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.

Causal chain reasoning (CCR) is an essential ability for many decision-making AI systems, which requires the model to build reliable causal chains by connecting causal pairs. However, CCR suffers from two main transitive problems: threshold effect and scene drift. In other words, the causal pairs to be spliced may have a conflicting threshold boundary or scenario. To address these issues, we propose a novel Reliable Causal chain reasoning framework~(ReCo), which introduces exogenous variables to represent the threshold and scene factors of each causal pair within the causal chain, and estimates the threshold and scene contradictions across exogenous variables via structural causal recurrent neural networks~(SRNN). Experiments show that ReCo outperforms a series of strong baselines on both Chinese and English CCR datasets. Moreover, by injecting reliable causal chain knowledge distilled by ReCo, BERT can achieve better performances on four downstream causal-related tasks than BERT models enhanced by other kinds of knowledge.

Earth observation, aiming at monitoring the state of planet Earth using remote sensing data, is critical for improving our daily lives and living environment. With a growing number of satellites in orbit, an increasing number of datasets with diverse sensors and research domains are being published to facilitate the research of the remote sensing community. In this paper, we present a comprehensive review of more than 400 publicly published datasets, including applications like land use/cover, change/disaster monitoring, scene understanding, agriculture, climate change, and weather forecasting. We systematically analyze these Earth observation datasets with respect to five aspects volume, bibliometric analysis, resolution distributions, research domains, and the correlation between datasets. Based on the dataset attributes, we propose to measure, rank, and select datasets to build a new benchmark for model evaluation. Furthermore, a new platform for Earth observation, termed EarthNets, is released as a means of achieving a fair and consistent evaluation of deep learning methods on remote sensing data. EarthNets supports standard dataset libraries and cutting-edge deep learning models to bridge the gap between the remote sensing and machine learning communities. Based on this platform, extensive deep learning methods are evaluated on the new benchmark. The insightful results are beneficial to future research. The platform and dataset collections are publicly available at https://earthnets.github.io/.

Models should be able to adapt to unseen data during test-time to avoid performance drops caused by inevitable distribution shifts in real-world deployment scenarios. In this work, we tackle the practical yet challenging test-time adaptation (TTA) problem, where a model adapts to the target domain without accessing the source data. We propose a simple recipe called \textit{Data-efficient Prompt Tuning} (DePT) with two key ingredients. First, DePT plugs visual prompts into the vision Transformer and only tunes these source-initialized prompts during adaptation. We find such parameter-efficient finetuning can efficiently adapt the model representation to the target domain without overfitting to the noise in the learning objective. Second, DePT bootstraps the source representation to the target domain by memory bank-based online pseudo-labeling. A hierarchical self-supervised regularization specially designed for prompts is jointly optimized to alleviate error accumulation during self-training. With much fewer tunable parameters, DePT demonstrates not only state-of-the-art performance on major adaptation benchmarks VisDA-C, ImageNet-C, and DomainNet-126, but also superior data efficiency, i.e., adaptation with only 1\% or 10\% data without much performance degradation compared to 100\% data. In addition, DePT is also versatile to be extended to online or multi-source TTA settings.

The peer merit review of research proposals has been the major mechanism for deciding grant awards. However, research proposals have become increasingly interdisciplinary. It has been a longstanding challenge to assign interdisciplinary proposals to appropriate reviewers, so proposals are fairly evaluated. One of the critical steps in reviewer assignment is to generate accurate interdisciplinary topic labels for proposal-reviewer matching. Existing systems mainly collect topic labels manually generated by principal investigators. However, such human-reported labels can be non-accurate, incomplete, labor intensive, and time costly. What role can AI play in developing a fair and precise proposal reviewer assignment system? In this study, we collaborate with the National Science Foundation of China to address the task of automated interdisciplinary topic path detection. For this purpose, we develop a deep Hierarchical Interdisciplinary Research Proposal Classification Network (HIRPCN). Specifically, we first propose a hierarchical transformer to extract the textual semantic information of proposals. We then design an interdisciplinary graph and leverage GNNs for learning representations of each discipline in order to extract interdisciplinary knowledge. After extracting the semantic and interdisciplinary knowledge, we design a level-wise prediction component to fuse the two types of knowledge representations and detect interdisciplinary topic paths for each proposal. We conduct extensive experiments and expert evaluations on three real-world datasets to demonstrate the effectiveness of our proposed model.

促性腺营养蛋白释放激素受体（GNRH1R）是治疗子宫疾病的有前途的治疗靶标。迄今为止，在临床研究中可以使用几个GNRH1R拮抗剂，而不满足多个财产约束。为了填补这一空白，我们旨在开发一个基于学习的框架，以促进有效，有效地发现具有理想特性的新的口服小型分子药物靶向GNRH1R。在目前的工作中，首先通过充分利用已知活性化合物和靶蛋白的结构的信息，首先提出了配体和结构组合模型，即LS-Molgen，首先提出了分子生成的方法，该信息通过其出色的性能证明了这一点。比分别基于配体或结构方法。然后，进行了A中的计算机筛选，包括活性预测，ADMET评估，分子对接和FEP计算，其中约30,000个生成的新型分子被缩小到8，以进行实验合成和验证。体外和体内实验表明，其中三个表现出有效的抑制活性（化合物5 IC50 = 0.856 nm，化合物6 IC50 = 0.901 nm，化合物7 IC50 = 2.54 nm对GNRH1R，并且化合物5在基本PK属性中表现良好例如半衰期，口服生物利用度和PPB等。我们认为，提议的配体和结构组合结合的分子生成模型和整个计算机辅助工作流程可能会扩展到从头开始的类似任务或铅优化的类似任务。

虽然微调预训练的网络已成为训练图像分割模型的流行方式，但这种用于图像分割的骨干网络经常使用图像分类源数据集（例如ImageNet）进行预训练。尽管图像分类数据集可以为骨干网络提供丰富的视觉特征和歧视能力，但它们无法以端到端的方式完全预训练目标模型（即骨干+分割模块）。由于分类数据集中缺乏分割标签，因此在微调过程中进行分割模块在微调过程中随机初始化。在我们的工作中，我们提出了一种利用伪语义分割标签（PSSL）的方法，以启用基于分类数据集的图像分割模型的端到端预训练。 PSSL的启发是受到观察的启发，即通过CAM，Smoothgrad和Lime等解释算法获得的分类模型的解释结果将接近视觉对象的像素簇。具体而言，通过解释分类结果并汇总了从多个分类器查询的解释集合来降低单个模型引起的偏差，从而为每个图像获得PSSL。使用PSSL，对于ImageNet的每个图像，提出的方法都利用加权分割学习程序来预先培训分割网络。实验结果表明，在Imagenet伴随PSSL作为源数据集的情况下，提出的端到端预训练策略成功地增强了各种分割模型的性能，即PSPNET-RESNET50，DEEPLABV3-RESNET50和OCRNET-HRNET-HRNETENET-HRNETENET-HRNETENET-HRNETENET-HRNETW18，和在许多细分任务上，例如CAMVID，VOC-A，VOC-C，ADE20K和CityScapes，并有重大改进。源代码可在https://github.com/paddlepaddle/paddleseg上使用。

超声（US）广泛用于实时成像，无辐射和便携性的优势。在临床实践中，分析和诊断通常依赖于美国序列，而不是单个图像来获得动态的解剖信息。对于新手来说，这是一项挑战，因为使用患者的足够视频进行练习是临床上不可行的。在本文中，我们提出了一个新颖的框架，以综合高保真美国视频。具体而言，合成视频是通过基于给定驾驶视频的动作来动画源内容图像来生成的。我们的亮点是三倍。首先，利用自我监督学习的优势，我们提出的系统以弱监督的方式进行了培训，以进行关键点检测。然后，这些关键点为处理美国视频中的复杂动态动作提供了重要信息。其次，我们使用双重解码器将内容和纹理学习解除，以有效地减少模型学习难度。最后，我们采用了对抗性训练策略，并采用了GAN损失，以进一步改善生成的视频的清晰度，从而缩小了真实和合成视频之间的差距。我们在具有高动态运动的大型内部骨盆数据集上验证我们的方法。广泛的评估指标和用户研究证明了我们提出的方法的有效性。

回归学习是经典的，是医学图像分析的基础。它为许多关键应用程序提供了连续的映射，例如属性估计，对象检测，分割和非刚性注册。但是，先前的研究主要以案例标准（如均方误差）为优化目标。他们忽略了非常重要的人口相关标准，这正是许多任务中的最终评估指标。在这项工作中，我们建议通过有关直接优化细粒相关损失的新型研究来重新审视经典回归任务。我们主要探索两个互补相关索引作为可学习的损失：Pearson线性相关（PLC）和Spearman等级相关性（SRC）。本文的贡献是两个折叠。首先，对于全球层面的PLC，我们提出了一项策略，以使其对异常值进行强大的态度并规范关键分布因素。这些努力显着稳定学习并扩大了PLC的功效。其次，对于本地级别的SRC，我们提出了一种粗到精细的方案，以减轻样品之间确切排名顺序的学习。具体而言，我们将样本排名的学习转换为样本之间相似关系的学习。我们在两个典型的超声图像回归任务上广泛验证了我们的方法，包括图像质量评估和生物措施测量。实验证明，通过直接优化相关性的细粒度指导，回归性能得到显着提高。我们提出的相关性损失是一般的，可以扩展到更重要的应用程序。