Graph neural networks (GNN) have become the default machine learning model for relational datasets, including protein interaction networks, biological neural networks, and scientific collaboration graphs. We use tools from statistical physics and random matrix theory to precisely characterize generalization in simple graph convolution networks on the contextual stochastic block model. The derived curves are phenomenologically rich: they explain the distinction between learning on homophilic and heterophilic graphs and they predict double descent whose existence in GNNs has been questioned by recent work. Our results are the first to accurately explain the behavior not only of a stylized graph learning model but also of complex GNNs on messy real-world datasets. To wit, we use our analytic insights about homophily and heterophily to improve performance of state-of-the-art graph neural networks on several heterophilic benchmarks by a simple addition of negative self-loop filters.

Network models are an essential block of modern networks. For example, they are widely used in network planning and optimization. However, as networks increase in scale and complexity, some models present limitations, such as the assumption of markovian traffic in queuing theory models, or the high computational cost of network simulators. Recent advances in machine learning, such as Graph Neural Networks (GNN), are enabling a new generation of network models that are data-driven and can learn complex non-linear behaviors. In this paper, we present RouteNet-Fermi, a custom GNN model that shares the same goals as queuing theory, while being considerably more accurate in the presence of realistic traffic models. The proposed model predicts accurately the delay, jitter, and loss in networks. We have tested RouteNet-Fermi in networks of increasing size (up to 300 nodes), including samples with mixed traffic profiles -- e.g., with complex non-markovian models -- and arbitrary routing and queue scheduling configurations. Our experimental results show that RouteNet-Fermi achieves similar accuracy as computationally-expensive packet-level simulators and it is able to accurately scale to large networks. For example, the model produces delay estimates with a mean relative error of 6.24% when applied to a test dataset with 1,000 samples, including network topologies one order of magnitude larger than those seen during training.

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Contrastive learning (CL), which can extract the information shared between different contrastive views, has become a popular paradigm for vision representation learning. Inspired by the success in computer vision, recent work introduces CL into graph modeling, dubbed as graph contrastive learning (GCL). However, generating contrastive views in graphs is more challenging than that in images, since we have little prior knowledge on how to significantly augment a graph without changing its labels. We argue that typical data augmentation techniques (e.g., edge dropping) in GCL cannot generate diverse enough contrastive views to filter out noises. Moreover, previous GCL methods employ two view encoders with exactly the same neural architecture and tied parameters, which further harms the diversity of augmented views. To address this limitation, we propose a novel paradigm named model augmented GCL (MA-GCL), which will focus on manipulating the architectures of view encoders instead of perturbing graph inputs. Specifically, we present three easy-to-implement model augmentation tricks for GCL, namely asymmetric, random and shuffling, which can respectively help alleviate high- frequency noises, enrich training instances and bring safer augmentations. All three tricks are compatible with typical data augmentations. Experimental results show that MA-GCL can achieve state-of-the-art performance on node classification benchmarks by applying the three tricks on a simple base model. Extensive studies also validate our motivation and the effectiveness of each trick. (Code, data and appendix are available at https://github.com/GXM1141/MA-GCL. )

Recently, the success of pre-training in text domain has been fully extended to vision, audio, and cross-modal scenarios. The proposed pre-training models of different modalities are showing a rising trend of homogeneity in their model structures, which brings the opportunity to implement different pre-training models within a uniform framework. In this paper, we present TencentPretrain, a toolkit supporting pre-training models of different modalities. The core feature of TencentPretrain is the modular design. The toolkit uniformly divides pre-training models into 5 components: embedding, encoder, target embedding, decoder, and target. As almost all of common modules are provided in each component, users can choose the desired modules from different components to build a complete pre-training model. The modular design enables users to efficiently reproduce existing pre-training models or build brand-new one. We test the toolkit on text, vision, and audio benchmarks and show that it can match the performance of the original implementations.

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

通过采用卷积神经网络（CNN）进行电路结构的分割，深度学习在具有挑战性的电路注释任务中取得了巨大的成功。深度学习方法需要大量手动注释的培训数据才能实现良好的性能，如果在给定数据集上培训的深度学习模型被应用于其他数据集，则可能导致性能降解。这通常称为电路注释的域移位问题，这源于不同图像数据集的分布的较大变化。可以从单个设备中的不同设备或不同层获得不同的图像数据集。为了解决域移位问题，我们提出了直方图门控图像翻译（HGIT），这是一个无监督的域适应框架，将图像从给定的源数据集转换为目标数据集的域，并利用转换的图像来训练段网络。具体而言，我们的HGIT执行基于生成的对抗网络（GAN）的图像翻译，并利用直方图统计数据进行数据策划。实验是在适应三个不同目标数据集（无标签的单个标记源数据集上进行的，并评估了每个目标数据集的分割性能。我们已经证明，与报道的域适应技术相比，我们的方法达到了最佳性能，并且还可以合理地接近完全监督的基准。

医学图像分类已在医学图像分析中广泛采用。但是，由于难以在医疗领域收集和标记数据，医疗图像数据集通常受到高度影响。为了解决这个问题，先前的工作利用类样本作为重新加权或重新采样的先验，但特征表示通常仍然不够歧视。在本文中，我们采用对比度学习来解决长尾医疗失衡问题。具体而言，我们首先提出类别原型和对抗性原型，以产生代表性的对比对。然后，提出了原型重新校准策略来解决高度不平衡的数据分布。最后，统一的原始损失旨在训练我们的框架。总体框架，即作为原型的对比学习（PROCO），以端到端方式统一为单级管道，以减轻医学图像分类中的不平衡问题，这也是与现有作品的独特进步当他们遵循传统的两阶段管道时。对两个高度平衡的医学图像分类数据集进行了广泛的实验表明，我们的方法的表现优于现有的最新方法。

变异量子算法（VQA）在NISQ时代表现出巨大的潜力。在VQA的工作流程中，Ansatz的参数迭代更新以近似所需的量子状态。我们已经看到了各种努力，以较少的大门起草更好的安萨兹。在量子计算机中，栅极Ansatz最终将转换为控制信号，例如TransMons上的微波脉冲。并且对照脉冲需要精心校准，以最大程度地减少误差（例如过度旋转和旋转）。在VQA的情况下，此过程将引入冗余，但是VQAS的变异性能自然可以通过更新幅度和频率参数来处理过度旋转和重组的问题。因此，我们提出了PAN，这是一种用于VQA的天然脉冲ANSATZ GENTARATOR框架。我们生成具有可训练参数用于振幅和频率的天然脉冲ansatz。在我们提出的锅中，我们正在调整参数脉冲，这些脉冲在NISQ计算机上得到了内在支持。考虑到本机 - 脉冲ANSATZ不符合参数迁移规则，我们需要部署非级别优化器。为了限制发送到优化器的参数数量，我们采用了一种生成本机 - 脉冲ANSATZ的渐进式方式。实验是在模拟器和量子设备上进行的，以验证我们的方法。当在NISQ机器上采用时，PAN获得的延迟平均提高了86％。 PAN在H2和HEH+上的VQE任务分别能够达到99.336％和96.482％的精度，即使NISQ机器中有很大的噪声。

磁共振图像（MRI）中的脑肿瘤分割（BTS）对于脑肿瘤诊断，癌症管理和研究目的至关重要。随着十年小型挑战的巨大成功以及CNN和Transformer算法的进步，已经提出了许多出色的BTS模型来解决BTS在不同技术方面的困难。但是，现有研究几乎没有考虑如何以合理的方式融合多模式图像。在本文中，我们利用了放射科医生如何从多种MRI模态诊断脑肿瘤的临床知识，并提出了一种称为CKD-TRANSBTS的临床知识驱动的脑肿瘤分割模型。我们没有直接串联所有模式，而是通过根据MRI的成像原理将输入方式分为两组来重新组织输入方式。具有拟议模态相关的跨意义块（MCCA）的双支支混合式编码器旨在提取多模式图像特征。所提出的模型以局部特征表示能力的能力来继承来自变压器和CNN的强度，以提供精确的病变边界和3D体积图像的远程特征提取。为了弥合变压器和CNN功能之间的间隙，我们提出了解码器中的反式和CNN功能校准块（TCFC）。我们将提出的模型与五个基于CNN的模型和六个基于Transformer的模型在Brats 2021挑战数据集上进行了比较。广泛的实验表明，与所有竞争对手相比，所提出的模型可实现最先进的脑肿瘤分割性能。