Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet, a supervised deep-learning model to predict the fitness for protein mutants by leveraging both sequence and structure information, and exploiting attention mechanism. Our model integrates local evolutionary context from homologous sequences, the global evolutionary context encoding rich semantic from the universal protein sequence space and the structure information accounting for the microenvironment around each residue in a protein. We show that SESNet outperforms state-of-the-art models for predicting the sequence-function relationship on 26 deep mutational scanning datasets. More importantly, we propose a data augmentation strategy by leveraging the data from unsupervised models to pre-train our model. After that, our model can achieve strikingly high accuracy in prediction of the fitness of protein mutants, especially for the higher order variants (> 4 mutation sites), when finetuned by using only a small number of experimental mutation data (<50). The strategy proposed is of great practical value as the required experimental effort, i.e., producing a few tens of experimental mutation data on a given protein, is generally affordable by an ordinary biochemical group and can be applied on almost any protein.

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.

Convolutional Neural Networks (CNNs) have demonstrated superiority in learning patterns, but are sensitive to label noises and may overfit noisy labels during training. The early stopping strategy averts updating CNNs during the early training phase and is widely employed in the presence of noisy labels. Motivated by biological findings that the amplitude spectrum (AS) and phase spectrum (PS) in the frequency domain play different roles in the animal's vision system, we observe that PS, which captures more semantic information, can increase the robustness of DNNs to label noise, more so than AS can. We thus propose early stops at different times for AS and PS by disentangling the features of some layer(s) into AS and PS using Discrete Fourier Transform (DFT) during training. Our proposed Phase-AmplituDe DisentangLed Early Stopping (PADDLES) method is shown to be effective on both synthetic and real-world label-noise datasets. PADDLES outperforms other early stopping methods and obtains state-of-the-art performance.

With the drive to create a decentralized digital economy, Web 3.0 has become a cornerstone of digital transformation, developed on the basis of computing-force networking, distributed data storage, and blockchain. With the rapid realization of quantum devices, Web 3.0 is being developed in parallel with the deployment of quantum cloud computing and quantum Internet. In this regard, quantum computing first disrupts the original cryptographic systems that protect data security while reshaping modern cryptography with the advantages of quantum computing and communication. Therefore, in this paper, we introduce a quantum blockchain-driven Web 3.0 framework that provides information-theoretic security for decentralized data transferring and payment transactions. First, we present the framework of quantum blockchain-driven Web 3.0 with future-proof security during the transmission of data and transaction information. Next, we discuss the potential applications and challenges of implementing quantum blockchain in Web 3.0. Finally, we describe a use case for quantum non-fungible tokens (NFTs) and propose a quantum deep learning-based optimal auction for NFT trading to maximize the achievable revenue for sufficient liquidity in Web 3.0. In this way, the proposed framework can achieve proven security and sustainability for the next-generation decentralized digital society.

Robust Model-Agnostic Meta-Learning (MAML) is usually adopted to train a meta-model which may fast adapt to novel classes with only a few exemplars and meanwhile remain robust to adversarial attacks. The conventional solution for robust MAML is to introduce robustness-promoting regularization during meta-training stage. With such a regularization, previous robust MAML methods simply follow the typical MAML practice that the number of training shots should match with the number of test shots to achieve an optimal adaptation performance. However, although the robustness can be largely improved, previous methods sacrifice clean accuracy a lot. In this paper, we observe that introducing robustness-promoting regularization into MAML reduces the intrinsic dimension of clean sample features, which results in a lower capacity of clean representations. This may explain why the clean accuracy of previous robust MAML methods drops severely. Based on this observation, we propose a simple strategy, i.e., increasing the number of training shots, to mitigate the loss of intrinsic dimension caused by robustness-promoting regularization. Though simple, our method remarkably improves the clean accuracy of MAML without much loss of robustness, producing a robust yet accurate model. Extensive experiments demonstrate that our method outperforms prior arts in achieving a better trade-off between accuracy and robustness. Besides, we observe that our method is less sensitive to the number of fine-tuning steps during meta-training, which allows for a reduced number of fine-tuning steps to improve training efficiency.

Large language models (LLMs) have been shown to be able to perform new tasks based on a few demonstrations or natural language instructions. While these capabilities have led to widespread adoption, most LLMs are developed by resource-rich organizations and are frequently kept from the public. As a step towards democratizing this powerful technology, we present BLOOM, a 176B-parameter open-access language model designed and built thanks to a collaboration of hundreds of researchers. BLOOM is a decoder-only Transformer language model that was trained on the ROOTS corpus, a dataset comprising hundreds of sources in 46 natural and 13 programming languages (59 in total). We find that BLOOM achieves competitive performance on a wide variety of benchmarks, with stronger results after undergoing multitask prompted finetuning. To facilitate future research and applications using LLMs, we publicly release our models and code under the Responsible AI License.

我们提出了一个基于神经网络的系统，用于长期，多动能人类运动合成。该系统被称为神经木偶，可以从简单的用户输入中平稳过渡，包括带有预期动作持续时间的动作标签，以及如果用户指定的话，则可以产生高质量和有意义的动作。我们系统的核心是一种基于变压器的新型运动生成模型，即Marionet，它可以在给定的动作标签给定不同的动作。与现有运动生成模型不同，Marionet利用了过去的运动剪辑和未来动作标签的上下文信息，专门用于生成可以平稳融合历史和未来动作的动作。具体而言，Marionet首先将目标动作标签和上下文信息编码为动作级潜在代码。该代码通过时间展开模块将代码展开为帧级控制信号，然后可以将其与其他帧级控制信号（如目标轨迹）结合使用。然后以自动回归方式生成运动帧。通过依次应用木偶，系统神经木偶可以借助两个简单的方案（即“影子开始”和“动作修订”）来稳健地产生长期的多动作运动。与新型系统一起，我们还提供了一个专门针对多动运动综合任务的新数据集，其中包含动作标签及其上下文信息。进行了广泛的实验，以研究我们系统产生的动作的动作准确性，自然主义和过渡平滑度。

透明的物体广泛用于工业自动化和日常生活中。但是，强大的视觉识别和对透明物体的感知一直是一个主要挑战。目前，由于光的折射和反射，大多数商用级深度摄像机仍然不擅长感知透明物体的表面。在这项工作中，我们从单个RGB-D输入中提出了一种基于变压器的透明对象深度估计方法。我们观察到，变压器的全球特征使得更容易提取上下文信息以执行透明区域的深度估计。此外，为了更好地增强细粒度的特征，功能融合模块（FFM）旨在帮助连贯的预测。我们的经验证据表明，与以前的最新基于卷积的数据集相比，我们的模型在最近的流行数据集中有了重大改进，例如RMSE增长25％，RER增长21％。广泛的结果表明，我们的基于变压器的模型可以更好地汇总对象的RGB和不准确的深度信息，以获得更好的深度表示。我们的代码和预培训模型将在https://github.com/yuchendoudou/tode上找到。

图形上的神经扩散是一类新型的图形神经网络，最近引起了越来越多的关注。图形神经偏微分方程（PDE）的能力在解决图形神经网络（GNN）的常见障碍方面的能力，例如过度平滑和瓶颈的问题，但尚未对其对逆性攻击的稳健性。在这项工作中，我们探讨了图神经PDE的稳健性。我们从经验上证明，与其他GNN相比，图形神经PDE在本质上对拓扑扰动更为强大。我们通过利用在图形拓扑扰动下利用热半群的稳定性来提供对这一现象的见解。我们讨论了各种图扩散操作员，并将它们与现有的图神经PDE相关联。此外，我们提出了一个一般图形神经PDE框架，可以通过该框架来定义新的强大GNN。我们验证了新模型在多个基准数据集上实现了可比的最新性能。

神经文本排名模型已经见证了显着的进步，并越来越多地在实践中部署。不幸的是，它们还继承了一般神经模型的对抗性脆弱性，这些神经模型已被检测到，但仍未被先前的研究所忽视。此外，Blackhat SEO可能会利用继承的对抗性漏洞来击败受保护的搜索引擎。在这项研究中，我们提出了对黑盒神经通道排名模型的模仿对抗攻击。我们首先表明，可以通过列举关键查询/候选者，然后训练排名模仿模型来透明和模仿目标段落排名模型。利用排名模仿模型，我们可以精心操纵排名结果并将操纵攻击转移到目标排名模型。为此，我们提出了一种由成对目标函数授权的基于创新的基于梯度的攻击方法，以产生对抗性触发器，该触发器会导致有预谋的混乱，而具有很少的令牌。为了配备触发器的伪装，我们将下一个句子预测损失和语言模型流利度限制添加到目标函数中。对通过排名的实验结果证明了对各种SOTA神经排名模型的排名模仿攻击模型和对抗触发器的有效性。此外，各种缓解分析和人类评估表明，在面对潜在的缓解方法时，伪装的有效性。为了激励其他学者进一步研究这一新颖和重要的问题，我们将实验数据和代码公开可用。