The prediction of protein structures from sequences is an important task for function prediction, drug design, and related biological processes understanding. Recent advances have proved the power of language models (LMs) in processing the protein sequence databases, which inherit the advantages of attention networks and capture useful information in learning representations for proteins. The past two years have witnessed remarkable success in tertiary protein structure prediction (PSP), including evolution-based and single-sequence-based PSP. It seems that instead of using energy-based models and sampling procedures, protein language model (pLM)-based pipelines have emerged as mainstream paradigms in PSP. Despite the fruitful progress, the PSP community needs a systematic and up-to-date survey to help bridge the gap between LMs in the natural language processing (NLP) and PSP domains and introduce their methodologies, advancements and practical applications. To this end, in this paper, we first introduce the similarities between protein and human languages that allow LMs extended to pLMs, and applied to protein databases. Then, we systematically review recent advances in LMs and pLMs from the perspectives of network architectures, pre-training strategies, applications, and commonly-used protein databases. Next, different types of methods for PSP are discussed, particularly how the pLM-based architectures function in the process of protein folding. Finally, we identify challenges faced by the PSP community and foresee promising research directions along with the advances of pLMs. This survey aims to be a hands-on guide for researchers to understand PSP methods, develop pLMs and tackle challenging problems in this field for practical purposes.

我们开发了一个概率框架，用于分析基于模型的加强学习在整个概念环境中。然后，我们将其应用于使用线性动力学但未知的系数和凸起的有限时间地平线随机控制问题，但可能是不规则的，客观的函数。使用概率表示，我们研究相关成本函数的规律性，并建立精确估计，用于应用估计和真实模型参数的最佳反馈控制之间的性能差距。我们确定这种性能差距是二次，提高近期工作的线性性能差距的条件[X.郭，A. Hu和Y. Zhang，Arxiv预印，arxiv：2104.09311，（2021）]，它与随机线性二次问题获得的结果相匹配。接下来，我们提出了一种基于阶段的学习算法，我们展示了如何优化探索剥削权衡，并在高概率和期望中实现索布林遗憾。当对二次性能间隙保持所需的假设时，该算法在一般情况下实现了订单$ \ mathcal {o}（\ sqrt {n \ ln n）$高概率后悔，以及订单$ \ mathcal {o} （（\ ln n）^ 2）$预期遗憾，在自我探索案例中，超过$ n $剧集，匹配文献中的最佳结果。分析需要新的浓度不等式，用于相关的连续时间观察，我们得出。

深层神经网络（DNN）是通过依次执行线性和非线性过程产生的。使用线性和非线性程序的组合对于生成足够深的特征空间至关重要。大多数非线性运算符是激活函数或合并函数的推导。数学形态是数学的一个分支，为各种图像处理问题提供了非线性操作员。我们调查了将这些操作集成到本文端到端深度学习框架中的实用性。 DNN旨在获得特定工作的现实代表。形态运算符给出拓扑描述符，以传达有关图像中描述的物体形状的显着信息。我们提出了一种基于元学习的方法，将形态算子纳入DNN。博学的结构展示了我们的新型形态操作如何显着提高各种任务（包括图片分类和边缘检测）的DNN性能。

我们研究有限的时间范围连续时间线性季节增强学习问题，在情节环境中，控制器的状态和控制系数都不清楚。我们首先提出了基于连续时间观察和控件的最小二乘算法，并建立对数的对数遗憾，以$ o（（\ ln m）（\ ln \ ln m））$，$ m $是数字学习情节。该分析由两个部分组成：扰动分析，这些分析利用了相关的riccati微分方程的规律性和鲁棒性；和参数估计误差，依赖于连续的最小二乘估计器的亚指数属性。我们进一步提出了一种基于离散时间观察和分段恒定控制的实际实现最小二乘算法，该算法根据算法中使用的时间步骤明确地取决于额外的术语，从而实现相似的对数后悔。

Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of sequence-structure data. With the development of Artificial Intelligence (AI) techniques, Protein Representation Learning (PRL) has recently emerged as a promising research topic for extracting informative knowledge from massive protein sequences or structures. To pave the way for AI researchers with little bioinformatics background, we present a timely and comprehensive review of PRL formulations and existing PRL methods from the perspective of model architectures, pretext tasks, and downstream applications. We first briefly introduce the motivations for protein representation learning and formulate it in a general and unified framework. Next, we divide existing PRL methods into three main categories: sequence-based, structure-based, and sequence-structure co-modeling. Finally, we discuss some technical challenges and potential directions for improving protein representation learning. The latest advances in PRL methods are summarized in a GitHub repository https://github.com/LirongWu/awesome-protein-representation-learning.

Negotiation is one of the crucial abilities in human communication, and there has been a resurgent research interest in negotiation dialogue systems recently, which goal is to empower intelligent agents with such ability that can efficiently help humans resolve conflicts or reach beneficial agreements. Although there have been many explorations in negotiation dialogue systems, a systematic review of this task has to date remained notably absent. To this end, we aim to fill this gap by reviewing contemporary studies in the emerging field of negotiation dialogue systems, covering benchmarks, evaluations, and methodologies. Furthermore, we also discuss potential future directions, including multi-modal, multi-party, and cross-cultural negotiation scenarios. Our goal is to provide the community with a systematic overview of negotiation dialogue systems and to inspire future research.

Our work targets at searching feasible adversarial perturbation to attack a classifier with high-dimensional categorical inputs in a domain-agnostic setting. This is intrinsically an NP-hard knapsack problem where the exploration space becomes explosively larger as the feature dimension increases. Without the help of domain knowledge, solving this problem via heuristic method, such as Branch-and-Bound, suffers from exponential complexity, yet can bring arbitrarily bad attack results. We address the challenge via the lens of multi-armed bandit based combinatorial search. Our proposed method, namely FEAT, treats modifying each categorical feature as pulling an arm in multi-armed bandit programming. Our objective is to achieve highly efficient and effective attack using an Orthogonal Matching Pursuit (OMP)-enhanced Upper Confidence Bound (UCB) exploration strategy. Our theoretical analysis bounding the regret gap of FEAT guarantees its practical attack performance. In empirical analysis, we compare FEAT with other state-of-the-art domain-agnostic attack methods over various real-world categorical data sets of different applications. Substantial experimental observations confirm the expected efficiency and attack effectiveness of FEAT applied in different application scenarios. Our work further hints the applicability of FEAT for assessing the adversarial vulnerability of classification systems with high-dimensional categorical inputs.

Recent deep learning methods have achieved promising results in image shadow removal. However, their restored images still suffer from unsatisfactory boundary artifacts, due to the lack of degradation prior embedding and the deficiency in modeling capacity. Our work addresses these issues by proposing a unified diffusion framework that integrates both the image and degradation priors for highly effective shadow removal. In detail, we first propose a shadow degradation model, which inspires us to build a novel unrolling diffusion model, dubbed ShandowDiffusion. It remarkably improves the model's capacity in shadow removal via progressively refining the desired output with both degradation prior and diffusive generative prior, which by nature can serve as a new strong baseline for image restoration. Furthermore, ShadowDiffusion progressively refines the estimated shadow mask as an auxiliary task of the diffusion generator, which leads to more accurate and robust shadow-free image generation. We conduct extensive experiments on three popular public datasets, including ISTD, ISTD+, and SRD, to validate our method's effectiveness. Compared to the state-of-the-art methods, our model achieves a significant improvement in terms of PSNR, increasing from 31.69dB to 34.73dB over SRD dataset.

Solving partial differential equations is difficult. Recently proposed neural resolution-invariant models, despite their effectiveness and efficiency, usually require equispaced spatial points of data. However, sampling in spatial domain is sometimes inevitably non-equispaced in real-world systems, limiting their applicability. In this paper, we propose a Non-equispaced Fourier PDE Solver (\textsc{NFS}) with adaptive interpolation on resampled equispaced points and a variant of Fourier Neural Operators as its components. Experimental results on complex PDEs demonstrate its advantages in accuracy and efficiency. Compared with the spatially-equispaced benchmark methods, it achieves superior performance with $42.85\%$ improvements on MAE, and is able to handle non-equispaced data with a tiny loss of accuracy. Besides, to our best knowledge, \textsc{NFS} is the first ML-based method with mesh invariant inference ability to successfully model turbulent flows in non-equispaced scenarios, with a minor deviation of the error on unseen spatial points.

In this paper, we show the surprisingly good properties of plain vision transformers for body pose estimation from various aspects, namely simplicity in model structure, scalability in model size, flexibility in training paradigm, and transferability of knowledge between models, through a simple baseline model dubbed ViTPose. Specifically, ViTPose employs the plain and non-hierarchical vision transformer as an encoder to encode features and a lightweight decoder to decode body keypoints in either a top-down or a bottom-up manner. It can be scaled up from about 20M to 1B parameters by taking advantage of the scalable model capacity and high parallelism of the vision transformer, setting a new Pareto front for throughput and performance. Besides, ViTPose is very flexible regarding the attention type, input resolution, and pre-training and fine-tuning strategy. Based on the flexibility, a novel ViTPose+ model is proposed to deal with heterogeneous body keypoint categories in different types of body pose estimation tasks via knowledge factorization, i.e., adopting task-agnostic and task-specific feed-forward networks in the transformer. We also empirically demonstrate that the knowledge of large ViTPose models can be easily transferred to small ones via a simple knowledge token. Experimental results show that our ViTPose model outperforms representative methods on the challenging MS COCO Human Keypoint Detection benchmark at both top-down and bottom-up settings. Furthermore, our ViTPose+ model achieves state-of-the-art performance simultaneously on a series of body pose estimation tasks, including MS COCO, AI Challenger, OCHuman, MPII for human keypoint detection, COCO-Wholebody for whole-body keypoint detection, as well as AP-10K and APT-36K for animal keypoint detection, without sacrificing inference speed.