with applications in healthcare and climate forecast.

Prevalent in many real-world settings such as healthcare, irregular time series are challenging to formulate predictions from. It is difficult to infer the value of a feature at any given time when observations are sporadic, as it could take on a range of values depending on when it was last observed. To characterize this uncertainty we present EDICT, a strategy that learns an evidential distribution over irregular time series in continuous time. This distribution enables well-calibrated and flexible inference of partially observed features at any time of interest, while expanding uncertainty temporally for sparse, irregular observations. We demonstrate that EDICT attains competitive performance on challenging time series classification tasks and enabling uncertainty-guided inference when encountering noisy data.

Dosing models often use differential equations to model biological dynamics. Neural differential equations in particular can learn to predict the derivative of a process, which permits predictions at irregular points of time. However, this temporal flexibility often comes with a high sensitivity to noise, whereas medical problems often present high noise and limited data. Moreover, medical dosing models must generalize reliably over individual patients and changing treatment policies. To address these challenges, we introduce the Neural Eigen Stochastic Differential Equation algorithm (NESDE). NESDE provides individualized modeling (using a hypernetwork over patient-level parameters); generalization to new treatment policies (using decoupled control); tunable expressiveness according to the noise level (using piecewise linearity); and fast, continuous, closed-form prediction (using spectral representation). We demonstrate the robustness of NESDE in both synthetic and real medical problems, and use the learned dynamics to publish simulated medical gym environments.