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Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design by high-throughput (HT) simulations is another forefront of MD. In these areas, the Martini coarse-grained force field, especially the latest version (i.e. v3), is being actively explored because it offers enhanced spatial-temporal resolution. However, the automation tools for preparing simulations with the Martini force field, accompanying the previous version, were not designed for HT simulations or studies of complex cellular systems. Therefore, they become a major limiting factor. To address these shortcomings, we present the open-source vermouth python library. Vermouth is designed to become the unified framework for developing programs, which prepare, run, and analyze Martini simulations of complex systems. To demonstrate the power of the vermouth library, the martinize2 program is showcased as a generalization of the martinize script, originally aimed to set up simulations of proteins. In contrast to the previous version, martinize2 automatically handles protonation states in proteins and post-translation modifications, offers more options to fine-tune structural biases such as the elastic network, and can convert non-protein molecules such as ligands. Finally, martinize2 is used in two high-complexity benchmarks. The entire I-TASSER protein template database as well as a subset of 200,000 structures from the AlphaFold Protein Structure Database are converted to CG resolution and we illustrate how the checks on input structure quality can safeguard HT applications.

Government development projects vary significantly from private sector initiatives in scope, stakeholder complexity, and regulatory requirements. There is a lack of empirical studies focusing on requirements engineering (RE) activities specifically for government projects. We addressed this gap by conducting a series of semi-structured interviews with 12 professional software practitioners working on government projects. These interviewees are employed by two types of companies, each serving different government departments. Our findings uncover differences in the requirements elicitation phase between government projects, particularly for data visualization aspects, and other software projects, such as stakeholders and policy requirements. Additionally, we explore the coverage of human and social aspects in requirements elicitation, finding that culture, team dynamics, and policy implications are critical considerations. Our findings also pinpoint the main challenges encountered during the requirements elicitation phase for government projects. Our findings highlight future research work that is important to bridge the gap in RE activities for government software projects.

Automated data labeling techniques are crucial for accelerating the development of deep learning models, particularly in complex medical imaging applications. However, ensuring accuracy and efficiency remains challenging. This paper presents iterative refinement strategies for automated data labeling in facial landmark diagnosis to enhance accuracy and efficiency for deep learning models in medical applications, including dermatology, plastic surgery, and ophthalmology. Leveraging feedback mechanisms and advanced algorithms, our approach iteratively refines initial labels, reducing reliance on manual intervention while improving label quality. Through empirical evaluation and case studies, we demonstrate the effectiveness of our proposed strategies in deep learning tasks across medical imaging domains. Our results highlight the importance of iterative refinement in automated data labeling to enhance the capabilities of deep learning systems in medical imaging applications.

Automatically generating human-readable text describing the functionality of a program is the intent of source code summarization. Although neural language models achieve significant performance in this field, they are limited by their inability to access external knowledge. To address this limitation, an emerging trend is combining neural models with external knowledge through retrieval methods. Previous methods have relied on the sentence-level retrieval paradigm on the encoder side. However, this paradigm is coarse-grained, noise-filled and cannot directly take advantage of the high-quality retrieved summary tokens on the decoder side. In this paper, we propose a fine-grained Token-level retrieval-augmented mechanism (Tram) on the decoder side rather than the encoder side to enhance the performance of neural models and produce more low-frequency tokens in generating summaries. Furthermore, to overcome the challenge of token-level retrieval in capturing contextual code semantics, we also propose integrating code semantics into individual summary tokens. The results of extensive experiments and human evaluation show that our token-level retrieval-augmented approach significantly improves performance and is more interpretable.

Edge computing facilitates low-latency services at the network's edge by distributing computation, communication, and storage resources within the geographic proximity of mobile and Internet-of-Things (IoT) devices. The recent advancement in Unmanned Aerial Vehicles (UAVs) technologies has opened new opportunities for edge computing in military operations, disaster response, or remote areas where traditional terrestrial networks are limited or unavailable. In such environments, UAVs can be deployed as aerial edge servers or relays to facilitate edge computing services. This form of computing is also known as UAV-enabled Edge Computing (UEC), which offers several unique benefits such as mobility, line-of-sight, flexibility, computational capability, and cost-efficiency. However, the resources on UAVs, edge servers, and IoT devices are typically very limited in the context of UEC. Efficient resource management is, therefore, a critical research challenge in UEC. In this article, we present a survey on the existing research in UEC from the resource management perspective. We identify a conceptual architecture, different types of collaborations, wireless communication models, research directions, key techniques and performance indicators for resource management in UEC. We also present a taxonomy of resource management in UEC. Finally, we identify and discuss some open research challenges that can stimulate future research directions for resource management in UEC.

Existing recommender systems extract the user preference based on learning the correlation in data, such as behavioral correlation in collaborative filtering, feature-feature, or feature-behavior correlation in click-through rate prediction. However, regretfully, the real world is driven by causality rather than correlation, and correlation does not imply causation. For example, the recommender systems can recommend a battery charger to a user after buying a phone, in which the latter can serve as the cause of the former, and such a causal relation cannot be reversed. Recently, to address it, researchers in recommender systems have begun to utilize causal inference to extract causality, enhancing the recommender system. In this survey, we comprehensively review the literature on causal inference-based recommendation. At first, we present the fundamental concepts of both recommendation and causal inference as the basis of later content. We raise the typical issues that the non-causality recommendation is faced. Afterward, we comprehensively review the existing work of causal inference-based recommendation, based on a taxonomy of what kind of problem causal inference addresses. Last, we discuss the open problems in this important research area, along with interesting future works.

The incredible development of federated learning (FL) has benefited various tasks in the domains of computer vision and natural language processing, and the existing frameworks such as TFF and FATE has made the deployment easy in real-world applications. However, federated graph learning (FGL), even though graph data are prevalent, has not been well supported due to its unique characteristics and requirements. The lack of FGL-related framework increases the efforts for accomplishing reproducible research and deploying in real-world applications. Motivated by such strong demand, in this paper, we first discuss the challenges in creating an easy-to-use FGL package and accordingly present our implemented package FederatedScope-GNN (FS-G), which provides (1) a unified view for modularizing and expressing FGL algorithms; (2) comprehensive DataZoo and ModelZoo for out-of-the-box FGL capability; (3) an efficient model auto-tuning component; and (4) off-the-shelf privacy attack and defense abilities. We validate the effectiveness of FS-G by conducting extensive experiments, which simultaneously gains many valuable insights about FGL for the community. Moreover, we employ FS-G to serve the FGL application in real-world E-commerce scenarios, where the attained improvements indicate great potential business benefits. We publicly release FS-G, as submodules of FederatedScope, at //github.com/alibaba/FederatedScope to promote FGL's research and enable broad applications that would otherwise be infeasible due to the lack of a dedicated package.

Autonomic computing investigates how systems can achieve (user) specified control outcomes on their own, without the intervention of a human operator. Autonomic computing fundamentals have been substantially influenced by those of control theory for closed and open-loop systems. In practice, complex systems may exhibit a number of concurrent and inter-dependent control loops. Despite research into autonomic models for managing computer resources, ranging from individual resources (e.g., web servers) to a resource ensemble (e.g., multiple resources within a data center), research into integrating Artificial Intelligence (AI) and Machine Learning (ML) to improve resource autonomy and performance at scale continues to be a fundamental challenge. The integration of AI/ML to achieve such autonomic and self-management of systems can be achieved at different levels of granularity, from full to human-in-the-loop automation. In this article, leading academics, researchers, practitioners, engineers, and scientists in the fields of cloud computing, AI/ML, and quantum computing join to discuss current research and potential future directions for these fields. Further, we discuss challenges and opportunities for leveraging AI and ML in next generation computing for emerging computing paradigms, including cloud, fog, edge, serverless and quantum computing environments.

The cross-domain recommendation technique is an effective way of alleviating the data sparsity in recommender systems by leveraging the knowledge from relevant domains. Transfer learning is a class of algorithms underlying these techniques. In this paper, we propose a novel transfer learning approach for cross-domain recommendation by using neural networks as the base model. We assume that hidden layers in two base networks are connected by cross mappings, leading to the collaborative cross networks (CoNet). CoNet enables dual knowledge transfer across domains by introducing cross connections from one base network to another and vice versa. CoNet is achieved in multi-layer feedforward networks by adding dual connections and joint loss functions, which can be trained efficiently by back-propagation. The proposed model is evaluated on two real-world datasets and it outperforms baseline models by relative improvements of 3.56\% in MRR and 8.94\% in NDCG, respectively.