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Mass spectra, which are agglomerations of ionized fragments from targeted molecules, play a crucial role across various fields for the identification of molecular structures. A prevalent analysis method involves spectral library searches,where unknown spectra are cross-referenced with a database. The effectiveness of such search-based approaches, however, is restricted by the scope of the existing mass spectra database, underscoring the need to expand the database via mass spectra prediction. In this research, we propose the Motif-based Mass Spectrum Prediction Network (MoMS-Net), a system that predicts mass spectra using the information derived from structural motifs and the implementation of Graph Neural Networks (GNNs). We have tested our model across diverse mass spectra and have observed its superiority over other existing models. MoMS-Net considers substructure at the graph level, which facilitates the incorporation of long-range dependencies while using less memory compared to the graph transformer model.

Robotic manipulation, in particular in-hand object manipulation, often requires an accurate estimate of the object's 6D pose. To improve the accuracy of the estimated pose, state-of-the-art approaches in 6D object pose estimation use observational data from one or more modalities, e.g., RGB images, depth, and tactile readings. However, existing approaches make limited use of the underlying geometric structure of the object captured by these modalities, thereby, increasing their reliance on visual features. This results in poor performance when presented with objects that lack such visual features or when visual features are simply occluded. Furthermore, current approaches do not take advantage of the proprioceptive information embedded in the position of the fingers. To address these limitations, in this paper: (1) we introduce a hierarchical graph neural network architecture for combining multimodal (vision and touch) data that allows for a geometrically informed 6D object pose estimation, (2) we introduce a hierarchical message passing operation that flows the information within and across modalities to learn a graph-based object representation, and (3) we introduce a method that accounts for the proprioceptive information for in-hand object representation. We evaluate our model on a diverse subset of objects from the YCB Object and Model Set, and show that our method substantially outperforms existing state-of-the-art work in accuracy and robustness to occlusion. We also deploy our proposed framework on a real robot and qualitatively demonstrate successful transfer to real settings.

In the autonomous driving system, trajectory prediction plays a vital role in ensuring safety and facilitating smooth navigation. However, we observe a substantial discrepancy between the accuracy of predictors on fixed datasets and their driving performance when used in downstream tasks. This discrepancy arises from two overlooked factors in the current evaluation protocols of trajectory prediction: 1) the dynamics gap between the dataset and real driving scenario; and 2) the computational efficiency of predictors. In real-world scenarios, prediction algorithms influence the behavior of autonomous vehicles, which, in turn, alter the behaviors of other agents on the road. This interaction results in predictor-specific dynamics that directly impact prediction results. As other agents' responses are predetermined on datasets, a significant dynamics gap arises between evaluations conducted on fixed datasets and actual driving scenarios. Furthermore, focusing solely on accuracy fails to address the demand for computational efficiency, which is critical for the real-time response required by the autonomous driving system. Therefore, in this paper, we demonstrate that an interactive, task-driven evaluation approach for trajectory prediction is crucial to reflect its efficacy for autonomous driving.

Predicting future trajectories of surrounding agents is essential for safety-critical autonomous driving. Most existing work focuses on predicting marginal trajectories for each agent independently. However, it has rarely been explored in predicting joint trajectories for interactive agents. In this work, we propose Bi-level Future Fusion (BiFF) to explicitly capture future interactions between interactive agents. Concretely, BiFF fuses the high-level future intentions followed by low-level future behaviors. Then the polyline-based coordinate is specifically designed for multi-agent prediction to ensure data efficiency, frame robustness, and prediction accuracy. Experiments show that BiFF achieves state-of-the-art performance on the interactive prediction benchmark of Waymo Open Motion Dataset.

Most iterative neural network training methods use estimates of the loss function over small random subsets (or minibatches) of the data to update the parameters, which aid in decoupling the training time from the (often very large) size of the training datasets. Here, we show that a minibatch approach can also be used to train neural network ensembles (NNEs) via trajectory methods in a highly efficent manner. We illustrate this approach by training NNEs to classify images in the MNIST datasets. This method gives an improvement to the training times, allowing it to scale as the ratio of the size of the dataset to that of the average minibatch size which, in the case of MNIST, gives a computational improvement typically of two orders of magnitude. We highlight the advantage of using longer trajectories to represent NNEs, both for improved accuracy in inference and reduced update cost in terms of the samples needed in minibatch updates.

Message-passing Graph Neural Networks (GNNs), which collect information from adjacent nodes achieve dismal performance on heterophilic graphs. Various schemes have been proposed to solve this problem, and propagating signed information on heterophilic edges has gained great attention. Recently, some works provided theoretical analysis that signed propagation always leads to performance improvement under a binary class scenario. However, we notice that prior analyses do not align well with multi-class benchmark datasets. This paper provides a new understanding of signed propagation for multi-class scenarios and points out two drawbacks in terms of message-passing and parameter update: (1) Message-passing: if two nodes belong to different classes but have a high similarity, signed propagation can decrease the separability. (2) Parameter update: the prediction uncertainty (e.g., conflict evidence) of signed neighbors increases during training, which can impede the stability of the algorithm. Based on the observation, we introduce two novel strategies for improving signed propagation under multi-class graphs. The proposed scheme combines calibration to secure robustness while reducing uncertainty. We show the efficacy of our theorem through extensive experiments on six benchmark graph datasets.

Graph Neural Networks (GNNs) have been successfully used in many problems involving graph-structured data, achieving state-of-the-art performance. GNNs typically employ a message-passing scheme, in which every node aggregates information from its neighbors using a permutation-invariant aggregation function. Standard well-examined choices such as the mean or sum aggregation functions have limited capabilities, as they are not able to capture interactions among neighbors. In this work, we formalize these interactions using an information-theoretic framework that notably includes synergistic information. Driven by this definition, we introduce the Graph Ordering Attention (GOAT) layer, a novel GNN component that captures interactions between nodes in a neighborhood. This is achieved by learning local node orderings via an attention mechanism and processing the ordered representations using a recurrent neural network aggregator. This design allows us to make use of a permutation-sensitive aggregator while maintaining the permutation-equivariance of the proposed GOAT layer. The GOAT model demonstrates its increased performance in modeling graph metrics that capture complex information, such as the betweenness centrality and the effective size of a node. In practical use-cases, its superior modeling capability is confirmed through its success in several real-world node classification benchmarks.

Graph Convolutional Network (GCN) has been widely applied in transportation demand prediction due to its excellent ability to capture non-Euclidean spatial dependence among station-level or regional transportation demands. However, in most of the existing research, the graph convolution was implemented on a heuristically generated adjacency matrix, which could neither reflect the real spatial relationships of stations accurately, nor capture the multi-level spatial dependence of demands adaptively. To cope with the above problems, this paper provides a novel graph convolutional network for transportation demand prediction. Firstly, a novel graph convolution architecture is proposed, which has different adjacency matrices in different layers and all the adjacency matrices are self-learned during the training process. Secondly, a layer-wise coupling mechanism is provided, which associates the upper-level adjacency matrix with the lower-level one. It also reduces the scale of parameters in our model. Lastly, a unitary network is constructed to give the final prediction result by integrating the hidden spatial states with gated recurrent unit, which could capture the multi-level spatial dependence and temporal dynamics simultaneously. Experiments have been conducted on two real-world datasets, NYC Citi Bike and NYC Taxi, and the results demonstrate the superiority of our model over the state-of-the-art ones.

Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect subgraphs, rendering subgraph prediction tasks challenging to tackle in many impactful applications. Further, subgraph prediction tasks present several unique challenges, because subgraphs can have non-trivial internal topology, but also carry a notion of position and external connectivity information relative to the underlying graph in which they exist. Here, we introduce SUB-GNN, a subgraph neural network to learn disentangled subgraph representations. In particular, we propose a novel subgraph routing mechanism that propagates neural messages between the subgraph's components and randomly sampled anchor patches from the underlying graph, yielding highly accurate subgraph representations. SUB-GNN specifies three channels, each designed to capture a distinct aspect of subgraph structure, and we provide empirical evidence that the channels encode their intended properties. We design a series of new synthetic and real-world subgraph datasets. Empirical results for subgraph classification on eight datasets show that SUB-GNN achieves considerable performance gains, outperforming strong baseline methods, including node-level and graph-level GNNs, by 12.4% over the strongest baseline. SUB-GNN performs exceptionally well on challenging biomedical datasets when subgraphs have complex topology and even comprise multiple disconnected components.

Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.