数据驱动的预测方法可以有效，准确地将蛋白质序列转化为生物活性结构，对于科学研究和治疗发展非常有价值。使用共同进化信息确定准确的折叠格局是现代蛋白质结构预测方法的成功基础。作为最新的状态，AlphaFold2显着提高了准确性，而无需进行明确的共同进化分析。然而，其性能仍然显示出对可用序列同源物的强烈依赖。我们研究了这种依赖性的原因，并提出了一种元生成模型Evogen，以弥补较差的MSA靶标的Alphafold2的表现不佳。 Evogen使我们能够通过降低搜索的MSA或生成虚拟MSA来操纵折叠景观，并帮助Alphafold2在低数据表方面准确地折叠，甚至通过单序预测来实现令人鼓舞的性能。能够用很少的MSA做出准确的预测，不仅可以更好地概括为孤儿序列的Alphafold2，而且使其在高通量应用程序中的使用民主化。此外，Evogen与AlphaFold2结合产生了一种概率结构生成方法，该方法可以探索蛋白质序列的替代构象，并且序列生成的任务意识可区分算法将使包括蛋白质设计在内的其他相关任务受益。

蛋白质是人类生命的重要组成部分，其结构对于功能和机制分析很重要。最近的工作表明了AI驱动方法对蛋白质结构预测的潜力。但是，新模型的开发受到数据集和基准测试培训程序的限制。据我们所知，现有的开源数据集远不足以满足现代蛋白质序列相关研究的需求。为了解决这个问题，我们介绍了具有高覆盖率和多样性的第一个百万级蛋白质结构预测数据集，称为PSP。该数据集由570K真实结构序列（10TB）和745K互补蒸馏序列（15TB）组成。此外，我们还提供了该数据集上SOTA蛋白结构预测模型的基准测试训练程序。我们通过参与客串比赛验证该数据集的实用程序进行培训，我们的模特赢得了第一名。我们希望我们的PSP数据集以及培训基准能够为AI驱动的蛋白质相关研究提供更广泛的AI/生物学研究人员社区。

Few Shot Instance Segmentation (FSIS) requires models to detect and segment novel classes with limited several support examples. In this work, we explore a simple yet unified solution for FSIS as well as its incremental variants, and introduce a new framework named Reference Twice (RefT) to fully explore the relationship between support/query features based on a Transformer-like framework. Our key insights are two folds: Firstly, with the aid of support masks, we can generate dynamic class centers more appropriately to re-weight query features. Secondly, we find that support object queries have already encoded key factors after base training. In this way, the query features can be enhanced twice from two aspects, i.e., feature-level and instance-level. In particular, we firstly design a mask-based dynamic weighting module to enhance support features and then propose to link object queries for better calibration via cross-attention. After the above steps, the novel classes can be improved significantly over our strong baseline. Additionally, our new framework can be easily extended to incremental FSIS with minor modification. When benchmarking results on the COCO dataset for FSIS, gFSIS, and iFSIS settings, our method achieves a competitive performance compared to existing approaches across different shots, e.g., we boost nAP by noticeable +8.2/+9.4 over the current state-of-the-art FSIS method for 10/30-shot. We further demonstrate the superiority of our approach on Few Shot Object Detection. Code and model will be available.

This paper focuses on designing efficient models with low parameters and FLOPs for dense predictions. Even though CNN-based lightweight methods have achieved stunning results after years of research, trading-off model accuracy and constrained resources still need further improvements. This work rethinks the essential unity of efficient Inverted Residual Block in MobileNetv2 and effective Transformer in ViT, inductively abstracting a general concept of Meta-Mobile Block, and we argue that the specific instantiation is very important to model performance though sharing the same framework. Motivated by this phenomenon, we deduce a simple yet efficient modern \textbf{I}nverted \textbf{R}esidual \textbf{M}obile \textbf{B}lock (iRMB) for mobile applications, which absorbs CNN-like efficiency to model short-distance dependency and Transformer-like dynamic modeling capability to learn long-distance interactions. Furthermore, we design a ResNet-like 4-phase \textbf{E}fficient \textbf{MO}del (EMO) based only on a series of iRMBs for dense applications. Massive experiments on ImageNet-1K, COCO2017, and ADE20K benchmarks demonstrate the superiority of our EMO over state-of-the-art methods, \eg, our EMO-1M/2M/5M achieve 71.5, 75.1, and 78.4 Top-1 that surpass \textbf{SoTA} CNN-/Transformer-based models, while trading-off the model accuracy and efficiency well.

Despite significant progress in object categorization, in recent years, a number of important challenges remain; mainly, the ability to learn from limited labeled data and to recognize object classes within large, potentially open, set of labels. Zero-shot learning is one way of addressing these challenges, but it has only been shown to work with limited sized class vocabularies and typically requires separation between supervised and unsupervised classes, allowing former to inform the latter but not vice versa. We propose the notion of vocabulary-informed learning to alleviate the above mentioned challenges and address problems of supervised, zero-shot, generalized zero-shot and open set recognition using a unified framework. Specifically, we propose a weighted maximum margin framework for semantic manifold-based recognition that incorporates distance constraints from (both supervised and unsupervised) vocabulary atoms. Distance constraints ensure that labeled samples are projected closer to their correct prototypes, in the embedding space, than to others. We illustrate that resulting model shows improvements in supervised, zero-shot, generalized zero-shot, and large open set recognition, with up to 310K class vocabulary on Animal with Attributes and ImageNet datasets.

Deploying reliable deep learning techniques in interdisciplinary applications needs learned models to output accurate and ({even more importantly}) explainable predictions. Existing approaches typically explicate network outputs in a post-hoc fashion, under an implicit assumption that faithful explanations come from accurate predictions/classifications. We have an opposite claim that explanations boost (or even determine) classification. That is, end-to-end learning of explanation factors to augment discriminative representation extraction could be a more intuitive strategy to inversely assure fine-grained explainability, e.g., in those neuroimaging and neuroscience studies with high-dimensional data containing noisy, redundant, and task-irrelevant information. In this paper, we propose such an explainable geometric deep network dubbed as NeuroExplainer, with applications to uncover altered infant cortical development patterns associated with preterm birth. Given fundamental cortical attributes as network input, our NeuroExplainer adopts a hierarchical attention-decoding framework to learn fine-grained attentions and respective discriminative representations to accurately recognize preterm infants from term-born infants at term-equivalent age. NeuroExplainer learns the hierarchical attention-decoding modules under subject-level weak supervision coupled with targeted regularizers deduced from domain knowledge regarding brain development. These prior-guided constraints implicitly maximizes the explainability metrics (i.e., fidelity, sparsity, and stability) in network training, driving the learned network to output detailed explanations and accurate classifications. Experimental results on the public dHCP benchmark suggest that NeuroExplainer led to quantitatively reliable explanation results that are qualitatively consistent with representative neuroimaging studies.

Improving the visual quality of the given degraded observation by correcting exposure level is a fundamental task in the computer vision community. Existing works commonly lack adaptability towards unknown scenes because of the data-driven patterns (deep networks) and limited regularization (traditional optimization), and they usually need time-consuming inference. These two points heavily limit their practicability. In this paper, we establish a Practical Exposure Corrector (PEC) that assembles the characteristics of efficiency and performance. To be concrete, we rethink the exposure correction to provide a linear solution with exposure-sensitive compensation. Around generating the compensation, we introduce an exposure adversarial function as the key engine to fully extract valuable information from the observation. By applying the defined function, we construct a segmented shrinkage iterative scheme to generate the desired compensation. Its shrinkage nature supplies powerful support for algorithmic stability and robustness. Extensive experimental evaluations fully reveal the superiority of our proposed PEC. The code is available at https://rsliu.tech/PEC.

Sparse principal component analysis (SPCA) has been widely used for dimensionality reduction and feature extraction in high-dimensional data analysis. Despite there are many methodological and theoretical developments in the past two decades, the theoretical guarantees of the popular SPCA algorithm proposed by Zou, Hastie & Tibshirani (2006) based on the elastic net are still unknown. We aim to close this important theoretical gap in this paper. We first revisit the SPCA algorithm of Zou et al. (2006) and present our implementation. Also, we study a computationally more efficient variant of the SPCA algorithm in Zou et al. (2006) that can be considered as the limiting case of SPCA. We provide the guarantees of convergence to a stationary point for both algorithms. We prove that, under a sparse spiked covariance model, both algorithms can recover the principal subspace consistently under mild regularity conditions. We show that their estimation error bounds match the best available bounds of existing works or the minimax rates up to some logarithmic factors. Moreover, we demonstrate the numerical performance of both algorithms in simulation studies.

During training, reinforcement learning systems interact with the world without considering the safety of their actions. When deployed into the real world, such systems can be dangerous and cause harm to their surroundings. Often, dangerous situations can be mitigated by defining a set of rules that the system should not violate under any conditions. For example, in robot navigation, one safety rule would be to avoid colliding with surrounding objects and people. In this work, we define safety rules in terms of the relationships between the agent and objects and use them to prevent reinforcement learning systems from performing potentially harmful actions. We propose a new safe epsilon-greedy algorithm that uses safety rules to override agents' actions if they are considered to be unsafe. In our experiments, we show that a safe epsilon-greedy policy significantly increases the safety of the agent during training, improves the learning efficiency resulting in much faster convergence, and achieves better performance than the base model.

Due to the issue that existing wireless sensor network (WSN)-based anomaly detection methods only consider and analyze temporal features, in this paper, a self-supervised learning-based anomaly node detection method based on an autoencoder is designed. This method integrates temporal WSN data flow feature extraction, spatial position feature extraction and intermodal WSN correlation feature extraction into the design of the autoencoder to make full use of the spatial and temporal information of the WSN for anomaly detection. First, a fully connected network is used to extract the temporal features of nodes by considering a single mode from a local spatial perspective. Second, a graph neural network (GNN) is used to introduce the WSN topology from a global spatial perspective for anomaly detection and extract the spatial and temporal features of the data flows of nodes and their neighbors by considering a single mode. Then, the adaptive fusion method involving weighted summation is used to extract the relevant features between different models. In addition, this paper introduces a gated recurrent unit (GRU) to solve the long-term dependence problem of the time dimension. Eventually, the reconstructed output of the decoder and the hidden layer representation of the autoencoder are fed into a fully connected network to calculate the anomaly probability of the current system. Since the spatial feature extraction operation is advanced, the designed method can be applied to the task of large-scale network anomaly detection by adding a clustering operation. Experiments show that the designed method outperforms the baselines, and the F1 score reaches 90.6%, which is 5.2% higher than those of the existing anomaly detection methods based on unsupervised reconstruction and prediction. Code and model are available at https://github.com/GuetYe/anomaly_detection/GLSL