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In this contribution we investigate in mathematical modeling and efficient simulation of biological cells with a particular emphasis on effective modeling of structural properties that originate from active forces generated from polymerization and depolymerization of cytoskeletal components. In detail, we propose a nonlinear continuum approach to model microtubule-based forces which have recently been established as central components of cell mechanics during early fruit fly wing development. The model is discretized in space using the finite-element method. Although the individual equations are decoupled by a semi-implicit time discretization, the discrete model is still computationally demanding. In addition, the parameters needed for the effective model equations are not easily available and have to be estimated or determined by repeatedly solving the model and fitting the results to measurements. This drastically increases the computational cost. Reduced basis methods have been used successfully to speed up such repeated solves, often by several orders of magnitude. However, for the complex nonlinear models regarded here, the application of these model order reduction methods is not always straight-forward and comes with its own set of challenges. In particular, subspace construction using the Proper Orthogonal Decomposition (POD) becomes prohibitively expensive for reasonably fine grids. We thus propose to combine the Hierarchical Approximate POD, which is a general, easy-to-implement approach to compute an approximate POD, with an Empirical Interpolation Method to efficiently generate a fast to evaluate reduced order model. Numerical experiments are given to demonstrate the applicability and efficiency of the proposed modeling and simulation approach.

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ACM/IEEE第23屆模型驅動工程語言和系統國際會議,是模型驅動軟件和系統工程的首要會議系列,由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來,模型涵蓋了建模的各個方面,從語言和方法到工具和應用程序。模特的參加者來自不同的背景,包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇,參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會,并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。 官網鏈接: · MoDELS · 目標函數 · 泛函 · AIM ·
2021 年 7 月 14 日

Computational design problems arise in a number of settings, from synthetic biology to computer architectures. In this paper, we aim to solve data-driven model-based optimization (MBO) problems, where the goal is to find a design input that maximizes an unknown objective function provided access to only a static dataset of prior experiments. Such data-driven optimization procedures are the only practical methods in many real-world domains where active data collection is expensive (e.g., when optimizing over proteins) or dangerous (e.g., when optimizing over aircraft designs). Typical methods for MBO that optimize the design against a learned model suffer from distributional shift: it is easy to find a design that "fools" the model into predicting a high value. To overcome this, we propose conservative objective models (COMs), a method that learns a model of the objective function that lower bounds the actual value of the ground-truth objective on out-of-distribution inputs, and uses it for optimization. Structurally, COMs resemble adversarial training methods used to overcome adversarial examples. COMs are simple to implement and outperform a number of existing methods on a wide range of MBO problems, including optimizing protein sequences, robot morphologies, neural network weights, and superconducting materials.

Accelerating learning processes for complex tasks by leveraging previously learned tasks has been one of the most challenging problems in reinforcement learning, especially when the similarity between source and target tasks is low. This work proposes REPresentation And INstance Transfer (REPAINT) algorithm for knowledge transfer in deep reinforcement learning. REPAINT not only transfers the representation of a pre-trained teacher policy in the on-policy learning, but also uses an advantage-based experience selection approach to transfer useful samples collected following the teacher policy in the off-policy learning. Our experimental results on several benchmark tasks show that REPAINT significantly reduces the total training time in generic cases of task similarity. In particular, when the source tasks are dissimilar to, or sub-tasks of, the target tasks, REPAINT outperforms other baselines in both training-time reduction and asymptotic performance of return scores.

Sequence-to-sequence models are a powerful workhorse of NLP. Most variants employ a softmax transformation in both their attention mechanism and output layer, leading to dense alignments and strictly positive output probabilities. This density is wasteful, making models less interpretable and assigning probability mass to many implausible outputs. In this paper, we propose sparse sequence-to-sequence models, rooted in a new family of $\alpha$-entmax transformations, which includes softmax and sparsemax as particular cases, and is sparse for any $\alpha > 1$. We provide fast algorithms to evaluate these transformations and their gradients, which scale well for large vocabulary sizes. Our models are able to produce sparse alignments and to assign nonzero probability to a short list of plausible outputs, sometimes rendering beam search exact. Experiments on morphological inflection and machine translation reveal consistent gains over dense models.

Most Deep Reinforcement Learning (Deep RL) algorithms require a prohibitively large number of training samples for learning complex tasks. Many recent works on speeding up Deep RL have focused on distributed training and simulation. While distributed training is often done on the GPU, simulation is not. In this work, we propose using GPU-accelerated RL simulations as an alternative to CPU ones. Using NVIDIA Flex, a GPU-based physics engine, we show promising speed-ups of learning various continuous-control, locomotion tasks. With one GPU and CPU core, we are able to train the Humanoid running task in less than 20 minutes, using 10-1000x fewer CPU cores than previous works. We also demonstrate the scalability of our simulator to multi-GPU settings to train more challenging locomotion tasks.

Deep reinforcement learning has recently shown many impressive successes. However, one major obstacle towards applying such methods to real-world problems is their lack of data-efficiency. To this end, we propose the Bottleneck Simulator: a model-based reinforcement learning method which combines a learned, factorized transition model of the environment with rollout simulations to learn an effective policy from few examples. The learned transition model employs an abstract, discrete (bottleneck) state, which increases sample efficiency by reducing the number of model parameters and by exploiting structural properties of the environment. We provide a mathematical analysis of the Bottleneck Simulator in terms of fixed points of the learned policy, which reveals how performance is affected by four distinct sources of error: an error related to the abstract space structure, an error related to the transition model estimation variance, an error related to the transition model estimation bias, and an error related to the transition model class bias. Finally, we evaluate the Bottleneck Simulator on two natural language processing tasks: a text adventure game and a real-world, complex dialogue response selection task. On both tasks, the Bottleneck Simulator yields excellent performance beating competing approaches.

This work considers the problem of provably optimal reinforcement learning for episodic finite horizon MDPs, i.e. how an agent learns to maximize his/her long term reward in an uncertain environment. The main contribution is in providing a novel algorithm --- Variance-reduced Upper Confidence Q-learning (vUCQ) --- which enjoys a regret bound of $\widetilde{O}(\sqrt{HSAT} + H^5SA)$, where the $T$ is the number of time steps the agent acts in the MDP, $S$ is the number of states, $A$ is the number of actions, and $H$ is the (episodic) horizon time. This is the first regret bound that is both sub-linear in the model size and asymptotically optimal. The algorithm is sub-linear in that the time to achieve $\epsilon$-average regret for any constant $\epsilon$ is $O(SA)$, which is a number of samples that is far less than that required to learn any non-trivial estimate of the transition model (the transition model is specified by $O(S^2A)$ parameters). The importance of sub-linear algorithms is largely the motivation for algorithms such as $Q$-learning and other "model free" approaches. vUCQ algorithm also enjoys minimax optimal regret in the long run, matching the $\Omega(\sqrt{HSAT})$ lower bound. Variance-reduced Upper Confidence Q-learning (vUCQ) is a successive refinement method in which the algorithm reduces the variance in $Q$-value estimates and couples this estimation scheme with an upper confidence based algorithm. Technically, the coupling of both of these techniques is what leads to the algorithm enjoying both the sub-linear regret property and the asymptotically optimal regret.

Image foreground extraction is a classical problem in image processing and vision, with a large range of applications. In this dissertation, we focus on the extraction of text and graphics in mixed-content images, and design novel approaches for various aspects of this problem. We first propose a sparse decomposition framework, which models the background by a subspace containing smooth basis vectors, and foreground as a sparse and connected component. We then formulate an optimization framework to solve this problem, by adding suitable regularizations to the cost function to promote the desired characteristics of each component. We present two techniques to solve the proposed optimization problem, one based on alternating direction method of multipliers (ADMM), and the other one based on robust regression. Promising results are obtained for screen content image segmentation using the proposed algorithm. We then propose a robust subspace learning algorithm for the representation of the background component using training images that could contain both background and foreground components, as well as noise. With the learnt subspace for the background, we can further improve the segmentation results, compared to using a fixed subspace. Lastly, we investigate a different class of signal/image decomposition problem, where only one signal component is active at each signal element. In this case, besides estimating each component, we need to find their supports, which can be specified by a binary mask. We propose a mixed-integer programming problem, that jointly estimates the two components and their supports through an alternating optimization scheme. We show the application of this algorithm on various problems, including image segmentation, video motion segmentation, and also separation of text from textured images.

We consider the task of learning the parameters of a {\em single} component of a mixture model, for the case when we are given {\em side information} about that component, we call this the "search problem" in mixture models. We would like to solve this with computational and sample complexity lower than solving the overall original problem, where one learns parameters of all components. Our main contributions are the development of a simple but general model for the notion of side information, and a corresponding simple matrix-based algorithm for solving the search problem in this general setting. We then specialize this model and algorithm to four common scenarios: Gaussian mixture models, LDA topic models, subspace clustering, and mixed linear regression. For each one of these we show that if (and only if) the side information is informative, we obtain parameter estimates with greater accuracy, and also improved computation complexity than existing moment based mixture model algorithms (e.g. tensor methods). We also illustrate several natural ways one can obtain such side information, for specific problem instances. Our experiments on real data sets (NY Times, Yelp, BSDS500) further demonstrate the practicality of our algorithms showing significant improvement in runtime and accuracy.

Methods that align distributions by minimizing an adversarial distance between them have recently achieved impressive results. However, these approaches are difficult to optimize with gradient descent and they often do not converge well without careful hyperparameter tuning and proper initialization. We investigate whether turning the adversarial min-max problem into an optimization problem by replacing the maximization part with its dual improves the quality of the resulting alignment and explore its connections to Maximum Mean Discrepancy. Our empirical results suggest that using the dual formulation for the restricted family of linear discriminators results in a more stable convergence to a desirable solution when compared with the performance of a primal min-max GAN-like objective and an MMD objective under the same restrictions. We test our hypothesis on the problem of aligning two synthetic point clouds on a plane and on a real-image domain adaptation problem on digits. In both cases, the dual formulation yields an iterative procedure that gives more stable and monotonic improvement over time.

Word Sense Disambiguation is an open problem in Natural Language Processing which is particularly challenging and useful in the unsupervised setting where all the words in any given text need to be disambiguated without using any labeled data. Typically WSD systems use the sentence or a small window of words around the target word as the context for disambiguation because their computational complexity scales exponentially with the size of the context. In this paper, we leverage the formalism of topic model to design a WSD system that scales linearly with the number of words in the context. As a result, our system is able to utilize the whole document as the context for a word to be disambiguated. The proposed method is a variant of Latent Dirichlet Allocation in which the topic proportions for a document are replaced by synset proportions. We further utilize the information in the WordNet by assigning a non-uniform prior to synset distribution over words and a logistic-normal prior for document distribution over synsets. We evaluate the proposed method on Senseval-2, Senseval-3, SemEval-2007, SemEval-2013 and SemEval-2015 English All-Word WSD datasets and show that it outperforms the state-of-the-art unsupervised knowledge-based WSD system by a significant margin.

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