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Background, enhancing interoperability of bioinformatics knowledge bases is a high priority requirement to maximize data reusability, and thus increase their utility such as the return on investment for biomedical research. A knowledge base may provide useful information for life scientists and other knowledge bases, but it only acquires exchange value once the knowledge base is (re)used, and without interoperability the utility lies dormant. Results, in this article, we discuss several approaches to boost interoperability depending on the interoperable parts. The findings are driven by several real-world scenario examples that were mostly implemented by Bgee, a well-established gene expression database. Moreover, we discuss ten general main lessons learnt. These lessons can be applied in the context of any bioinformatics knowledge base to foster data reusability. Conclusions, this work provides pragmatic methods and transferable skills to promote reusability of bioinformatics knowledge bases by focusing on interoperability.

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Effective communication is crucial for deploying robots in mission-specific tasks, but inadequate or unreliable communication can greatly reduce mission efficacy, for example in search and rescue missions where communication-denied conditions may occur. In such missions, robots are deployed to locate targets, such as human survivors, but they might get trapped at hazardous locations, such as in a trapping pit or by debris. Thus, the information the robot collected is lost owing to the lack of communication. In our prior work, we developed the notion of a path-based sensor. A path-based sensor detects whether or not an event has occurred along a particular path, but it does not provide the exact location of the event. Such path-based sensor observations are well-suited to communication-denied environments, and various studies have explored methods to improve information gathering in such settings. In some missions it is typical for target elements to be in close proximity to hazardous factors that hinder the information-gathering process. In this study, we examine a similar scenario and conduct experiments to determine if additional knowledge about the correlation between hazards and targets improves the efficiency of information gathering. To incorporate this knowledge, we utilize a Bayesian network representation of domain knowledge and develop an algorithm based on this representation. Our empirical investigation reveals that such additional information on correlation is beneficial only in environments with moderate hazard lethality, suggesting that while knowledge of correlation helps, further research and development is necessary for optimal outcomes.

Surrogate-assisted evolutionary algorithms (SAEAs) aim to use efficient computational models with the goal of approximating the fitness function in evolutionary computation systems. This area of research has been active for over two decades and has received significant attention from the specialised research community in different areas, for example, single and many objective optimisation or dynamic and stationary optimisation problems. An emergent and exciting area that has received little attention from the SAEAs community is in neuroevolution. This refers to the use of evolutionary algorithms in the automatic configuration of artificial neural network (ANN) architectures, hyper-parameters and/or the training of ANNs. However, ANNs suffer from two major issues: (a) the use of highly-intense computational power for their correct training, and (b) the highly specialised human expertise required to correctly configure ANNs necessary to get a well-performing network. This work aims to fill this important research gap in SAEAs in neuroevolution by addressing these two issues. We demonstrate how one can use a Kriging Partial Least Squares method that allows efficient computation of good approximate surrogate models compared to the well-known Kriging method, which normally cannot be used in neuroevolution due to the high dimensionality of the data.

Continuous-time models such as Neural ODEs and Neural Flows have shown promising results in analyzing irregularly sampled time series frequently encountered in electronic health records. Based on these models, time series are typically processed with a hybrid of an initial value problem (IVP) solver and a recurrent neural network within the variational autoencoder architecture. Sequentially solving IVPs makes such models computationally less efficient. In this paper, we propose to model time series purely with continuous processes whose state evolution can be approximated directly by IVPs. This eliminates the need for recurrent computation and enables multiple states to evolve in parallel. We further fuse the encoder and decoder with one IVP solver based on its invertibility, which leads to fewer parameters and faster convergence. Experiments on three real-world datasets show that the proposed approach achieves comparable extrapolation and classification performance while gaining more than one order of magnitude speedup over other continuous-time counterparts.

When building a new application we are increasingly confronted with the need of reusing and integrating pre-existing knowledge. Nevertheless, it is a fact that this prior knowledge is virtually impossible to reuse as-is. This is true also in domains, e.g., eHealth, where a lot of effort has been put into developing high-quality standards and reference ontologies, e.g. FHIR1. In this paper, we propose an integrated methodology, called iTelos, which enables data and knowledge reuse towards the construction of Interoperable Electronic Health Records (iEHR). The key intuition is that the data level and the schema level of an application should be developed independently, thus allowing for maximum flexibility in the reuse of the prior knowledge, but under the overall guidance of the needs to be satisfied, formalized as competence queries. This intuition is implemented by codifying all the requirements, including those concerning reuse, as part of a purpose defined a priori, which is then used to drive a middle-out development process where the application schema and data are continuously aligned. The proposed methodology is validated through its application to a large-scale case study.

Federated Learning (FL) is a widely embraced paradigm for distilling artificial intelligence from distributed mobile data. However, the deployment of FL in mobile networks can be compromised by exposure to interference from neighboring cells or jammers. Existing interference mitigation techniques require multi-cell cooperation or at least interference channel state information, which is expensive in practice. On the other hand, power control that treats interference as noise may not be effective due to limited power budgets, and also that this mechanism can trigger countermeasures by interference sources. As a practical approach for protecting FL against interference, we propose Spectrum Breathing, which cascades stochastic-gradient pruning and spread spectrum to suppress interference without bandwidth expansion. The cost is higher learning latency by exploiting the graceful degradation of learning speed due to pruning. We synchronize the two operations such that their levels are controlled by the same parameter, Breathing Depth. To optimally control the parameter, we develop a martingale-based approach to convergence analysis of Over-the-Air FL with spectrum breathing, termed AirBreathing FL. We show a performance tradeoff between gradient-pruning and interference-induced error as regulated by the breathing depth. Given receive SIR and model size, the optimization of the tradeoff yields two schemes for controlling the breathing depth that can be either fixed or adaptive to channels and the learning process. As shown by experiments, in scenarios where traditional Over-the-Air FL fails to converge in the presence of strong interference, AirBreahing FL with either fixed or adaptive breathing depth can ensure convergence where the adaptive scheme achieves close-to-ideal performance.

Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering and recommendation systems, etc. According to the graph types, the existing KGR models can be roughly divided into three categories, \textit{i.e.,} static models, temporal models, and multi-modal models. The early works in this domain mainly focus on static KGR and tend to directly apply general knowledge graph embedding models to the reasoning task. However, these models are not suitable for more complex but practical tasks, such as inductive static KGR, temporal KGR, and multi-modal KGR. To this end, multiple works have been developed recently, but no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the preliminaries, summaries of KGR models, and typical datasets are introduced and discussed consequently. Moreover, we discuss the challenges and potential opportunities. The corresponding open-source repository is shared on GitHub: //github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.

Knowledge graph embedding models learn the representations of entities and relations in the knowledge graphs for predicting missing links (relations) between entities. Their effectiveness are deeply affected by the ability of modeling and inferring different relation patterns such as symmetry, asymmetry, inversion, composition and transitivity. Although existing models are already able to model many of these relations patterns, transitivity, a very common relation pattern, is still not been fully supported. In this paper, we first theoretically show that the transitive relations can be modeled with projections. We then propose the Rot-Pro model which combines the projection and relational rotation together. We prove that Rot-Pro can infer all the above relation patterns. Experimental results show that the proposed Rot-Pro model effectively learns the transitivity pattern and achieves the state-of-the-art results on the link prediction task in the datasets containing transitive relations.

In this paper we provide a comprehensive introduction to knowledge graphs, which have recently garnered significant attention from both industry and academia in scenarios that require exploiting diverse, dynamic, large-scale collections of data. After a general introduction, we motivate and contrast various graph-based data models and query languages that are used for knowledge graphs. We discuss the roles of schema, identity, and context in knowledge graphs. We explain how knowledge can be represented and extracted using a combination of deductive and inductive techniques. We summarise methods for the creation, enrichment, quality assessment, refinement, and publication of knowledge graphs. We provide an overview of prominent open knowledge graphs and enterprise knowledge graphs, their applications, and how they use the aforementioned techniques. We conclude with high-level future research directions for knowledge graphs.

Knowledge graph completion aims to predict missing relations between entities in a knowledge graph. While many different methods have been proposed, there is a lack of a unifying framework that would lead to state-of-the-art results. Here we develop PathCon, a knowledge graph completion method that harnesses four novel insights to outperform existing methods. PathCon predicts relations between a pair of entities by: (1) Considering the Relational Context of each entity by capturing the relation types adjacent to the entity and modeled through a novel edge-based message passing scheme; (2) Considering the Relational Paths capturing all paths between the two entities; And, (3) adaptively integrating the Relational Context and Relational Path through a learnable attention mechanism. Importantly, (4) in contrast to conventional node-based representations, PathCon represents context and path only using the relation types, which makes it applicable in an inductive setting. Experimental results on knowledge graph benchmarks as well as our newly proposed dataset show that PathCon outperforms state-of-the-art knowledge graph completion methods by a large margin. Finally, PathCon is able to provide interpretable explanations by identifying relations that provide the context and paths that are important for a given predicted relation.

Graph convolutional neural networks have recently shown great potential for the task of zero-shot learning. These models are highly sample efficient as related concepts in the graph structure share statistical strength allowing generalization to new classes when faced with a lack of data. However, multi-layer architectures, which are required to propagate knowledge to distant nodes in the graph, dilute the knowledge by performing extensive Laplacian smoothing at each layer and thereby consequently decrease performance. In order to still enjoy the benefit brought by the graph structure while preventing dilution of knowledge from distant nodes, we propose a Dense Graph Propagation (DGP) module with carefully designed direct links among distant nodes. DGP allows us to exploit the hierarchical graph structure of the knowledge graph through additional connections. These connections are added based on a node's relationship to its ancestors and descendants. A weighting scheme is further used to weigh their contribution depending on the distance to the node to improve information propagation in the graph. Combined with finetuning of the representations in a two-stage training approach our method outperforms state-of-the-art zero-shot learning approaches.

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