10,16,2021

 MRI Image Reconstruction via Learning Optimization Using Neural ODEs2020-06-30   ${\displaystyle \cong }$ We propose to formulate MRI image reconstruction as an optimization problem and model the optimization trajectory as a dynamic process using ordinary differential equations (ODEs). We model the dynamics in ODE with a neural network and solve the desired ODE with the off-the-shelf (fixed) solver to obtain reconstructed images. We extend this model and incorporate the knowledge of off-the-shelf ODE solvers into the network design (learned solvers). We investigate several models based on three ODE solvers and compare models with fixed solvers and learned solvers. Our models achieve better reconstruction results and are more parameter efficient than other popular methods such as UNet and cascaded CNN. We introduce a new way of tackling the MRI reconstruction problem by modeling the continuous optimization dynamics using neural ODEs. Meta-Solver for Neural Ordinary Differential Equations2021-03-15   ${\displaystyle \cong }$ A conventional approach to train neural ordinary differential equations (ODEs) is to fix an ODE solver and then learn the neural network's weights to optimize a target loss function. However, such an approach is tailored for a specific discretization method and its properties, which may not be optimal for the selected application and yield the overfitting to the given solver. In our paper, we investigate how the variability in solvers' space can improve neural ODEs performance. We consider a family of Runge-Kutta methods that are parameterized by no more than two scalar variables. Based on the solvers' properties, we propose an approach to decrease neural ODEs overfitting to the pre-defined solver, along with a criterion to evaluate such behaviour. Moreover, we show that the right choice of solver parameterization can significantly affect neural ODEs models in terms of robustness to adversarial attacks. Recently it was shown that neural ODEs demonstrate superiority over conventional CNNs in terms of robustness. Our work demonstrates that the model robustness can be further improved by optimizing solver choice for a given task. The source code to reproduce our experiments is available at https://github.com/juliagusak/neural-ode-metasolver. When are Neural ODE Solutions Proper ODEs?2020-07-30   ${\displaystyle \cong }$ A key appeal of the recently proposed Neural Ordinary Differential Equation(ODE) framework is that it seems to provide a continuous-time extension of discrete residual neural networks. As we show herein, though, trained Neural ODE models actually depend on the specific numerical method used during training. If the trained model is supposed to be a flow generated from an ODE, it should be possible to choose another numerical solver with equal or smaller numerical error without loss of performance. We observe that if training relies on a solver with overly coarse discretization, then testing with another solver of equal or smaller numerical error results in a sharp drop in accuracy. In such cases, the combination of vector field and numerical method cannot be interpreted as a flow generated from an ODE, which arguably poses a fatal breakdown of the Neural ODE concept. We observe, however, that there exists a critical step size beyond which the training yields a valid ODE vector field. We propose a method that monitors the behavior of the ODE solver during training to adapt its step size, aiming to ensure a valid ODE without unnecessarily increasing computational cost. We verify this adaption algorithm on two common bench mark datasets as well as a synthetic dataset. Furthermore, we introduce a novel synthetic dataset in which the underlying ODE directly generates a classification task. Differentiable Likelihoods for Fast Inversion of 'Likelihood-Free' Dynamical Systems2020-06-29   ${\displaystyle \cong }$ Likelihood-free (a.k.a. simulation-based) inference problems are inverse problems with expensive, or intractable, forward models. ODE inverse problems are commonly treated as likelihood-free, as their forward map has to be numerically approximated by an ODE solver. This, however, is not a fundamental constraint but just a lack of functionality in classic ODE solvers, which do not return a likelihood but a point estimate. To address this shortcoming, we employ Gaussian ODE filtering (a probabilistic numerical method for ODEs) to construct a local Gaussian approximation to the likelihood. This approximation yields tractable estimators for the gradient and Hessian of the (log-)likelihood. Insertion of these estimators into existing gradient-based optimization and sampling methods engenders new solvers for ODE inverse problems. We demonstrate that these methods outperform standard likelihood-free approaches on three benchmark-systems. Neural Ordinary Differential Equation based Recurrent Neural Network Model2020-05-19   ${\displaystyle \cong }$ Neural differential equations are a promising new member in the neural network family. They show the potential of differential equations for time series data analysis. In this paper, the strength of the ordinary differential equation (ODE) is explored with a new extension. The main goal of this work is to answer the following questions: (i)~can ODE be used to redefine the existing neural network model? (ii)~can Neural ODEs solve the irregular sampling rate challenge of existing neural network models for a continuous time series, i.e., length and dynamic nature, (iii)~how to reduce the training and evaluation time of existing Neural ODE systems? This work leverages the mathematical foundation of ODEs to redesign traditional RNNs such as Long Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU). The main contribution of this paper is to illustrate the design of two new ODE-based RNN models (GRU-ODE model and LSTM-ODE) which can compute the hidden state and cell state at any point of time using an ODE solver. These models reduce the computation overhead of hidden state and cell state by a vast amount. The performance evaluation of these two new models for learning continuous time series with irregular sampling rate is then demonstrated. Experiments show that these new ODE based RNN models require less training time than Latent ODEs and conventional Neural ODEs. They can achieve higher accuracy quickly, and the design of the neural network is simpler than, previous neural ODE systems. A Probabilistic State Space Model for Joint Inference from Differential Equations and Data2021-03-18   ${\displaystyle \cong }$ Mechanistic models with differential equations are a key component of scientific applications of machine learning. Inference in such models is usually computationally demanding, because it involves repeatedly solving the differential equation. The main problem here is that the numerical solver is hard to combine with standard inference techniques. Recent work in probabilistic numerics has developed a new class of solvers for ordinary differential equations (ODEs) that phrase the solution process directly in terms of Bayesian filtering. We here show that this allows such methods to be combined very directly, with conceptual and numerical ease, with latent force models in the ODE itself. It then becomes possible to perform approximate Bayesian inference on the latent force as well as the ODE solution in a single, linear complexity pass of an extended Kalman filter / smoother - that is, at the cost of computing a single ODE solution. We demonstrate the expressiveness and performance of the algorithm by training a non-parametric SIRD model on data from the COVID-19 outbreak. Predicting dynamical system evolution with residual neural networks2019-10-11   ${\displaystyle \cong }$ Forecasting time series and time-dependent data is a common problem in many applications. One typical example is solving ordinary differential equation (ODE) systems $\dot{x}=F(x)$. Oftentimes the right hand side function $F(x)$ is not known explicitly and the ODE system is described by solution samples taken at some time points. Hence, ODE solvers cannot be used. In this paper, a data-driven approach to learning the evolution of dynamical systems is considered. We show how by training neural networks with ResNet-like architecture on the solution samples, models can be developed to predict the ODE system solution further in time. By evaluating the proposed approaches on three test ODE systems, we demonstrate that the neural network models are able to reproduce the main dynamics of the systems qualitatively well. Moreover, the predicted solution remains stable for much longer times than for other currently known models. Neural Ordinary Differential Equations2019-12-13   ${\displaystyle \cong }$ We introduce a new family of deep neural network models. Instead of specifying a discrete sequence of hidden layers, we parameterize the derivative of the hidden state using a neural network. The output of the network is computed using a black-box differential equation solver. These continuous-depth models have constant memory cost, adapt their evaluation strategy to each input, and can explicitly trade numerical precision for speed. We demonstrate these properties in continuous-depth residual networks and continuous-time latent variable models. We also construct continuous normalizing flows, a generative model that can train by maximum likelihood, without partitioning or ordering the data dimensions. For training, we show how to scalably backpropagate through any ODE solver, without access to its internal operations. This allows end-to-end training of ODEs within larger models. Augmenting Neural Differential Equations to Model Unknown Dynamical Systems with Incomplete State Information2020-08-18   ${\displaystyle \cong }$ Neural Ordinary Differential Equations replace the right-hand side of a conventional ODE with a neural net, which by virtue of the universal approximation theorem, can be trained to the representation of any function. When we do not know the function itself, but have state trajectories (time evolution) of the ODE system we can still train the neural net to learn the representation of the underlying but unknown ODE. However if the state of the system is incompletely known then the right-hand side of the ODE cannot be calculated. The derivatives to propagate the system are unavailable. We show that a specially augmented Neural ODE can learn the system when given incomplete state information. As a worked example we apply neural ODEs to the Lotka-Voltera problem of 3 species, rabbits, wolves, and bears. We show that even when the data for the bear time series is removed the remaining time series of the rabbits and wolves is sufficient to learn the dynamical system despite the missing the incomplete state information. This is surprising since a conventional ODE system cannot output the correct derivatives without the full state as the input. We implement augmented neural ODEs and differential equation solvers in the julia programming language. Active Uncertainty Calibration in Bayesian ODE Solvers2018-11-03   ${\displaystyle \cong }$ There is resurging interest, in statistics and machine learning, in solvers for ordinary differential equations (ODEs) that return probability measures instead of point estimates. Recently, Conrad et al. introduced a sampling-based class of methods that are 'well-calibrated' in a specific sense. But the computational cost of these methods is significantly above that of classic methods. On the other hand, Schober et al. pointed out a precise connection between classic Runge-Kutta ODE solvers and Gaussian filters, which gives only a rough probabilistic calibration, but at negligible cost overhead. By formulating the solution of ODEs as approximate inference in linear Gaussian SDEs, we investigate a range of probabilistic ODE solvers, that bridge the trade-off between computational cost and probabilistic calibration, and identify the inaccurate gradient measurement as the crucial source of uncertainty. We propose the novel filtering-based method Bayesian Quadrature filtering (BQF) which uses Bayesian quadrature to actively learn the imprecision in the gradient measurement by collecting multiple gradient evaluations. Generative ODE Modeling with Known Unknowns2020-03-24   ${\displaystyle \cong }$ In several crucial applications, domain knowledge is encoded by a system of ordinary differential equations (ODE). A motivating example is intensive care unit patients: The dynamics of some vital physiological variables such as heart rate, blood pressure and arterial compliance can be approximately described by a known system of ODEs. Typically, some of the ODE variables are directly observed while some are unobserved, and in addition many other variables are observed but not modeled by the ODE, for example body temperature. Importantly, the unobserved ODE variables are known-unknowns'': We know they exist and their functional dynamics, but cannot measure them directly, nor do we know the function tying them to all observed measurements. Estimating these known-unknowns is often highly valuable to physicians. Under this scenario we wish to: (i) learn the static parameters of the ODE generating each observed time-series (ii) infer the dynamic sequence of all ODE variables including the known-unknowns, and (iii) extrapolate the future of the ODE variables and the observations of the time-series. We address this task with a variational autoencoder incorporating the known ODE function, called GOKU-net for Generative ODE modeling with Known Unknowns. We test our method on videos of pendulums with unknown length, and a model of the cardiovascular system. Time Dependence in Non-Autonomous Neural ODEs2020-05-06   ${\displaystyle \cong }$ Neural Ordinary Differential Equations (ODEs) are elegant reinterpretations of deep networks where continuous time can replace the discrete notion of depth, ODE solvers perform forward propagation, and the adjoint method enables efficient, constant memory backpropagation. Neural ODEs are universal approximators only when they are non-autonomous, that is, the dynamics depends explicitly on time. We propose a novel family of Neural ODEs with time-varying weights, where time-dependence is non-parametric, and the smoothness of weight trajectories can be explicitly controlled to allow a tradeoff between expressiveness and efficiency. Using this enhanced expressiveness, we outperform previous Neural ODE variants in both speed and representational capacity, ultimately outperforming standard ResNet and CNN models on select image classification and video prediction tasks. GENO -- GENeric Optimization for Classical Machine Learning2019-05-31   ${\displaystyle \cong }$ Although optimization is the longstanding algorithmic backbone of machine learning, new models still require the time-consuming implementation of new solvers. As a result, there are thousands of implementations of optimization algorithms for machine learning problems. A natural question is, if it is always necessary to implement a new solver, or if there is one algorithm that is sufficient for most models. Common belief suggests that such a one-algorithm-fits-all approach cannot work, because this algorithm cannot exploit model specific structure and thus cannot be efficient and robust on a wide variety of problems. Here, we challenge this common belief. We have designed and implemented the optimization framework GENO (GENeric Optimization) that combines a modeling language with a generic solver. GENO generates a solver from the declarative specification of an optimization problem class. The framework is flexible enough to encompass most of the classical machine learning problems. We show on a wide variety of classical but also some recently suggested problems that the automatically generated solvers are (1) as efficient as well-engineered specialized solvers, (2) more efficient by a decent margin than recent state-of-the-art solvers, and (3) orders of magnitude more efficient than classical modeling language plus solver approaches. How to train your neural ODE: the world of Jacobian and kinetic regularization2020-06-23   ${\displaystyle \cong }$ Training neural ODEs on large datasets has not been tractable due to the necessity of allowing the adaptive numerical ODE solver to refine its step size to very small values. In practice this leads to dynamics equivalent to many hundreds or even thousands of layers. In this paper, we overcome this apparent difficulty by introducing a theoretically-grounded combination of both optimal transport and stability regularizations which encourage neural ODEs to prefer simpler dynamics out of all the dynamics that solve a problem well. Simpler dynamics lead to faster convergence and to fewer discretizations of the solver, considerably decreasing wall-clock time without loss in performance. Our approach allows us to train neural ODE-based generative models to the same performance as the unregularized dynamics, with significant reductions in training time. This brings neural ODEs closer to practical relevance in large-scale applications. Stiff Neural Ordinary Differential Equations2021-03-29   ${\displaystyle \cong }$ Neural Ordinary Differential Equations (ODE) are a promising approach to learn dynamic models from time-series data in science and engineering applications. This work aims at learning Neural ODE for stiff systems, which are usually raised from chemical kinetic modeling in chemical and biological systems. We first show the challenges of learning neural ODE in the classical stiff ODE systems of Robertson's problem and propose techniques to mitigate the challenges associated with scale separations in stiff systems. We then present successful demonstrations in stiff systems of Robertson's problem and an air pollution problem. The demonstrations show that the usage of deep networks with rectified activations, proper scaling of the network outputs as well as loss functions, and stabilized gradient calculations are the key techniques enabling the learning of stiff neural ODE. The success of learning stiff neural ODE opens up possibilities of using neural ODEs in applications with widely varying time-scales, like chemical dynamics in energy conversion, environmental engineering, and the life sciences. On-line Non-Convex Constrained Optimization2019-09-16   ${\displaystyle \cong }$ Time-varying non-convex continuous-valued non-linear constrained optimization is a fundamental problem. We study conditions wherein a momentum-like regularising term allow for the tracking of local optima by considering an ordinary differential equation (ODE). We then derive an efficient algorithm based on a predictor-corrector method, to track the ODE solution. STEER: Simple Temporal Regularization For Neural ODEs2020-07-01   ${\displaystyle \cong }$ Training Neural Ordinary Differential Equations (ODEs) is often computationally expensive. Indeed, computing the forward pass of such models involves solving an ODE which can become arbitrarily complex during training. Recent works have shown that regularizing the dynamics of the ODE can partially alleviate this. In this paper we propose a new regularization technique: randomly sampling the end time of the ODE during training. The proposed regularization is simple to implement, has negligible overhead and is effective across a wide variety of tasks. Further, the technique is orthogonal to several other methods proposed to regularize the dynamics of ODEs and as such can be used in conjunction with them. We show through experiments on normalizing flows, time series models and image recognition that the proposed regularization can significantly decrease training time and even improve performance over baseline models. Probabilistic ODE Solvers with Runge-Kutta Means2014-10-24   ${\displaystyle \cong }$ Runge-Kutta methods are the classic family of solvers for ordinary differential equations (ODEs), and the basis for the state of the art. Like most numerical methods, they return point estimates. We construct a family of probabilistic numerical methods that instead return a Gauss-Markov process defining a probability distribution over the ODE solution. In contrast to prior work, we construct this family such that posterior means match the outputs of the Runge-Kutta family exactly, thus inheriting their proven good properties. Remaining degrees of freedom not identified by the match to Runge-Kutta are chosen such that the posterior probability measure fits the observed structure of the ODE. Our results shed light on the structure of Runge-Kutta solvers from a new direction, provide a richer, probabilistic output, have low computational cost, and raise new research questions. Theoretical Guarantees for Learning Conditional Expectation using Controlled ODE-RNN2020-06-08   ${\displaystyle \cong }$ Continuous stochastic processes are widely used to model time series that exhibit a random behaviour. Predictions of the stochastic process can be computed by the conditional expectation given the current information. To this end, we introduce the controlled ODE-RNN that provides a data-driven approach to learn the conditional expectation of a stochastic process. Our approach extends the ODE-RNN framework which models the latent state of a recurrent neural network (RNN) between two observations with a neural ordinary differential equation (neural ODE). We show that controlled ODEs provide a general framework which can in particular describe the ODE-RNN, combining in a single equation the continuous neural ODE part with the jumps introduced by RNN. We demonstrate the predictive capabilities of this model by proving that, under some regularities assumptions, the output process converges to the conditional expectation process. Combining GANs and AutoEncoders for Efficient Anomaly Detection2020-11-16   ${\displaystyle \cong }$ Deep learned models are now largely adopted in different fields, and they generally provide superior performances with respect to classical signal-based approaches. Notwithstanding this, their actual reliability when working in an unprotected environment is far enough to be proven. In this work, we consider a novel deep neural network architecture, named Neural Ordinary Differential Equations (N-ODE), that is getting particular attention due to an attractive property --- a test-time tunable trade-off between accuracy and efficiency. This paper analyzes the robustness of N-ODE image classifiers when faced against a strong adversarial attack and how its effectiveness changes when varying such a tunable trade-off. We show that adversarial robustness is increased when the networks operate in different tolerance regimes during test time and training time. On this basis, we propose a novel adversarial detection strategy for N-ODE nets based on the randomization of the adaptive ODE solver tolerance. Our evaluation performed on standard image classification benchmarks shows that our detection technique provides high rejection of adversarial examples while maintaining most of the original samples under white-box attacks and zero-knowledge adversaries.