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In predictive modeling with simulation or machine learning, it is critical to accurately assess the quality of estimated values through output analysis. In recent decades output analysis has become enriched with methods that quantify the impact of input data uncertainty in the model outputs to increase robustness. However, most developments are applicable assuming that the input data adheres to a parametric family of distributions. We propose a unified output analysis framework for simulation and machine learning outputs through the lens of Monte Carlo sampling. This framework provides nonparametric quantification of the variance and bias induced in the outputs with higher-order accuracy. Our new bias-corrected estimation from the model outputs leverages the extension of fast iterative bootstrap sampling and higher-order influence functions. For the scalability of the proposed estimation methods, we devise budget-optimal rules and leverage control variates for variance reduction. Our theoretical and numerical results demonstrate a clear advantage in building more robust confidence intervals from the model outputs with higher coverage probability.

In reliable decision-making systems based on machine learning, models have to be robust to distributional shifts or provide the uncertainty of their predictions. In node-level problems of graph learning, distributional shifts can be especially complex since the samples are interdependent. To evaluate the performance of graph models, it is important to test them on diverse and meaningful distributional shifts. However, most graph benchmarks considering distributional shifts for node-level problems focus mainly on node features, while structural properties are also essential for graph problems. In this work, we propose a general approach for inducing diverse distributional shifts based on graph structure. We use this approach to create data splits according to several structural node properties: popularity, locality, and density. In our experiments, we thoroughly evaluate the proposed distributional shifts and show that they can be quite challenging for existing graph models. We also reveal that simple models often outperform more sophisticated methods on the considered structural shifts. Finally, our experiments provide evidence that there is a trade-off between the quality of learned representations for the base classification task under structural distributional shift and the ability to separate the nodes from different distributions using these representations.

Our ability to use deep learning approaches to decipher neural activity would likely benefit from greater scale, in terms of both model size and datasets. However, the integration of many neural recordings into one unified model is challenging, as each recording contains the activity of different neurons from different individual animals. In this paper, we introduce a training framework and architecture designed to model the population dynamics of neural activity across diverse, large-scale neural recordings. Our method first tokenizes individual spikes within the dataset to build an efficient representation of neural events that captures the fine temporal structure of neural activity. We then employ cross-attention and a PerceiverIO backbone to further construct a latent tokenization of neural population activities. Utilizing this architecture and training framework, we construct a large-scale multi-session model trained on large datasets from seven nonhuman primates, spanning over 158 different sessions of recording from over 27,373 neural units and over 100 hours of recordings. In a number of different tasks, we demonstrate that our pretrained model can be rapidly adapted to new, unseen sessions with unspecified neuron correspondence, enabling few-shot performance with minimal labels. This work presents a powerful new approach for building deep learning tools to analyze neural data and stakes out a clear path to training at scale.

The growing proliferation of customized and pretrained generative models has made it infeasible for a user to be fully cognizant of every model in existence. To address this need, we introduce the task of content-based model search: given a query and a large set of generative models, finding the models that best match the query. As each generative model produces a distribution of images, we formulate the search task as an optimization problem to select the model with the highest probability of generating similar content as the query. We introduce a formulation to approximate this probability given the query from different modalities, e.g., image, sketch, and text. Furthermore, we propose a contrastive learning framework for model retrieval, which learns to adapt features for various query modalities. We demonstrate that our method outperforms several baselines on Generative Model Zoo, a new benchmark we create for the model retrieval task.

Recently, automatic speaker verification (ASV) based on deep learning is easily contaminated by adversarial attacks, which is a new type of attack that injects imperceptible perturbations to audio signals so as to make ASV produce wrong decisions. This poses a significant threat to the security and reliability of ASV systems. To address this issue, we propose a Diffusion-Based Adversarial Purification (DAP) method that enhances the robustness of ASV systems against such adversarial attacks. Our method leverages a conditional denoising diffusion probabilistic model to effectively purify the adversarial examples and mitigate the impact of perturbations. DAP first introduces controlled noise into adversarial examples, and then performs a reverse denoising process to reconstruct clean audio. Experimental results demonstrate the efficacy of the proposed DAP in enhancing the security of ASV and meanwhile minimizing the distortion of the purified audio signals.

As machine learning models become more capable, they have exhibited increased potential in solving complex tasks. One of the most promising directions uses deep reinforcement learning to train autonomous agents in computer network defense tasks. This work studies the impact of the reward signal that is provided to the agents when training for this task. Due to the nature of cybersecurity tasks, the reward signal is typically 1) in the form of penalties (e.g., when a compromise occurs), and 2) distributed sparsely across each defense episode. Such reward characteristics are atypical of classic reinforcement learning tasks where the agent is regularly rewarded for progress (cf. to getting occasionally penalized for failures). We investigate reward shaping techniques that could bridge this gap so as to enable agents to train more sample-efficiently and potentially converge to a better performance. We first show that deep reinforcement learning algorithms are sensitive to the magnitude of the penalties and their relative size. Then, we combine penalties with positive external rewards and study their effect compared to penalty-only training. Finally, we evaluate intrinsic curiosity as an internal positive reward mechanism and discuss why it might not be as advantageous for high-level network monitoring tasks.

The quality of explanations for the predictions of complex machine learning predictors is often measured using insertion and deletion metrics, which assess the faithfulness of the explanations, i.e., how correctly the explanations reflect the predictor's behavior. To improve the faithfulness, we propose insertion/deletion metric-aware explanation-based optimization (ID-ExpO), which optimizes differentiable predictors to improve both insertion and deletion scores of the explanations while keeping their predictive accuracy. Since the original insertion and deletion metrics are indifferentiable with respect to the explanations and directly unavailable for gradient-based optimization, we extend the metrics to be differentiable and use them to formalize insertion and deletion metric-based regularizers. The experimental results on image and tabular datasets show that the deep neural networks-based predictors fine-tuned using ID-ExpO enable popular post-hoc explainers to produce more faithful and easy-to-interpret explanations while keeping high predictive accuracy.

Offline constrained reinforcement learning (RL) aims to learn a policy that maximizes the expected cumulative reward subject to constraints on expected cumulative cost using an existing dataset. In this paper, we propose Primal-Dual-Critic Algorithm (PDCA), a novel algorithm for offline constrained RL with general function approximation. PDCA runs a primal-dual algorithm on the Lagrangian function estimated by critics. The primal player employs a no-regret policy optimization oracle to maximize the Lagrangian estimate and the dual player acts greedily to minimize the Lagrangian estimate. We show that PDCA can successfully find a near saddle point of the Lagrangian, which is nearly optimal for the constrained RL problem. Unlike previous work that requires concentrability and a strong Bellman completeness assumption, PDCA only requires concentrability and realizability assumptions for sample-efficient learning.

The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.

Data augmentation has been widely used to improve generalizability of machine learning models. However, comparatively little work studies data augmentation for graphs. This is largely due to the complex, non-Euclidean structure of graphs, which limits possible manipulation operations. Augmentation operations commonly used in vision and language have no analogs for graphs. Our work studies graph data augmentation for graph neural networks (GNNs) in the context of improving semi-supervised node-classification. We discuss practical and theoretical motivations, considerations and strategies for graph data augmentation. Our work shows that neural edge predictors can effectively encode class-homophilic structure to promote intra-class edges and demote inter-class edges in given graph structure, and our main contribution introduces the GAug graph data augmentation framework, which leverages these insights to improve performance in GNN-based node classification via edge prediction. Extensive experiments on multiple benchmarks show that augmentation via GAug improves performance across GNN architectures and datasets.