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Register a new userPopulation-Based Black-Box Optimization for Biological Sequence Design
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Added by
Christof Angermueller
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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The use of black-box optimization for the design of new biological sequences is an emerging research area with potentially revolutionary impact. The cost and latency of wet-lab experiments requires methods that find good sequences in few experimental rounds of large batches of sequences--a setting that off-the-shelf black-box optimization methods are ill-equipped to handle. We find that the performance of existing methods varies drastically across optimization tasks, posing a significant obstacle to real-world applications. To improve robustness, we propose Population-Based Black-Box Optimization (P3BO), which generates batches of sequences by sampling from an ensemble of methods. The number of sequences sampled from any method is proportional to the quality of sequences it previously proposed, allowing P3BO to combine the strengths of individual methods while hedging against their innate brittleness. Adapting the hyper-parameters of each of the methods online using evolutionary optimization further improves performance. Through extensive experiments on in-silico optimization tasks, we show that P3BO outperforms any single method in its population, proposing higher quality sequences as well as more diverse batches. As such, P3BO and Adaptive-P3BO are a crucial step towards deploying ML to real-world sequence design.
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This paper investigates the control of an ML component within the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) devoted to black-box optimization. The known CMA-ES weakness is its sample complexity, the number of evaluations of the objective function needed to approximate the global optimum. This weakness is commonly addressed through surrogate optimization, learning an estimate of the objective function a.k.a. surrogate model, and replacing most evaluations of the true objective function with the (inexpensive) evaluation of the surrogate model. This paper presents a principled control of the learning schedule (when to relearn the surrogate model), based on the Kullback-Leibler divergence of the current search distribution and the training distribution of the former surrogate model. The experimental validation of the proposed approach shows significant performance gains on a comprehensive set of ill-conditioned benchmark problems, compared to the best state of the art including the quasi-Newton high-precision BFGS method.
Zeroth-order optimization is an important research topic in machine learning. In recent years, it has become a key tool in black-box adversarial attack to neural network based image classifiers. However, existing zeroth-order optimization algorithms rarely extract second-order information of the model function. In this paper, we utilize the second-order information of the objective function and propose a novel textit{Hessian-aware zeroth-order algorithm} called texttt{ZO-HessAware}. Our theoretical result shows that texttt{ZO-HessAware} has an improved zeroth-order convergence rate and query complexity under structured Hessian approximation, where we propose a few approximation methods for estimating Hessian. Our empirical studies on the black-box adversarial attack problem validate that our algorithm can achieve improved success rates with a lower query complexity.
The adaptive momentum method (AdaMM), which uses past gradients to update descent directions and learning rates simultaneously, has become one of the most popular first-order optimization methods for solving machine learning problems. However, AdaMM is not suited for solving black-box optimization problems, where explicit gradient forms are difficult or infeasible to obtain. In this paper, we propose a zeroth-order AdaMM (ZO-AdaMM) algorithm, that generalizes AdaMM to the gradient-free regime. We show that the convergence rate of ZO-AdaMM for both convex and nonconvex optimization is roughly a factor of $O(sqrt{d})$ worse than that of the first-order AdaMM algorithm, where $d$ is problem size. In particular, we provide a deep understanding on why Mahalanobis distance matters in convergence of ZO-AdaMM and other AdaMM-type methods. As a byproduct, our analysis makes the first step toward understanding adaptive learning rate methods for nonconvex constrained optimization. Furthermore, we demonstrate two applications, designing per-image and universal adversarial attacks from black-box neural networks, respectively. We perform extensive experiments on ImageNet and empirically show that ZO-AdaMM converges much faster to a solution of high accuracy compared with $6$ state-of-the-art ZO optimization methods.
Gradient-based meta-learning and hyperparameter optimization have seen significant progress recently, enabling practical end-to-end training of neural networks together with many hyperparameters. Nevertheless, existing approaches are relatively expensive as they need to compute second-order derivatives and store a longer computational graph. This cost prevents scaling them to larger network architectures. We present EvoGrad, a new approach to meta-learning that draws upon evolutionary techniques to more efficiently compute hypergradients. EvoGrad estimates hypergradient with respect to hyperparameters without calculating second-order gradients, or storing a longer computational graph, leading to significant improvements in efficiency. We evaluate EvoGrad on two substantial recent meta-learning applications, namely cross-domain few-shot learning with feature-wise transformations and noisy label learning with MetaWeightNet. The results show that EvoGrad significantly improves efficiency and enables scaling meta-learning to bigger CNN architectures such as from ResNet18 to ResNet34.
We derive an optimal policy for adaptively restarting a randomized algorithm, based on observed features of the run-so-far, so as to minimize the expected time required for the algorithm to successfully terminate. Given a suitable Bayesian prior, this result can be used to select the optimal black-box optimization algorithm from among a large family of algorithms that includes random search, Successive Halving, and Hyperband. On CIFAR-10 and ImageNet hyperparameter tuning problems, the proposed policies offer up to a factor of 13 improvement over random search in terms of expected time to reach a given target accuracy, and up to a factor of 3 improvement over a baseline adaptive policy that terminates a run whenever its accuracy is below-median.
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