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.

营销活动是一系列战略活动，可以促进企业的目标。在真正的工业场景中，营销活动的效果预测非常复杂且具有挑战性，因为通常从观察数据中学到了先验知识，而没有任何营销活动干预。此外，每个主题始终在几个营销活动的干预下同时受到干扰。因此，我们无法轻松解析和评估单个营销活动的效果。据我们所知，目前尚无有效的方法来解决此类问题，即，基于具有多个相互缠绕事件的层次结构对个体级别的预测任务进行建模。在本文中，我们对效果预测任务中涉及的基础解析树的结构进行了深入的分析，并进一步建立了一个层次结构胶囊预测网络（HAPNET）来预测营销活动的影响。基于合成数据和实际数据的广泛结果证明了我们模型比最新方法的优越性，并在实际工业应用中表现出显着的实用性。

图表神经网络（GNNS）在各种机器学习任务中获得了表示学习的提高。然而，应用邻域聚合的大多数现有GNN通常在图中的图表上执行不良，其中相邻的节点属于不同的类。在本文中，我们示出了在典型的异界图中，边缘可以被引导，以及是否像是处理边缘，也可以使它们过度地影响到GNN模型的性能。此外，由于异常的限制，节点对来自本地邻域之外的类似节点的消息非常有益。这些激励我们开发一个自适应地学习图表的方向性的模型，并利用潜在的长距离相关性节点之间。我们首先将图拉普拉斯概括为基于所提出的特征感知PageRank算法向数字化，该算法同时考虑节点之间的图形方向性和长距离特征相似性。然后，Digraph Laplacian定义了一个图形传播矩阵，导致一个名为{\ em diglaciangcn}的模型。基于此，我们进一步利用节点之间的通勤时间测量的节点接近度，以便在拓扑级别上保留节点的远距离相关性。具有不同级别的10个数据集的广泛实验，同意级别展示了我们在节点分类任务任务中对现有解决方案的有效性。

Although many studies have successfully applied transfer learning to medical image segmentation, very few of them have investigated the selection strategy when multiple source tasks are available for transfer. In this paper, we propose a prior knowledge guided and transferability based framework to select the best source tasks among a collection of brain image segmentation tasks, to improve the transfer learning performance on the given target task. The framework consists of modality analysis, RoI (region of interest) analysis, and transferability estimation, such that the source task selection can be refined step by step. Specifically, we adapt the state-of-the-art analytical transferability estimation metrics to medical image segmentation tasks and further show that their performance can be significantly boosted by filtering candidate source tasks based on modality and RoI characteristics. Our experiments on brain matter, brain tumor, and white matter hyperintensities segmentation datasets reveal that transferring from different tasks under the same modality is often more successful than transferring from the same task under different modalities. Furthermore, within the same modality, transferring from the source task that has stronger RoI shape similarity with the target task can significantly improve the final transfer performance. And such similarity can be captured using the Structural Similarity index in the label space.

Rankings are widely collected in various real-life scenarios, leading to the leakage of personal information such as users' preferences on videos or news. To protect rankings, existing works mainly develop privacy protection on a single ranking within a set of ranking or pairwise comparisons of a ranking under the $\epsilon$-differential privacy. This paper proposes a novel notion called $\epsilon$-ranking differential privacy for protecting ranks. We establish the connection between the Mallows model (Mallows, 1957) and the proposed $\epsilon$-ranking differential privacy. This allows us to develop a multistage ranking algorithm to generate synthetic rankings while satisfying the developed $\epsilon$-ranking differential privacy. Theoretical results regarding the utility of synthetic rankings in the downstream tasks, including the inference attack and the personalized ranking tasks, are established. For the inference attack, we quantify how $\epsilon$ affects the estimation of the true ranking based on synthetic rankings. For the personalized ranking task, we consider varying privacy preferences among users and quantify how their privacy preferences affect the consistency in estimating the optimal ranking function. Extensive numerical experiments are carried out to verify the theoretical results and demonstrate the effectiveness of the proposed synthetic ranking algorithm.

Modern deep neural networks have achieved superhuman performance in tasks from image classification to game play. Surprisingly, these various complex systems with massive amounts of parameters exhibit the same remarkable structural properties in their last-layer features and classifiers across canonical datasets. This phenomenon is known as "Neural Collapse," and it was discovered empirically by Papyan et al. \cite{Papyan20}. Recent papers have theoretically shown the global solutions to the training network problem under a simplified "unconstrained feature model" exhibiting this phenomenon. We take a step further and prove the Neural Collapse occurrence for deep linear network for the popular mean squared error (MSE) and cross entropy (CE) loss. Furthermore, we extend our research to imbalanced data for MSE loss and present the first geometric analysis for Neural Collapse under this setting.

In this paper we derive a PAC-Bayesian-Like error bound for a class of stochastic dynamical systems with inputs, namely, for linear time-invariant stochastic state-space models (stochastic LTI systems for short). This class of systems is widely used in control engineering and econometrics, in particular, they represent a special case of recurrent neural networks. In this paper we 1) formalize the learning problem for stochastic LTI systems with inputs, 2) derive a PAC-Bayesian-Like error bound for such systems, 3) discuss various consequences of this error bound.

Denoising Diffusion Probabilistic Models (DDPMs) are emerging in text-to-speech (TTS) synthesis because of their strong capability of generating high-fidelity samples. However, their iterative refinement process in high-dimensional data space results in slow inference speed, which restricts their application in real-time systems. Previous works have explored speeding up by minimizing the number of inference steps but at the cost of sample quality. In this work, to improve the inference speed for DDPM-based TTS model while achieving high sample quality, we propose ResGrad, a lightweight diffusion model which learns to refine the output spectrogram of an existing TTS model (e.g., FastSpeech 2) by predicting the residual between the model output and the corresponding ground-truth speech. ResGrad has several advantages: 1) Compare with other acceleration methods for DDPM which need to synthesize speech from scratch, ResGrad reduces the complexity of task by changing the generation target from ground-truth mel-spectrogram to the residual, resulting into a more lightweight model and thus a smaller real-time factor. 2) ResGrad is employed in the inference process of the existing TTS model in a plug-and-play way, without re-training this model. We verify ResGrad on the single-speaker dataset LJSpeech and two more challenging datasets with multiple speakers (LibriTTS) and high sampling rate (VCTK). Experimental results show that in comparison with other speed-up methods of DDPMs: 1) ResGrad achieves better sample quality with the same inference speed measured by real-time factor; 2) with similar speech quality, ResGrad synthesizes speech faster than baseline methods by more than 10 times. Audio samples are available at https://resgrad1.github.io/.

Deep neural networks (DNNs) are found to be vulnerable to adversarial attacks, and various methods have been proposed for the defense. Among these methods, adversarial training has been drawing increasing attention because of its simplicity and effectiveness. However, the performance of the adversarial training is greatly limited by the architectures of target DNNs, which often makes the resulting DNNs with poor accuracy and unsatisfactory robustness. To address this problem, we propose DSARA to automatically search for the neural architectures that are accurate and robust after adversarial training. In particular, we design a novel cell-based search space specially for adversarial training, which improves the accuracy and the robustness upper bound of the searched architectures by carefully designing the placement of the cells and the proportional relationship of the filter numbers. Then we propose a two-stage search strategy to search for both accurate and robust neural architectures. At the first stage, the architecture parameters are optimized to minimize the adversarial loss, which makes full use of the effectiveness of the adversarial training in enhancing the robustness. At the second stage, the architecture parameters are optimized to minimize both the natural loss and the adversarial loss utilizing the proposed multi-objective adversarial training method, so that the searched neural architectures are both accurate and robust. We evaluate the proposed algorithm under natural data and various adversarial attacks, which reveals the superiority of the proposed method in terms of both accurate and robust architectures. We also conclude that accurate and robust neural architectures tend to deploy very different structures near the input and the output, which has great practical significance on both hand-crafting and automatically designing of accurate and robust neural architectures.

People with diabetes are more likely to develop diabetic retinopathy (DR) than healthy people. However, DR is the leading cause of blindness. At present, the diagnosis of diabetic retinopathy mainly relies on the experienced clinician to recognize the fine features in color fundus images. This is a time-consuming task. Therefore, in this paper, to promote the development of UW-OCTA DR automatic detection, we propose a novel semi-supervised semantic segmentation method for UW-OCTA DR image grade assessment. This method, first, uses the MAE algorithm to perform semi-supervised pre-training on the UW-OCTA DR grade assessment dataset to mine the supervised information in the UW-OCTA images, thereby alleviating the need for labeled data. Secondly, to more fully mine the lesion features of each region in the UW-OCTA image, this paper constructs a cross-algorithm ensemble DR tissue segmentation algorithm by deploying three algorithms with different visual feature processing strategies. The algorithm contains three sub-algorithms, namely pre-trained MAE, ConvNeXt, and SegFormer. Based on the initials of these three sub-algorithms, the algorithm can be named MCS-DRNet. Finally, we use the MCS-DRNet algorithm as an inspector to check and revise the results of the preliminary evaluation of the DR grade evaluation algorithm. The experimental results show that the mean dice similarity coefficient of MCS-DRNet v1 and v2 are 0.5161 and 0.5544, respectively. The quadratic weighted kappa of the DR grading evaluation is 0.7559. Our code will be released soon.