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Error-bounded lossy compression is one of the most effective techniques for scientific data reduction. However, the traditional trial-and-error approach used to configure lossy compressors for finding the optimal trade-off between reconstructed data quality and compression ratio is prohibitively expensive. To resolve this issue, we develop a general-purpose analytical ratio-quality model based on the prediction-based lossy compression framework, which can effectively foresee the reduced data quality and compression ratio, as well as the impact of the lossy compressed data on post-hoc analysis quality. Our analytical model significantly improves the prediction-based lossy compression in three use-cases: (1) optimization of predictor by selecting the best-fit predictor; (2) memory compression with a target ratio; and (3) in-situ compression optimization by fine-grained error-bound tuning of various data partitions. We evaluate our analytical model on 10 scientific datasets, demonstrating its high accuracy (93.47% accuracy on average) and low computational cost (up to 18.7X lower than the trial-and-error approach) for estimating the compression ratio and the impact of lossy compression on post-hoc analysis quality. We also verified the high efficiency of our ratio-quality model using different applications across the three use-cases. In addition, the experiment demonstrates that our modeling based approach reduces the time to store the 3D Reverse Time Migration data by up to 3.4X over the traditional solution using 128 CPU cores from 8 compute nodes.

Score-based generative models and diffusion probabilistic models have been successful at generating high-quality samples in continuous domains such as images and audio. However, due to their Langevin-inspired sampling mechanisms, their application to discrete and sequential data has been limited. In this work, we present a technique for training diffusion models on sequential data by parameterizing the discrete domain in the continuous latent space of a pre-trained variational autoencoder. Our method is non-autoregressive and learns to generate sequences of latent embeddings through the reverse process and offers parallel generation with a constant number of iterative refinement steps. We apply this technique to modeling symbolic music and show strong unconditional generation and post-hoc conditional infilling results compared to autoregressive language models operating over the same continuous embeddings.

Controllable generation is one of the key requirements for successful adoption of deep generative models in real-world applications, but it still remains as a great challenge. In particular, the compositional ability to generate novel concept combinations is out of reach for most current models. In this work, we use energy-based models (EBMs) to handle compositional generation over a set of attributes. To make them scalable to high-resolution image generation, we introduce an EBM in the latent space of a pre-trained generative model such as StyleGAN. We propose a novel EBM formulation representing the joint distribution of data and attributes together, and we show how sampling from it is formulated as solving an ordinary differential equation (ODE). Given a pre-trained generator, all we need for controllable generation is to train an attribute classifier. Sampling with ODEs is done efficiently in the latent space and is robust to hyperparameters. Thus, our method is simple, fast to train, and efficient to sample. Experimental results show that our method outperforms the state-of-the-art in both conditional sampling and sequential editing. In compositional generation, our method excels at zero-shot generation of unseen attribute combinations. Also, by composing energy functions with logical operators, this work is the first to achieve such compositionality in generating photo-realistic images of resolution 1024x1024.

Molecular graph generation is a fundamental problem for drug discovery and has been attracting growing attention. The problem is challenging since it requires not only generating chemically valid molecular structures but also optimizing their chemical properties in the meantime. Inspired by the recent progress in deep generative models, in this paper we propose a flow-based autoregressive model for graph generation called GraphAF. GraphAF combines the advantages of both autoregressive and flow-based approaches and enjoys: (1) high model flexibility for data density estimation; (2) efficient parallel computation for training; (3) an iterative sampling process, which allows leveraging chemical domain knowledge for valency checking. Experimental results show that GraphAF is able to generate 68% chemically valid molecules even without chemical knowledge rules and 100% valid molecules with chemical rules. The training process of GraphAF is two times faster than the existing state-of-the-art approach GCPN. After fine-tuning the model for goal-directed property optimization with reinforcement learning, GraphAF achieves state-of-the-art performance on both chemical property optimization and constrained property optimization.

Graph convolution is the core of most Graph Neural Networks (GNNs) and usually approximated by message passing between direct (one-hop) neighbors. In this work, we remove the restriction of using only the direct neighbors by introducing a powerful, yet spatially localized graph convolution: Graph diffusion convolution (GDC). GDC leverages generalized graph diffusion, examples of which are the heat kernel and personalized PageRank. It alleviates the problem of noisy and often arbitrarily defined edges in real graphs. We show that GDC is closely related to spectral-based models and thus combines the strengths of both spatial (message passing) and spectral methods. We demonstrate that replacing message passing with graph diffusion convolution consistently leads to significant performance improvements across a wide range of models on both supervised and unsupervised tasks and a variety of datasets. Furthermore, GDC is not limited to GNNs but can trivially be combined with any graph-based model or algorithm (e.g. spectral clustering) without requiring any changes to the latter or affecting its computational complexity. Our implementation is available online.

With the capability of modeling bidirectional contexts, denoising autoencoding based pretraining like BERT achieves better performance than pretraining approaches based on autoregressive language modeling. However, relying on corrupting the input with masks, BERT neglects dependency between the masked positions and suffers from a pretrain-finetune discrepancy. In light of these pros and cons, we propose XLNet, a generalized autoregressive pretraining method that (1) enables learning bidirectional contexts by maximizing the expected likelihood over all permutations of the factorization order and (2) overcomes the limitations of BERT thanks to its autoregressive formulation. Furthermore, XLNet integrates ideas from Transformer-XL, the state-of-the-art autoregressive model, into pretraining. Empirically, XLNet outperforms BERT on 20 tasks, often by a large margin, and achieves state-of-the-art results on 18 tasks including question answering, natural language inference, sentiment analysis, and document ranking.

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.

Topic models are one of the most frequently used models in machine learning due to its high interpretability and modular structure. However extending the model to include supervisory signal, incorporate pre-trained word embedding vectors and add nonlinear output function to the model is not an easy task because one has to resort to highly intricate approximate inference procedure. In this paper, we show that topic models could be viewed as performing a neighborhood aggregation algorithm where the messages are passed through a network defined over words. Under the network view of topic models, nodes corresponds to words in a document and edges correspond to either a relationship describing co-occurring words in a document or a relationship describing same word in the corpus. The network view allows us to extend the model to include supervisory signals, incorporate pre-trained word embedding vectors and add nonlinear output function to the model in a simple manner. Moreover, we describe a simple way to train the model that is well suited in a semi-supervised setting where we only have supervisory signals for some portion of the corpus and the goal is to improve prediction performance in the held-out data. Through careful experiments we show that our approach outperforms state-of-the-art supervised Latent Dirichlet Allocation implementation in both held-out document classification tasks and topic coherence.

Scientific publications have evolved several features for mitigating vocabulary mismatch when indexing, retrieving, and computing similarity between articles. These mitigation strategies range from simply focusing on high-value article sections, such as titles and abstracts, to assigning keywords, often from controlled vocabularies, either manually or through automatic annotation. Various document representation schemes possess different cost-benefit tradeoffs. In this paper, we propose to model different representations of the same article as translations of each other, all generated from a common latent representation in a multilingual topic model. We start with a methodological overview on latent variable models for parallel document representations that could be used across many information science tasks. We then show how solving the inference problem of mapping diverse representations into a shared topic space allows us to evaluate representations based on how topically similar they are to the original article. In addition, our proposed approach provides means to discover where different concept vocabularies require improvement.