一种感染细菌和古代的原核病毒是微生物社区的关键球员。预测原核病毒的宿主有助于破译微生物之间的动态关系。虽然存在用于宿主鉴定的实验方法，但它们是劳动密集型或需要培养宿主细胞，从而产生对计算宿主预测的需求。尽管结果有一些有希望的结果，但计算宿主预测仍然是挑战，因为通过高通量测序技术通过有限的已知的相互作用和纯粹的测序量。最先进的方法只能在物种级别达到43％的精度。这项工作呈现樱桃，该工具配制主机预测作为知识图中的链路预测。作为病毒原核相互作用预测工具，可以应用樱桃以预测新发现病毒的宿主以及感染抗生素抗菌细菌的病毒。我们展示了樱桃对既有应用的效用，并将其性能与不同情景中的最先进的方法进行了比较。为了我们最好的知识，樱桃在识别病毒 - 原核互动方面具有最高的准确性。它优于物种水平的所有现有方法，精度增加37％。此外，樱桃的性能比其他工具更短的Contig。

近年来，由于强大的3D CNN，基于体素的方法已成为室内场景3D语义分割的最新方法。然而，基于体素的方法忽略了基础的几何形状，由于缺乏地理位置信息而在空间上闭合物体上的模棱两可的特征遭受了含糊的特征，并努力处理复杂和不规则的几何形状。鉴于此，我们提出了Voxel-Mesh网络（VMNET），这是一种新颖的3D深度体系结构，该架构在Voxel和网格表示上运行，并利用了欧几里得和地球信息。从直觉上讲，从体素中提取的欧几里得信息可以提供代表附近对象之间交互的上下文提示，而从网格中提取的地理信息可以帮助空间上接近但断开表面的分离对象。为了合并两个域中的此类信息，我们设计了一个内域的专注模块，以进行有效的特征聚集和一个用于自适应特征融合的专注于域间的模块。实验结果验证了VMNET的有效性：具体而言，在具有挑战性的扫描仪数据集上，用于大规模的室内场景分割，它的表现优于最先进的Sparseconvnet和Minkowskownet（74.6％vs 72.5％和73.6％）更简单的网络结构（17m vs 30m和38m参数）。代码发布：https：//github.com/hzykent/vmnet

背景：感染细菌和古代的原核病毒是生物圈中最丰富和多样化的生物实体。要了解各种生态系统中的监管作用，并利用治疗中使用的噬菌体的潜力，需要了解有病毒宿主关系的知识。高通量测序及其对微生物组的应用已经为预测宿主特定病毒可能感染的预测提供了新的机会。但是，计算宿主预测存在两个主要挑战。首先，经验上已知的病毒 - 宿主关系非常有限。其次，虽然病毒与其原核寄存器之间的序列相似度被用作宿主预测的主要特征，但在许多情况下，对齐在丢失或含糊不清。因此，仍然需要提高宿主预测的准确性。结果：在这项工作中，我们提出了一个半监督的学习模型，名为Hostg，为新颖病毒进行主机预测。我们通过利用病毒病毒蛋白质相似性和病毒宿主DNA序列相似性构建知识图。然后采用图形卷积网络（GCN）来利用或没有已知主机在培训中进行病毒来提高学习能力。在GCN培训期间，我们最小化预期的校准错误（ECE），以确保预测的信心。我们在模拟和实际测序数据上测试了HostG，并将其性能与其他用于病毒主机分类（VHM-Net，Wish，PHP，Hophage，Rafah，VHulk和VPF-Class）设计的最先进的方法。结论：Hostg优于其他流行的方法，展示了使用基于GCN的半监督学习方法的功效。 Hostg的特殊优势是它能够从新的分类群中预测主机。

Existing federated classification algorithms typically assume the local annotations at every client cover the same set of classes. In this paper, we aim to lift such an assumption and focus on a more general yet practical non-IID setting where every client can work on non-identical and even disjoint sets of classes (i.e., client-exclusive classes), and the clients have a common goal which is to build a global classification model to identify the union of these classes. Such heterogeneity in client class sets poses a new challenge: how to ensure different clients are operating in the same latent space so as to avoid the drift after aggregation? We observe that the classes can be described in natural languages (i.e., class names) and these names are typically safe to share with all parties. Thus, we formulate the classification problem as a matching process between data representations and class representations and break the classification model into a data encoder and a label encoder. We leverage the natural-language class names as the common ground to anchor the class representations in the label encoder. In each iteration, the label encoder updates the class representations and regulates the data representations through matching. We further use the updated class representations at each round to annotate data samples for locally-unaware classes according to similarity and distill knowledge to local models. Extensive experiments on four real-world datasets show that the proposed method can outperform various classical and state-of-the-art federated learning methods designed for learning with non-IID data.

Existing measures and representations for trajectories have two longstanding fundamental shortcomings, i.e., they are computationally expensive and they can not guarantee the `uniqueness' property of a distance function: dist(X,Y) = 0 if and only if X=Y, where $X$ and $Y$ are two trajectories. This paper proposes a simple yet powerful way to represent trajectories and measure the similarity between two trajectories using a distributional kernel to address these shortcomings. It is a principled approach based on kernel mean embedding which has a strong theoretical underpinning. It has three distinctive features in comparison with existing approaches. (1) A distributional kernel is used for the very first time for trajectory representation and similarity measurement. (2) It does not rely on point-to-point distances which are used in most existing distances for trajectories. (3) It requires no learning, unlike existing learning and deep learning approaches. We show the generality of this new approach in three applications: (a) trajectory anomaly detection, (b) anomalous sub-trajectory detection, and (c) trajectory pattern mining. We identify that the distributional kernel has (i) a unique data-dependent property and the above uniqueness property which are the key factors that lead to its superior task-specific performance; and (ii) runtime orders of magnitude faster than existing distance measures.

Natural Language Processing (NLP) has been revolutionized by the use of Pre-trained Language Models (PLMs) such as BERT. Despite setting new records in nearly every NLP task, PLMs still face a number of challenges including poor interpretability, weak reasoning capability, and the need for a lot of expensive annotated data when applied to downstream tasks. By integrating external knowledge into PLMs, \textit{\underline{K}nowledge-\underline{E}nhanced \underline{P}re-trained \underline{L}anguage \underline{M}odels} (KEPLMs) have the potential to overcome the above-mentioned limitations. In this paper, we examine KEPLMs systematically through a series of studies. Specifically, we outline the common types and different formats of knowledge to be integrated into KEPLMs, detail the existing methods for building and evaluating KEPLMS, present the applications of KEPLMs in downstream tasks, and discuss the future research directions. Researchers will benefit from this survey by gaining a quick and comprehensive overview of the latest developments in this field.

Autonomous robotic surgery has advanced significantly based on analysis of visual and temporal cues in surgical workflow, but relational cues from domain knowledge remain under investigation. Complex relations in surgical annotations can be divided into intra- and inter-relations, both valuable to autonomous systems to comprehend surgical workflows. Intra- and inter-relations describe the relevance of various categories within a particular annotation type and the relevance of different annotation types, respectively. This paper aims to systematically investigate the importance of relational cues in surgery. First, we contribute the RLLS12M dataset, a large-scale collection of robotic left lateral sectionectomy (RLLS), by curating 50 videos of 50 patients operated by 5 surgeons and annotating a hierarchical workflow, which consists of 3 inter- and 6 intra-relations, 6 steps, 15 tasks, and 38 activities represented as the triplet of 11 instruments, 8 actions, and 16 objects, totaling 2,113,510 video frames and 12,681,060 annotation entities. Correspondingly, we propose a multi-relation purification hybrid network (MURPHY), which aptly incorporates novel relation modules to augment the feature representation by purifying relational features using the intra- and inter-relations embodied in annotations. The intra-relation module leverages a R-GCN to implant visual features in different graph relations, which are aggregated using a targeted relation purification with affinity information measuring label consistency and feature similarity. The inter-relation module is motivated by attention mechanisms to regularize the influence of relational features based on the hierarchy of annotation types from the domain knowledge. Extensive experimental results on the curated RLLS dataset confirm the effectiveness of our approach, demonstrating that relations matter in surgical workflow analysis.

In the era of Internet of Things (IoT), network-wide anomaly detection is a crucial part of monitoring IoT networks due to the inherent security vulnerabilities of most IoT devices. Principal Components Analysis (PCA) has been proposed to separate network traffics into two disjoint subspaces corresponding to normal and malicious behaviors for anomaly detection. However, the privacy concerns and limitations of devices' computing resources compromise the practical effectiveness of PCA. We propose a federated PCA-based Grassmannian optimization framework that coordinates IoT devices to aggregate a joint profile of normal network behaviors for anomaly detection. First, we introduce a privacy-preserving federated PCA framework to simultaneously capture the profile of various IoT devices' traffic. Then, we investigate the alternating direction method of multipliers gradient-based learning on the Grassmann manifold to guarantee fast training and the absence of detecting latency using limited computational resources. Empirical results on the NSL-KDD dataset demonstrate that our method outperforms baseline approaches. Finally, we show that the Grassmann manifold algorithm is highly adapted for IoT anomaly detection, which permits drastically reducing the analysis time of the system. To the best of our knowledge, this is the first federated PCA algorithm for anomaly detection meeting the requirements of IoT networks.

Deep learning-based methods have achieved significant performance for image defogging. However, existing methods are mainly developed for land scenes and perform poorly when dealing with overwater foggy images, since overwater scenes typically contain large expanses of sky and water. In this work, we propose a Prior map Guided CycleGAN (PG-CycleGAN) for defogging of images with overwater scenes. To promote the recovery of the objects on water in the image, two loss functions are exploited for the network where a prior map is designed to invert the dark channel and the min-max normalization is used to suppress the sky and emphasize objects. However, due to the unpaired training set, the network may learn an under-constrained domain mapping from foggy to fog-free image, leading to artifacts and loss of details. Thus, we propose an intuitive Upscaling Inception Module (UIM) and a Long-range Residual Coarse-to-fine framework (LRC) to mitigate this issue. Extensive experiments on qualitative and quantitative comparisons demonstrate that the proposed method outperforms the state-of-the-art supervised, semi-supervised, and unsupervised defogging approaches.

Code generation models have achieved impressive performance. However, they tend to be brittle as slight edits to a prompt could lead to very different generations; these robustness properties, critical for user experience when deployed in real-life applications, are not well understood. Most existing works on robustness in text or code tasks have focused on classification, while robustness in generation tasks is an uncharted area and to date there is no comprehensive benchmark for robustness in code generation. In this paper, we propose ReCode, a comprehensive robustness evaluation benchmark for code generation models. We customize over 30 transformations specifically for code on docstrings, function and variable names, code syntax, and code format. They are carefully designed to be natural in real-life coding practice, preserve the original semantic meaning, and thus provide multifaceted assessments of a model's robustness performance. With human annotators, we verified that over 90% of the perturbed prompts do not alter the semantic meaning of the original prompt. In addition, we define robustness metrics for code generation models considering the worst-case behavior under each type of perturbation, taking advantage of the fact that executing the generated code can serve as objective evaluation. We demonstrate ReCode on SOTA models using HumanEval, MBPP, as well as function completion tasks derived from them. Interesting observations include: better robustness for CodeGen over InCoder and GPT-J; models are most sensitive to syntax perturbations; more challenging robustness evaluation on MBPP over HumanEval.