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Recently, methods that represent data as a graph, such as graph neural networks (GNNs) have been successfully used to learn data representations and structures to solve classification and link prediction problems. The applications of such methods are vast and diverse, but most of the current work relies on the assumption of a static graph. This assumption does not hold for many highly dynamic systems, where the underlying connectivity structure is non-stationary and is mostly unobserved. Using a static model in these situations may result in sub-optimal performance. In contrast, modeling changes in graph structure with time can provide information about the system whose applications go beyond classification. Most work of this type does not learn effective connectivity and focuses on cross-correlation between nodes to generate undirected graphs. An undirected graph is unable to capture direction of an interaction which is vital in many fields, including neuroscience. To bridge this gap, we developed dynamic effective connectivity estimation via neural network training (DECENNT), a novel model to learn an interpretable directed and dynamic graph induced by the downstream classification/prediction task. DECENNT outperforms state-of-the-art (SOTA) methods on five different tasks and infers interpretable task-specific dynamic graphs. The dynamic graphs inferred from functional neuroimaging data align well with the existing literature and provide additional information. Additionally, the temporal attention module of DECENNT identifies time-intervals crucial for predictive downstream task from multivariate time series data.

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Graph Convolutional Networks (GCNs) are one of the most popular architectures that are used to solve classification problems accompanied by graphical information. We present a rigorous theoretical understanding of the effects of graph convolutions in multi-layer networks. We study these effects through the node classification problem of a non-linearly separable Gaussian mixture model coupled with a stochastic block model. First, we show that a single graph convolution expands the regime of the distance between the means where multi-layer networks can classify the data by a factor of at least $1/\sqrt[4]{\mathbb{E}{\rm deg}}$, where $\mathbb{E}{\rm deg}$ denotes the expected degree of a node. Second, we show that with a slightly stronger graph density, two graph convolutions improve this factor to at least $1/\sqrt[4]{n}$, where $n$ is the number of nodes in the graph. Finally, we provide both theoretical and empirical insights into the performance of graph convolutions placed in different combinations among the layers of a network, concluding that the performance is mutually similar for all combinations of the placement. We present extensive experiments on both synthetic and real-world data that illustrate our results.

Computing a maximum independent set (MaxIS) is a fundamental NP-hard problem in graph theory, which has important applications in a wide spectrum of fields. Since graphs in many applications are changing frequently over time, the problem of maintaining a MaxIS over dynamic graphs has attracted increasing attention over the past few years. Due to the intractability of maintaining an exact MaxIS, this paper aims to develop efficient algorithms that can maintain an approximate MaxIS with an accuracy guarantee theoretically. In particular, we propose a framework that maintains a $(\frac{\Delta}{2} + 1)$-approximate MaxIS over dynamic graphs and prove that it achieves a constant approximation ratio in many real-world networks. To the best of our knowledge, this is the first non-trivial approximability result for the dynamic MaxIS problem. Following the framework, we implement an efficient linear-time dynamic algorithm and a more effective dynamic algorithm with near-linear expected time complexity. Our thorough experiments over real and synthetic graphs demonstrate the effectiveness and efficiency of the proposed algorithms, especially when the graph is highly dynamic.

Consider the problem of training robustly capable agents. One approach is to generate a diverse collection of agent polices. Training can then be viewed as a quality diversity (QD) optimization problem, where we search for a collection of performant policies that are diverse with respect to quantified behavior. Recent work shows that differentiable quality diversity (DQD) algorithms greatly accelerate QD optimization when exact gradients are available. However, agent policies typically assume that the environment is not differentiable. To apply DQD algorithms to training agent policies, we must approximate gradients for performance and behavior. We propose two variants of the current state-of-the-art DQD algorithm that compute gradients via approximation methods common in reinforcement learning (RL). We evaluate our approach on four simulated locomotion tasks. One variant achieves results comparable to the current state-of-the-art in combining QD and RL, while the other performs comparably in two locomotion tasks. These results provide insight into the limitations of current DQD algorithms in domains where gradients must be approximated. Source code is available at //github.com/icaros-usc/dqd-rl

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.

Graph Neural Networks (GNNs) are widely used for analyzing graph-structured data. Most GNN methods are highly sensitive to the quality of graph structures and usually require a perfect graph structure for learning informative embeddings. However, the pervasiveness of noise in graphs necessitates learning robust representations for real-world problems. To improve the robustness of GNN models, many studies have been proposed around the central concept of Graph Structure Learning (GSL), which aims to jointly learn an optimized graph structure and corresponding representations. Towards this end, in the presented survey, we broadly review recent progress of GSL methods for learning robust representations. Specifically, we first formulate a general paradigm of GSL, and then review state-of-the-art methods classified by how they model graph structures, followed by applications that incorporate the idea of GSL in other graph tasks. Finally, we point out some issues in current studies and discuss future directions.

Graph Neural Networks (GNNs) have recently become increasingly popular due to their ability to learn complex systems of relations or interactions arising in a broad spectrum of problems ranging from biology and particle physics to social networks and recommendation systems. Despite the plethora of different models for deep learning on graphs, few approaches have been proposed thus far for dealing with graphs that present some sort of dynamic nature (e.g. evolving features or connectivity over time). In this paper, we present Temporal Graph Networks (TGNs), a generic, efficient framework for deep learning on dynamic graphs represented as sequences of timed events. Thanks to a novel combination of memory modules and graph-based operators, TGNs are able to significantly outperform previous approaches being at the same time more computationally efficient. We furthermore show that several previous models for learning on dynamic graphs can be cast as specific instances of our framework. We perform a detailed ablation study of different components of our framework and devise the best configuration that achieves state-of-the-art performance on several transductive and inductive prediction tasks for dynamic graphs.

Modeling multivariate time series has long been a subject that has attracted researchers from a diverse range of fields including economics, finance, and traffic. A basic assumption behind multivariate time series forecasting is that its variables depend on one another but, upon looking closely, it is fair to say that existing methods fail to fully exploit latent spatial dependencies between pairs of variables. In recent years, meanwhile, graph neural networks (GNNs) have shown high capability in handling relational dependencies. GNNs require well-defined graph structures for information propagation which means they cannot be applied directly for multivariate time series where the dependencies are not known in advance. In this paper, we propose a general graph neural network framework designed specifically for multivariate time series data. Our approach automatically extracts the uni-directed relations among variables through a graph learning module, into which external knowledge like variable attributes can be easily integrated. A novel mix-hop propagation layer and a dilated inception layer are further proposed to capture the spatial and temporal dependencies within the time series. The graph learning, graph convolution, and temporal convolution modules are jointly learned in an end-to-end framework. Experimental results show that our proposed model outperforms the state-of-the-art baseline methods on 3 of 4 benchmark datasets and achieves on-par performance with other approaches on two traffic datasets which provide extra structural information.

In structure learning, the output is generally a structure that is used as supervision information to achieve good performance. Considering the interpretation of deep learning models has raised extended attention these years, it will be beneficial if we can learn an interpretable structure from deep learning models. In this paper, we focus on Recurrent Neural Networks (RNNs) whose inner mechanism is still not clearly understood. We find that Finite State Automaton (FSA) that processes sequential data has more interpretable inner mechanism and can be learned from RNNs as the interpretable structure. We propose two methods to learn FSA from RNN based on two different clustering methods. We first give the graphical illustration of FSA for human beings to follow, which shows the interpretability. From the FSA's point of view, we then analyze how the performance of RNNs are affected by the number of gates, as well as the semantic meaning behind the transition of numerical hidden states. Our results suggest that RNNs with simple gated structure such as Minimal Gated Unit (MGU) is more desirable and the transitions in FSA leading to specific classification result are associated with corresponding words which are understandable by human beings.

Graphs, which describe pairwise relations between objects, are essential representations of many real-world data such as social networks. In recent years, graph neural networks, which extend the neural network models to graph data, have attracted increasing attention. Graph neural networks have been applied to advance many different graph related tasks such as reasoning dynamics of the physical system, graph classification, and node classification. Most of the existing graph neural network models have been designed for static graphs, while many real-world graphs are inherently dynamic. For example, social networks are naturally evolving as new users joining and new relations being created. Current graph neural network models cannot utilize the dynamic information in dynamic graphs. However, the dynamic information has been proven to enhance the performance of many graph analytical tasks such as community detection and link prediction. Hence, it is necessary to design dedicated graph neural networks for dynamic graphs. In this paper, we propose DGNN, a new {\bf D}ynamic {\bf G}raph {\bf N}eural {\bf N}etwork model, which can model the dynamic information as the graph evolving. In particular, the proposed framework can keep updating node information by capturing the sequential information of edges, the time intervals between edges and information propagation coherently. Experimental results on various dynamic graphs demonstrate the effectiveness of the proposed framework.

Multivariate time series forecasting is extensively studied throughout the years with ubiquitous applications in areas such as finance, traffic, environment, etc. Still, concerns have been raised on traditional methods for incapable of modeling complex patterns or dependencies lying in real word data. To address such concerns, various deep learning models, mainly Recurrent Neural Network (RNN) based methods, are proposed. Nevertheless, capturing extremely long-term patterns while effectively incorporating information from other variables remains a challenge for time-series forecasting. Furthermore, lack-of-explainability remains one serious drawback for deep neural network models. Inspired by Memory Network proposed for solving the question-answering task, we propose a deep learning based model named Memory Time-series network (MTNet) for time series forecasting. MTNet consists of a large memory component, three separate encoders, and an autoregressive component to train jointly. Additionally, the attention mechanism designed enable MTNet to be highly interpretable. We can easily tell which part of the historic data is referenced the most.

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