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Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. We present pyPESTO, a modular framework for systematic parameter estimation, with scalable algorithms for optimization and uncertainty quantification. While tailored to ordinary differential equation problems, pyPESTO is broadly applicable to black-box parameter estimation problems. Besides own implementations, it provides a unified interface to various popular simulation and inference methods. pyPESTO is implemented in Python, open-source under a 3-Clause BSD license. Code and documentation are available on GitHub (//github.com/icb-dcm/pypesto).

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This paper introduces a modular framework for Mixed-variable and Combinatorial Bayesian Optimization (MCBO) to address the lack of systematic benchmarking and standardized evaluation in the field. Current MCBO papers often introduce non-diverse or non-standard benchmarks to evaluate their methods, impeding the proper assessment of different MCBO primitives and their combinations. Additionally, papers introducing a solution for a single MCBO primitive often omit benchmarking against baselines that utilize the same methods for the remaining primitives. This omission is primarily due to the significant implementation overhead involved, resulting in a lack of controlled assessments and an inability to showcase the merits of a contribution effectively. To overcome these challenges, our proposed framework enables an effortless combination of Bayesian Optimization components, and provides a diverse set of synthetic and real-world benchmarking tasks. Leveraging this flexibility, we implement 47 novel MCBO algorithms and benchmark them against seven existing MCBO solvers and five standard black-box optimization algorithms on ten tasks, conducting over 4000 experiments. Our findings reveal a superior combination of MCBO primitives outperforming existing approaches and illustrate the significance of model fit and the use of a trust region. We make our MCBO library available under the MIT license at \url{//github.com/huawei-noah/HEBO/tree/master/MCBO}.

High-Performance Computing (HPC) processors are nowadays integrated Cyber-Physical Systems demanding complex and high-bandwidth closed-loop power and thermal control strategies. To efficiently satisfy real-time multi-input multi-output (MIMO) optimal power requirements, high-end processors integrate an on-die power controller system (PCS). While traditional PCSs are based on a simple microcontroller (MCU)-class core, more scalable and flexible PCS architectures are required to support advanced MIMO control algorithms for managing the ever-increasing number of cores, power states, and process, voltage, and temperature variability. This paper presents ControlPULP, an open-source, HW/SW RISC-V parallel PCS platform consisting of a single-core MCU with fast interrupt handling coupled with a scalable multi-core programmable cluster accelerator and a specialized DMA engine for the parallel acceleration of real-time power management policies. ControlPULP relies on FreeRTOS to schedule a reactive power control firmware (PCF) application layer. We demonstrate ControlPULP in a power management use-case targeting a next-generation 72-core HPC processor. We first show that the multi-core cluster accelerates the PCF, achieving 4.9x speedup compared to single-core execution, enabling more advanced power management algorithms within the control hyper-period at a shallow area overhead, about 0.1\% the area of a modern HPC CPU die. We then assess the PCS and PCF by designing an FPGA-based, closed-loop emulation framework that leverages the heterogeneous SoCs paradigm, achieving DVFS tracking with a mean deviation within 3\% the plant's thermal design power (TDP) against a software-equivalent model-in-the-loop approach. Finally, we show that the proposed PCF compares favorably with an industry-grade control algorithm under computational-intensive workloads.

Reliable probabilistic primality tests are fundamental in public-key cryptography. In adversarial scenarios, a composite with a high probability of passing a specific primality test could be chosen. In such cases, we need worst-case error estimates for the test. However, in many scenarios the numbers are randomly chosen and thus have significantly smaller error probability. Therefore, we are interested in average case error estimates. In this paper, we establish such bounds for the strong Lucas primality test, as only worst-case, but no average case error bounds, are currently available. This allows us to use this test with more confidence. We examine an algorithm that draws odd $k$-bit integers uniformly and independently, runs $t$ independent iterations of the strong Lucas test with randomly chosen parameters, and outputs the first number that passes all $t$ consecutive rounds. We attain numerical upper bounds on the probability on returing a composite. Furthermore, we consider a modified version of this algorithm that excludes integers divisible by small primes, resulting in improved bounds. Additionally, we classify the numbers that contribute most to our estimate.

We present an analysis of large-scale load balancing systems, where the processing time distribution of tasks depends on both the task and server types. Our study focuses on the asymptotic regime, where the number of servers and task types tend to infinity in proportion. In heterogeneous environments, commonly used load balancing policies such as Join Fastest Idle Queue and Join Fastest Shortest Queue exhibit poor performance and even shrink the stability region. Interestingly, prior to this work, finding a scalable policy with a provable performance guarantee in this setup remained an open question. To address this gap, we propose and analyze two asymptotically delay-optimal dynamic load balancing policies. The first policy efficiently reserves the processing capacity of each server for ``good" tasks and routes tasks using the vanilla Join Idle Queue policy. The second policy, called the speed-priority policy, significantly increases the likelihood of assigning tasks to the respective ``good" servers capable of processing them at high speeds. By leveraging a framework inspired by the graphon literature and employing the mean-field method and stochastic coupling arguments, we demonstrate that both policies achieve asymptotic zero queuing. Specifically, as the system scales, the probability of a typical task being assigned to an idle server approaches 1.

The quantum separability problem consists in deciding whether a bipartite density matrix is entangled or separable. In this work, we propose a machine learning pipeline for finding approximate solutions for this NP-hard problem in large-scale scenarios. We provide an efficient Frank-Wolfe-based algorithm to approximately seek the nearest separable density matrix and derive a systematic way for labeling density matrices as separable or entangled, allowing us to treat quantum separability as a classification problem. Our method is applicable to any two-qudit mixed states. Numerical experiments with quantum states of 3- and 7-dimensional qudits validate the efficiency of the proposed procedure, and demonstrate that it scales up to thousands of density matrices with a high quantum entanglement detection accuracy. This takes a step towards benchmarking quantum separability to support the development of more powerful entanglement detection techniques.

Learning to control unknown nonlinear dynamical systems is a fundamental problem in reinforcement learning and control theory. A commonly applied approach is to first explore the environment (exploration), learn an accurate model of it (system identification), and then compute an optimal controller with the minimum cost on this estimated system (policy optimization). While existing work has shown that it is possible to learn a uniformly good model of the system~\citep{mania2020active}, in practice, if we aim to learn a good controller with a low cost on the actual system, certain system parameters may be significantly more critical than others, and we therefore ought to focus our exploration on learning such parameters. In this work, we consider the setting of nonlinear dynamical systems and seek to formally quantify, in such settings, (a) which parameters are most relevant to learning a good controller, and (b) how we can best explore so as to minimize uncertainty in such parameters. Inspired by recent work in linear systems~\citep{wagenmaker2021task}, we show that minimizing the controller loss in nonlinear systems translates to estimating the system parameters in a particular, task-dependent metric. Motivated by this, we develop an algorithm able to efficiently explore the system to reduce uncertainty in this metric, and prove a lower bound showing that our approach learns a controller at a near-instance-optimal rate. Our algorithm relies on a general reduction from policy optimization to optimal experiment design in arbitrary systems, and may be of independent interest. We conclude with experiments demonstrating the effectiveness of our method in realistic nonlinear robotic systems.

In this paper, we use the optimization formulation of nonlinear Kalman filtering and smoothing problems to develop second-order variants of iterated Kalman smoother (IKS) methods. We show that Newton's method corresponds to a recursion over affine smoothing problems on a modified state-space model augmented by a pseudo measurement. The first and second derivatives required in this approach can be efficiently computed with widely available automatic differentiation tools. Furthermore, we show how to incorporate line-search and trust-region strategies into the proposed second-order IKS algorithm in order to regularize updates between iterations. Finally, we provide numerical examples to demonstrate the method's efficiency in terms of runtime compared to its batch counterpart.

Deep neural network (DNN) models have become increasingly crucial components in intelligent software systems. However, training a DNN model is typically expensive in terms of both time and money. To address this issue, researchers have recently focused on reusing existing DNN models - borrowing the idea of code reuse in software engineering. However, reusing an entire model could cause extra overhead or inherits the weakness from the undesired functionalities. Hence, existing work proposes to decompose an already trained model into modules, i.e., modularizing-after-training, and enable module reuse. Since trained models are not built for modularization, modularizing-after-training incurs huge overhead and model accuracy loss. In this paper, we propose a novel approach that incorporates modularization into the model training process, i.e., modularizing-while-training (MwT). We train a model to be structurally modular through two loss functions that optimize intra-module cohesion and inter-module coupling. We have implemented the proposed approach for modularizing Convolutional Neural Network (CNN) models in this work. The evaluation results on representative models demonstrate that MwT outperforms the state-of-the-art approach. Specifically, the accuracy loss caused by MwT is only 1.13 percentage points, which is 1.76 percentage points less than that of the baseline. The kernel retention rate of the modules generated by MwT is only 14.58%, with a reduction of 74.31% over the state-of-the-art approach. Furthermore, the total time cost required for training and modularizing is only 108 minutes, half of the baseline.

We consider the problem of estimating a scalar target parameter in the presence of nuisance parameters. Replacing the unknown nuisance parameter with a nonparametric estimator, e.g.,a machine learning (ML) model, is convenient but has shown to be inefficient due to large biases. Modern methods, such as the targeted minimum loss-based estimation (TMLE) and double machine learning (DML), achieve optimal performance under flexible assumptions by harnessing ML estimates while mitigating the plug-in bias. To avoid a sub-optimal bias-variance trade-off, these methods perform a debiasing step of the plug-in pre-estimate. Existing debiasing methods require the influence function of the target parameter as input. However, deriving the IF requires specialized expertise and thus obstructs the adaptation of these methods by practitioners. We propose a novel way to debias plug-in estimators which (i) is efficient, (ii) does not require the IF to be implemented, (iii) is computationally tractable, and therefore can be readily adapted to new estimation problems and automated without analytic derivations by the user. We build on the TMLE framework and update a plug-in estimate with a regularized likelihood maximization step over a nonparametric model constructed with a reproducing kernel Hilbert space (RKHS), producing an efficient plug-in estimate for any regular target parameter. Our method, thus, offers the efficiency of competing debiasing techniques without sacrificing the utility of the plug-in approach.

The proliferation of the Internet of Things (IoT) has led to the emergence of crowdsensing applications, where a multitude of interconnected devices collaboratively collect and analyze data. Ensuring the authenticity and integrity of the data collected by these devices is crucial for reliable decision-making and maintaining trust in the system. Traditional authentication methods are often vulnerable to attacks or can be easily duplicated, posing challenges to securing crowdsensing applications. Besides, current solutions leveraging device behavior are mostly focused on device identification, which is a simpler task than authentication. To address these issues, an individual IoT device authentication framework based on hardware behavior fingerprinting and Transformer autoencoders is proposed in this work. This solution leverages the inherent imperfections and variations in IoT device hardware to differentiate between devices with identical specifications. By monitoring and analyzing the behavior of key hardware components, such as the CPU, GPU, RAM, and Storage on devices, unique fingerprints for each device are created. The performance samples are considered as time series data and used to train anomaly detection transformer models, one per device. Then, the framework is validated within a spectrum crowdsensing system leveraging Raspberry Pi devices. After a pool of experiments, the model from each device is able to individually authenticate it between the 45 devices employed for validation. An average True Positive Rate (TPR) of 0.74+-0.13 and an average maximum False Positive Rate (FPR) of 0.06+-0.09 demonstrate the effectiveness of this approach in enhancing authentication, security, and trust in crowdsensing applications.

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