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Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible multi-task surrogate models of MD from data. By conditioning on appropriately chosen frames of the trajectory, we show such generative models can be adapted to diverse tasks such as forward simulation, transition path sampling, and trajectory upsampling. By alternatively conditioning on part of the molecular system and inpainting the rest, we also demonstrate the first steps towards dynamics-conditioned molecular design. We validate the full set of these capabilities on tetrapeptide simulations and show that our model can produce reasonable ensembles of protein monomers. Altogether, our work illustrates how generative modeling can unlock value from MD data towards diverse downstream tasks that are not straightforward to address with existing methods or even MD itself. Code is available at //github.com/bjing2016/mdgen.

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ACM/IEEE第23屆模型驅動工程語言和系統國際會議,是模型驅動軟件和系統工程的首要會議系列,由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來,模型涵蓋了建模的各個方面,從語言和方法到工具和應用程序。模特的參加者來自不同的背景,包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇,參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會,并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。 官網鏈接: · 優化器 · 線性的 · 情景 · 可約的 ·
2024 年 11 月 4 日

Scalarization is a general, parallizable technique that can be deployed in any multiobjective setting to reduce multiple objectives into one, yet some have dismissed this versatile approach because linear scalarizations cannot explore concave regions of the Pareto frontier. To that end, we aim to find simple non-linear scalarizations that provably explore a diverse set of $k$ objectives on the Pareto frontier, as measured by the dominated hypervolume. We show that hypervolume scalarizations with uniformly random weights achieves an optimal sublinear hypervolume regret bound of $O(T^{-1/k})$, with matching lower bounds that preclude any algorithm from doing better asymptotically. For the setting of multiobjective stochastic linear bandits, we utilize properties of hypervolume scalarizations to derive a novel non-Euclidean analysis to get regret bounds of $\tilde{O}( d T^{-1/2} + T^{-1/k})$, removing unnecessary $\text{poly}(k)$ dependencies. We support our theory with strong empirical performance of using non-linear scalarizations that outperforms both their linear counterparts and other standard multiobjective algorithms in a variety of natural settings.

General state-space models (SSMs) are widely used in statistical machine learning and are among the most classical generative models for sequential time-series data. SSMs, comprising latent Markovian states, can be subjected to variational inference (VI), but standard VI methods like the importance-weighted autoencoder (IWAE) lack functionality for streaming data. To enable online VI in SSMs when the observations are received in real time, we propose maximising an IWAE-type variational lower bound on the asymptotic contrast function, rather than the standard IWAE ELBO, using stochastic approximation. Unlike the recursive maximum likelihood method, which directly maximises the asymptotic contrast, our approach, called online sequential IWAE (OSIWAE), allows for online learning of both model parameters and a Markovian recognition model for inferring latent states. By approximating filter state posteriors and their derivatives using sequential Monte Carlo (SMC) methods, we create a particle-based framework for online VI in SSMs. This approach is more theoretically well-founded than recently proposed online variational SMC methods. We provide rigorous theoretical results on the learning objective and a numerical study demonstrating the method's efficiency in learning model parameters and particle proposal kernels.

Compromise estimation entails using a weighted average of outputs from several candidate models, and is a viable alternative to model selection when the choice of model is not obvious. As such, it is a tool used by both frequentists and Bayesians, and in both cases, the literature is vast and includes studies of performance in simulations and applied examples. However, frequentist researchers often prove oracle properties, showing that a proposed average asymptotically performs at least as well as any other average comprising the same candidates. On the Bayesian side, such oracle properties are yet to be established. This paper considers Bayesian stacking estimators, and evaluates their performance using frequentist asymptotics. Oracle properties are derived for estimators stacking Bayesian linear and logistic regression models, and combined with Monte Carlo experiments that show Bayesian stacking may outperform the best candidate model included in the stack. Thus, the result is not only a frequentist motivation of a fundamentally Bayesian procedure, but also an extended range of methods available to frequentist practitioners.

It is becoming increasingly difficult to improve the performance of a a single process (thread) on a computer due to physical limitations. Modern systems use multi-core processors in which multiple processes (threads) may run concurrently. A lock-free data structure can allow these processes to communicate with each other without requiring mutual exclusion, and may increase the amount of work they may perform in parallel rather than sequentially, thus improving the performance of the system as a whole. This paper contains an implementation of Ko's Lock-Free Binary Trie, which stores a dynamic set of keys from an ordered universe. It supports insert, remove, search and predecessor operations. One novel component of this implementation is a lock-free linked list which allows multiple processes to attempt to insert the same node, but which prevents a node from being reinserted once it has been removed from the list. The final section of this paper contains an experimental comparison of this implementation against other data structures which implement the same abstract data type (ADT) as the lock-free trie. Analysis of these experiments reveal that the implementation of Ko's Trie performs better than existing theoretical implementations of this ADT when the universe of keys is large, when removes are rare and when the number of processes performing operations concurrently is low.

Structured state-space models (SSMs) such as S4, stemming from the seminal work of Gu et al., are gaining popularity as effective approaches for modeling sequential data. Deep SSMs demonstrate outstanding performance across a diverse set of domains, at a reduced training and inference cost compared to attention-based transformers. Recent developments show that if the linear recurrence powering SSMs allows for multiplicative interactions between inputs and hidden states (e.g. GateLoop, Mamba, GLA), then the resulting architecture can surpass in both in accuracy and efficiency attention-powered foundation models trained on text, at scales of billion parameters. In this paper, we give theoretical grounding to this recent finding using tools from Rough Path Theory: we show that when random linear recurrences are equipped with simple input-controlled transitions (selectivity mechanism), then the hidden state is provably a low-dimensional projection of a powerful mathematical object called the signature of the input -- capturing non-linear interactions between tokens at distinct timescales. Our theory not only motivates the success of modern selective state-space models such as Mamba but also provides a solid framework to understand the expressive power of future SSM variants.

Classification is a pivotal task in deep learning not only because of its intrinsic importance, but also for providing embeddings with desirable properties in other tasks. To optimize these properties, a wide variety of loss functions have been proposed that attempt to minimize the intra-class distance and maximize the inter-class distance in the embeddings space. In this paper we argue that, in addition to these two, eliminating hierarchies within and among classes are two other desirable properties for classification embeddings. Furthermore, we propose the Angular Distance Distribution (ADD) Loss, which aims to enhance the four previous properties jointly. For this purpose, it imposes conditions on the first and second order statistical moments of the angular distance between embeddings. Finally, we perform experiments showing that our loss function improves all four properties and, consequently, performs better than other loss functions in audio classification tasks.

Large Language Models (LLMs) have shown excellent generalization capabilities that have led to the development of numerous models. These models propose various new architectures, tweaking existing architectures with refined training strategies, increasing context length, using high-quality training data, and increasing training time to outperform baselines. Analyzing new developments is crucial for identifying changes that enhance training stability and improve generalization in LLMs. This survey paper comprehensively analyses the LLMs architectures and their categorization, training strategies, training datasets, and performance evaluations and discusses future research directions. Moreover, the paper also discusses the basic building blocks and concepts behind LLMs, followed by a complete overview of LLMs, including their important features and functions. Finally, the paper summarizes significant findings from LLM research and consolidates essential architectural and training strategies for developing advanced LLMs. Given the continuous advancements in LLMs, we intend to regularly update this paper by incorporating new sections and featuring the latest LLM models.

Attention Model has now become an important concept in neural networks that has been researched within diverse application domains. This survey provides a structured and comprehensive overview of the developments in modeling attention. In particular, we propose a taxonomy which groups existing techniques into coherent categories. We review the different neural architectures in which attention has been incorporated, and also show how attention improves interpretability of neural models. Finally, we discuss some applications in which modeling attention has a significant impact. We hope this survey will provide a succinct introduction to attention models and guide practitioners while developing approaches for their applications.

It is important to detect anomalous inputs when deploying machine learning systems. The use of larger and more complex inputs in deep learning magnifies the difficulty of distinguishing between anomalous and in-distribution examples. At the same time, diverse image and text data are available in enormous quantities. We propose leveraging these data to improve deep anomaly detection by training anomaly detectors against an auxiliary dataset of outliers, an approach we call Outlier Exposure (OE). This enables anomaly detectors to generalize and detect unseen anomalies. In extensive experiments on natural language processing and small- and large-scale vision tasks, we find that Outlier Exposure significantly improves detection performance. We also observe that cutting-edge generative models trained on CIFAR-10 may assign higher likelihoods to SVHN images than to CIFAR-10 images; we use OE to mitigate this issue. We also analyze the flexibility and robustness of Outlier Exposure, and identify characteristics of the auxiliary dataset that improve performance.

Neural machine translation (NMT) is a deep learning based approach for machine translation, which yields the state-of-the-art translation performance in scenarios where large-scale parallel corpora are available. Although the high-quality and domain-specific translation is crucial in the real world, domain-specific corpora are usually scarce or nonexistent, and thus vanilla NMT performs poorly in such scenarios. Domain adaptation that leverages both out-of-domain parallel corpora as well as monolingual corpora for in-domain translation, is very important for domain-specific translation. In this paper, we give a comprehensive survey of the state-of-the-art domain adaptation techniques for NMT.

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