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The widespread dependency on open-source software makes it a fruitful target for malicious actors, as demonstrated by recurring attacks. The complexity of today's open-source supply chains results in a significant attack surface, giving attackers numerous opportunities to reach the goal of injecting malicious code into open-source artifacts that is then downloaded and executed by victims. This work proposes a general taxonomy for attacks on open-source supply chains, independent of specific programming languages or ecosystems, and covering all supply chain stages from code contributions to package distribution. Taking the form of an attack tree, it covers 107 unique vectors, linked to 94 real-world incidents, and mapped to 33 mitigating safeguards. User surveys conducted with 17 domain experts and 134 software developers positively validated the correctness, comprehensiveness and comprehensibility of the taxonomy, as well as its suitability for various use-cases. Survey participants also assessed the utility and costs of the identified safeguards, and whether they are used.

A fundamental problem in drug discovery is to design molecules that bind to specific proteins. To tackle this problem using machine learning methods, here we propose a novel and effective framework, known as GraphBP, to generate 3D molecules that bind to given proteins by placing atoms of specific types and locations to the given binding site one by one. In particular, at each step, we first employ a 3D graph neural network to obtain geometry-aware and chemically informative representations from the intermediate contextual information. Such context includes the given binding site and atoms placed in the previous steps. Second, to preserve the desirable equivariance property, we select a local reference atom according to the designed auxiliary classifiers and then construct a local spherical coordinate system. Finally, to place a new atom, we generate its atom type and relative location w.r.t. the constructed local coordinate system via a flow model. We also consider generating the variables of interest sequentially to capture the underlying dependencies among them. Experiments demonstrate that our GraphBP is effective to generate 3D molecules with binding ability to target protein binding sites. Our implementation is available at //github.com/divelab/GraphBP.

The irresponsible use of ML algorithms in practical settings has received a lot of deserved attention in the recent years. We posit that the traditional system analysis perspective is needed when designing and implementing ML algorithms and systems. Such perspective can provide a formal way for evaluating and enabling responsible ML practices. In this paper, we review components of the System Analysis methodology and highlight how they connect and enable responsible practices of ML design.

Microcosm, Hyper-G, and the Web were developed and released after 1989. There were strengths and weaknesses associate with each of these hypertext systems. The architectures of these systems were relatively different from one another. Standing above its competitors, the Web became the largest and most popular information system. This paper analyses the reasons for which the Web became the first successful hypermedia system by looking and evaluating the architecture of the Web, Hyper-G, and Microcosm systems. Three reasons will be given beyond this success with some lessons to learn. Currently, Semantic Web is a recent development of the Web to provide conceptual hypermedia. More importantly, study of the Web with its impact on technical, socio-cultural, and economical agendas is introduced as web science.

With the advent of open source software, a veritable treasure trove of previously proprietary software development data was made available. This opened the field of empirical software engineering research to anyone in academia. Data that is mined from software projects, however, requires extensive processing and needs to be handled with utmost care to ensure valid conclusions. Since the software development practices and tools have changed over two decades, we aim to understand the state-of-the-art research workflows and to highlight potential challenges. We employ a systematic literature review by sampling over one thousand papers from leading conferences and by analyzing the 286 most relevant papers from the perspective of data workflows, methodologies, reproducibility, and tools. We found that an important part of the research workflow involving dataset selection was particularly problematic, which raises questions about the generality of the results in existing literature. Furthermore, we found a considerable number of papers provide little or no reproducibility instructions -- a substantial deficiency for a data-intensive field. In fact, 33% of papers provide no information on how their data was retrieved. Based on these findings, we propose ways to address these shortcomings via existing tools and also provide recommendations to improve research workflows and the reproducibility of research.

Designers reportedly struggle with design optimization tasks where they are asked to find a combination of design parameters that maximizes a given set of objectives. In HCI, design optimization problems are often exceedingly complex, involving multiple objectives and expensive empirical evaluations. Model-based computational design algorithms assist designers by generating design examples during design, however they assume a model of the interaction domain. Black box methods for assistance, on the other hand, can work with any design problem. However, virtually all empirical studies of this human-in-the-loop approach have been carried out by either researchers or end-users. The question stands out if such methods can help designers in realistic tasks. In this paper, we study Bayesian optimization as an algorithmic method to guide the design optimization process. It operates by proposing to a designer which design candidate to try next, given previous observations. We report observations from a comparative study with 40 novice designers who were tasked to optimize a complex 3D touch interaction technique. The optimizer helped designers explore larger proportions of the design space and arrive at a better solution, however they reported lower agency and expressiveness. Designers guided by an optimizer reported lower mental effort but also felt less creative and less in charge of the progress. We conclude that human-in-the-loop optimization can support novice designers in cases where agency is not critical.

Music Structure Analysis (MSA) consists in segmenting a music piece in several distinct sections. We approach MSA within a compression framework, under the hypothesis that the structure is more easily revealed by a simplified representation of the original content of the song. More specifically, under the hypothesis that MSA is correlated with similarities occurring at the bar scale, this article introduces the use of linear and non-linear compression schemes on barwise audio signals. Compressed representations capture the most salient components of the different bars in the song and are then used to infer the song structure using a dynamic programming algorithm. This work explores both low-rank approximation models such as Principal Component Analysis or Nonnegative Matrix Factorization and "piece-specific" Auto-Encoding Neural Networks, with the objective to learn latent representations specific to a given song. Such approaches do not rely on supervision nor annotations, which are well-known to be tedious to collect and possibly ambiguous in MSA description. In our experiments, several unsupervised compression schemes achieve a level of performance comparable to that of state-of-the-art supervised methods (for 3s tolerance) on the RWC-Pop dataset, showcasing the importance of the barwise compression processing for MSA.

In recent years, large pre-trained transformers have led to substantial gains in performance over traditional retrieval models and feedback approaches. However, these results are primarily based on the MS Marco/TREC Deep Learning Track setup, with its very particular setup, and our understanding of why and how these models work better is fragmented at best. We analyze effective BERT-based cross-encoders versus traditional BM25 ranking for the passage retrieval task where the largest gains have been observed, and investigate two main questions. On the one hand, what is similar? To what extent does the neural ranker already encompass the capacity of traditional rankers? Is the gain in performance due to a better ranking of the same documents (prioritizing precision)? On the other hand, what is different? Can it retrieve effectively documents missed by traditional systems (prioritizing recall)? We discover substantial differences in the notion of relevance identifying strengths and weaknesses of BERT that may inspire research for future improvement. Our results contribute to our understanding of (black-box) neural rankers relative to (well-understood) traditional rankers, help understand the particular experimental setting of MS-Marco-based test collections.

Deep neural networks have revolutionized many machine learning tasks in power systems, ranging from pattern recognition to signal processing. The data in these tasks is typically represented in Euclidean domains. Nevertheless, there is an increasing number of applications in power systems, where data are collected from non-Euclidean domains and represented as the graph-structured data with high dimensional features and interdependency among nodes. The complexity of graph-structured data has brought significant challenges to the existing deep neural networks defined in Euclidean domains. Recently, many studies on extending deep neural networks for graph-structured data in power systems have emerged. In this paper, a comprehensive overview of graph neural networks (GNNs) in power systems is proposed. Specifically, several classical paradigms of GNNs structures (e.g., graph convolutional networks, graph recurrent neural networks, graph attention networks, graph generative networks, spatial-temporal graph convolutional networks, and hybrid forms of GNNs) are summarized, and key applications in power systems such as fault diagnosis, power prediction, power flow calculation, and data generation are reviewed in detail. Furthermore, main issues and some research trends about the applications of GNNs in power systems are discussed.

Reinforcement learning is one of the core components in designing an artificial intelligent system emphasizing real-time response. Reinforcement learning influences the system to take actions within an arbitrary environment either having previous knowledge about the environment model or not. In this paper, we present a comprehensive study on Reinforcement Learning focusing on various dimensions including challenges, the recent development of different state-of-the-art techniques, and future directions. The fundamental objective of this paper is to provide a framework for the presentation of available methods of reinforcement learning that is informative enough and simple to follow for the new researchers and academics in this domain considering the latest concerns. First, we illustrated the core techniques of reinforcement learning in an easily understandable and comparable way. Finally, we analyzed and depicted the recent developments in reinforcement learning approaches. My analysis pointed out that most of the models focused on tuning policy values rather than tuning other things in a particular state of reasoning.