Directed Evolution (DE), a landmark wet-lab method originated in 1960s, enables discovery of novel protein designs via evolving a population of candidate sequences. Recent advances in biotechnology has made it possible to collect high-throughput data, allowing the use of machine learning to map out a protein's sequence-to-function relation. There is a growing interest in machine learning-assisted DE for accelerating protein optimization. Yet the theoretical understanding of DE, as well as the use of machine learning in DE, remains limited. In this paper, we connect DE with the bandit learning theory and make a first attempt to study regret minimization in DE. We propose a Thompson Sampling-guided Directed Evolution (TS-DE) framework for sequence optimization, where the sequence-to-function mapping is unknown and querying a single value is subject to costly and noisy measurements. TS-DE updates a posterior of the function based on collected measurements. It uses a posterior-sampled function estimate to guide the crossover recombination and mutation steps in DE. In the case of a linear model, we show that TS-DE enjoys a Bayesian regret of order $\tilde O(d^{2}\sqrt{MT})$, where $d$ is feature dimension, $M$ is population size and $T$ is number of rounds. This regret bound is nearly optimal, confirming that bandit learning can provably accelerate DE. It may have implications for more general sequence optimization and evolutionary algorithms.
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Bayesian optimization (BO) is a widely popular approach for the hyperparameter optimization (HPO) in machine learning. At its core, BO iteratively evaluates promising configurations until a user-defined budget, such as wall-clock time or number of iterations, is exhausted. While the final performance after tuning heavily depends on the provided budget, it is hard to pre-specify an optimal value in advance. In this work, we propose an effective and intuitive termination criterion for BO that automatically stops the procedure if it is sufficiently close to the global optimum. Our key insight is that the discrepancy between the true objective (predictive performance on test data) and the computable target (validation performance) suggests stopping once the suboptimality in optimizing the target is dominated by the statistical estimation error. Across an extensive range of real-world HPO problems and baselines, we show that our termination criterion achieves a better trade-off between the test performance and optimization time. Additionally, we find that overfitting may occur in the context of HPO, which is arguably an overlooked problem in the literature, and show how our termination criterion helps to mitigate this phenomenon on both small and large datasets.
Changing conditions or environments can cause system dynamics to vary over time. To ensure optimal control performance, controllers should adapt to these changes. When the underlying cause and time of change is unknown, we need to rely on online data for this adaptation. In this paper, we will use time-varying Bayesian optimization (TVBO) to tune controllers online in changing environments using appropriate prior knowledge on the control objective and its changes. Two properties are characteristic of many online controller tuning problems: First, they exhibit incremental and lasting changes in the objective due to changes to the system dynamics, e.g., through wear and tear. Second, the optimization problem is convex in the tuning parameters. Current TVBO methods do not explicitly account for these properties, resulting in poor tuning performance and many unstable controllers through over-exploration of the parameter space. We propose a novel TVBO forgetting strategy using Uncertainty-Injection (UI), which incorporates the assumption of incremental and lasting changes. The control objective is modeled as a spatio-temporal Gaussian process (GP) with UI through a Wiener process in the temporal domain. Further, we explicitly model the convexity assumptions in the spatial dimension through GP models with linear inequality constraints. In numerical experiments, we show that our model outperforms the state-of-the-art method in TVBO, exhibiting reduced regret and fewer unstable parameter configurations.
This work presents a new procedure for obtaining predictive distributions in the context of Gaussian process (GP) modeling, with a relaxation of the interpolation constraints outside some ranges of interest: the mean of the predictive distributions no longer necessarily interpolates the observed values when they are outside ranges of interest, but are simply constrained to remain outside. This method called relaxed Gaussian process (reGP) interpolation provides better predictive distributions in ranges of interest, especially in cases where a stationarity assumption for the GP model is not appropriate. It can be viewed as a goal-oriented method and becomes particularly interesting in Bayesian optimization, for example, for the minimization of an objective function, where good predictive distributions for low function values are important. When the expected improvement criterion and reGP are used for sequentially choosing evaluation points, the convergence of the resulting optimization algorithm is theoretically guaranteed (provided that the function to be optimized lies in the reproducing kernel Hilbert spaces attached to the known covariance of the underlying Gaussian process). Experiments indicate that using reGP instead of stationary GP models in Bayesian optimization is beneficial.
In this paper, we study a sequential decision making problem faced by e-commerce carriers related to when to send out a vehicle from the central depot to serve customer requests, and in which order to provide the service, under the assumption that the time at which parcels arrive at the depot is stochastic and dynamic. The objective is to maximize the number of parcels that can be delivered during the service hours. We propose two reinforcement learning approaches for solving this problem, one based on a policy function approximation (PFA) and the second on a value function approximation (VFA). Both methods are combined with a look-ahead strategy, in which future release dates are sampled in a Monte-Carlo fashion and a tailored batch approach is used to approximate the value of future states. Our PFA and VFA make a good use of branch-and-cut-based exact methods to improve the quality of decisions. We also establish sufficient conditions for partial characterization of optimal policy and integrate them into PFA/VFA. In an empirical study based on 720 benchmark instances, we conduct a competitive analysis using upper bounds with perfect information and we show that PFA and VFA greatly outperform two alternative myopic approaches. Overall, PFA provides best solutions, while VFA (which benefits from a two-stage stochastic optimization model) achieves a better tradeoff between solution quality and computing time.
Lighting is a determining factor in photography that affects the style, expression of emotion, and even quality of images. Creating or finding satisfying lighting conditions, in reality, is laborious and time-consuming, so it is of great value to develop a technology to manipulate illumination in an image as post-processing. Although previous works have explored techniques based on the physical viewpoint for relighting images, extensive supervisions and prior knowledge are necessary to generate reasonable images, restricting the generalization ability of these works. In contrast, we take the viewpoint of image-to-image translation and implicitly merge ideas of the conventional physical viewpoint. In this paper, we present an Illumination-Aware Network (IAN) which follows the guidance from hierarchical sampling to progressively relight a scene from a single image with high efficiency. In addition, an Illumination-Aware Residual Block (IARB) is designed to approximate the physical rendering process and to extract precise descriptors of light sources for further manipulations. We also introduce a depth-guided geometry encoder for acquiring valuable geometry- and structure-related representations once the depth information is available. Experimental results show that our proposed method produces better quantitative and qualitative relighting results than previous state-of-the-art methods. The code and models are publicly available on //github.com/NK-CS-ZZL/IAN.
Spatial data can exhibit dependence structures more complicated than can be represented using models that rely on the traditional assumptions of stationarity and isotropy. Several statistical methods have been developed to relax these assumptions. One in particular, the "spatial deformation approach" defines a transformation from the geographic space in which data are observed, to a latent space in which stationarity and isotropy are assumed to hold. Taking inspiration from this class of models, we develop a new model for spatially dependent data observed on graphs. Our method implies an embedding of the graph into Euclidean space wherein the covariance can be modeled using traditional covariance functions such as those from the Mat\'{e}rn family. This is done via a class of graph metrics compatible with such covariance functions. By estimating the edge weights which underlie these metrics, we can recover the "intrinsic distance" between nodes of a graph. We compare our model to existing methods for spatially dependent graph data, primarily conditional autoregressive (CAR) models and their variants and illustrate the advantages our approach has over traditional methods. We fit our model and competitors to bird abundance data for several species in North Carolina. We find that our model fits the data best, and provides insight into the interaction between species-specific spatial distributions and geography.
Importance sampling (IS) is valuable in reducing the variance of Monte Carlo sampling for many areas, including finance, rare event simulation, and Bayesian inference. It is natural and obvious to combine quasi-Monte Carlo (QMC) methods with IS to achieve a faster rate of convergence. However, a naive replacement of Monte Carlo with QMC may not work well. This paper investigates the convergence rates of randomized QMC-based IS for estimating integrals with respect to a Gaussian measure, in which the IS measure is a Gaussian or $t$ distribution. We prove that if the target function satisfies the so-called boundary growth condition and the covariance matrix of the IS density has eigenvalues no smaller than 1, then randomized QMC with the Gaussian proposal has a root mean squared error of $O(N^{-1+\epsilon})$ for arbitrarily small $\epsilon>0$. Similar results of $t$ distribution as the proposal are also established. These sufficient conditions help to assess the effectiveness of IS in QMC. For some particular applications, we find that the Laplace IS, a very general approach to approximate the target function by a quadratic Taylor approximation around its mode, has eigenvalues smaller than 1, making the resulting integrand less favorable for QMC. From this point of view, when using Gaussian distributions as the IS proposal, a change of measure via Laplace IS may transform a favorable integrand into unfavorable one for QMC although the variance of Monte Carlo sampling is reduced. We also give some examples to verify our propositions and warn against naive replacement of MC with QMC under IS proposals. Numerical results suggest that using Laplace IS with $t$ distributions is more robust than that with Gaussian distributions.
This book develops an effective theory approach to understanding deep neural networks of practical relevance. Beginning from a first-principles component-level picture of networks, we explain how to determine an accurate description of the output of trained networks by solving layer-to-layer iteration equations and nonlinear learning dynamics. A main result is that the predictions of networks are described by nearly-Gaussian distributions, with the depth-to-width aspect ratio of the network controlling the deviations from the infinite-width Gaussian description. We explain how these effectively-deep networks learn nontrivial representations from training and more broadly analyze the mechanism of representation learning for nonlinear models. From a nearly-kernel-methods perspective, we find that the dependence of such models' predictions on the underlying learning algorithm can be expressed in a simple and universal way. To obtain these results, we develop the notion of representation group flow (RG flow) to characterize the propagation of signals through the network. By tuning networks to criticality, we give a practical solution to the exploding and vanishing gradient problem. We further explain how RG flow leads to near-universal behavior and lets us categorize networks built from different activation functions into universality classes. Altogether, we show that the depth-to-width ratio governs the effective model complexity of the ensemble of trained networks. By using information-theoretic techniques, we estimate the optimal aspect ratio at which we expect the network to be practically most useful and show how residual connections can be used to push this scale to arbitrary depths. With these tools, we can learn in detail about the inductive bias of architectures, hyperparameters, and optimizers.
Deep learning is usually described as an experiment-driven field under continuous criticizes of lacking theoretical foundations. This problem has been partially fixed by a large volume of literature which has so far not been well organized. This paper reviews and organizes the recent advances in deep learning theory. The literature is categorized in six groups: (1) complexity and capacity-based approaches for analyzing the generalizability of deep learning; (2) stochastic differential equations and their dynamic systems for modelling stochastic gradient descent and its variants, which characterize the optimization and generalization of deep learning, partially inspired by Bayesian inference; (3) the geometrical structures of the loss landscape that drives the trajectories of the dynamic systems; (4) the roles of over-parameterization of deep neural networks from both positive and negative perspectives; (5) theoretical foundations of several special structures in network architectures; and (6) the increasingly intensive concerns in ethics and security and their relationships with generalizability.
When and why can a neural network be successfully trained? This article provides an overview of optimization algorithms and theory for training neural networks. First, we discuss the issue of gradient explosion/vanishing and the more general issue of undesirable spectrum, and then discuss practical solutions including careful initialization and normalization methods. Second, we review generic optimization methods used in training neural networks, such as SGD, adaptive gradient methods and distributed methods, and theoretical results for these algorithms. Third, we review existing research on the global issues of neural network training, including results on bad local minima, mode connectivity, lottery ticket hypothesis and infinite-width analysis.
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