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.

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.

生物医学网络是与疾病网络的蛋白质相互作用的普遍描述符，从蛋白质相互作用，一直到医疗保健系统和科学知识。随着代表学习提供强大的预测和洞察的显着成功，我们目睹了表现形式学习技术的快速扩展，进入了这些网络的建模，分析和学习。在这篇综述中，我们提出了一个观察到生物学和医学中的网络长期原则 - 而在机器学习研究中经常出口 - 可以为代表学习提供概念基础，解释其当前的成功和限制，并告知未来进步。我们综合了一系列算法方法，即在其核心利用图形拓扑到将网络嵌入到紧凑的向量空间中，并捕获表示陈述学习证明有用的方式的广度。深远的影响包括鉴定复杂性状的变异性，单细胞的异心行为及其对健康的影响，协助患者的诊断和治疗以及制定安全有效的药物。

自然语言处理（NLP）是一个人工智能领域，它应用信息技术来处理人类语言，在一定程度上理解并在各种应用中使用它。在过去的几年中，该领域已经迅速发展，现在采用了深层神经网络的现代变体来从大型文本语料库中提取相关模式。这项工作的主要目的是调查NLP在药理学领域的最新使用。正如我们的工作所表明的那样，NLP是药理学高度相关的信息提取和处理方法。它已被广泛使用，从智能搜索到成千上万的医疗文件到在社交媒体中找到对抗性药物相互作用的痕迹。我们将覆盖范围分为五个类别，以调查现代NLP方法论，常见的任务，相关的文本数据，知识库和有用的编程库。我们将这五个类别分为适当的子类别，描述其主要属性和想法，并以表格形式进行总结。最终的调查介绍了该领域的全面概述，对从业者和感兴趣的观察者有用。

本次调查绘制了用于分析社交媒体数据的生成方法的研究状态的广泛的全景照片（Sota）。它填补了空白，因为现有的调查文章在其范围内或被约会。我们包括两个重要方面，目前正在挖掘和建模社交媒体的重要性：动态和网络。社会动态对于了解影响影响或疾病的传播，友谊的形成，友谊的形成等，另一方面，可以捕获各种复杂关系，提供额外的洞察力和识别否则将不会被注意的重要模式。

Geometric deep learning has recently achieved great success in non-Euclidean domains, and learning on 3D structures of large biomolecules is emerging as a distinct research area. However, its efficacy is largely constrained due to the limited quantity of structural data. Meanwhile, protein language models trained on substantial 1D sequences have shown burgeoning capabilities with scale in a broad range of applications. Nevertheless, no preceding studies consider combining these different protein modalities to promote the representation power of geometric neural networks. To address this gap, we make the foremost step to integrate the knowledge learned by well-trained protein language models into several state-of-the-art geometric networks. Experiments are evaluated on a variety of protein representation learning benchmarks, including protein-protein interface prediction, model quality assessment, protein-protein rigid-body docking, and binding affinity prediction, leading to an overall improvement of 20% over baselines and the new state-of-the-art performance. Strong evidence indicates that the incorporation of protein language models' knowledge enhances geometric networks' capacity by a significant margin and can be generalized to complex tasks.

连接视觉和语言在生成智能中起着重要作用。因此，已经致力于图像标题的大型研究工作，即用句法和语义有意义的句子描述图像。从2015年开始，该任务通常通过由Visual Encoder组成的管道和文本生成的语言模型来解决任务。在这些年来，两种组件通过对象区域，属性，介绍多模态连接，完全关注方法和伯特早期融合策略的利用而显着发展。但是，无论令人印象深刻的结果，图像标题的研究还没有达到结论性答案。这项工作旨在提供图像标题方法的全面概述，从视觉编码和文本生成到培训策略，数据集和评估度量。在这方面，我们量化地比较了许多相关的最先进的方法来确定架构和培训策略中最有影响力的技术创新。此外，讨论了问题的许多变体及其开放挑战。这项工作的最终目标是作为理解现有文献的工具，并突出显示计算机视觉和自然语言处理的研究领域的未来方向可以找到最佳的协同作用。

学习有效的蛋白质表示在生物学的各种任务中至关重要，例如预测蛋白质功能或结构。现有的方法通常在大量未标记的氨基酸序列上预先蛋白质语言模型，然后在下游任务中使用一些标记的数据来对模型进行修复。尽管基于序列的方法具有有效性，但尚未探索蛋白质性能预测的已知蛋白质结构的预处理功能，尽管蛋白质结构已知是蛋白质功能的决定因素，但尚未探索。在本文中，我们建议根据其3D结构预处理蛋白质。我们首先提出一个简单而有效的编码器，以学习蛋白质的几何特征。我们通过利用多视图对比学习和不同的自我预测任务来预先蛋白质图编码器。对功能预测和折叠分类任务的实验结果表明，我们提出的预处理方法表现优于或与最新的基于最新的序列方法相提并论，同时使用较少的数据。我们的实施可在https://github.com/deepgraphlearning/gearnet上获得。

基于神经网络的深层语言模型（LMS）越来越多地应用于大规模蛋白质序列数据以预测蛋白质功能。然而，作为黑框模型，当前的蛋白质LM方法并不促进对序列功能映射的基本理解，而阻碍了基于规则的生物治疗药物开发，因此目前的蛋白质LM方法不大。我们认为，从语言学中得出的指导是从自然语言数据中提取分析规则的领域，可以帮助构建学习相关领域特定规则的更容易解释的蛋白质LM。与自然语言LMS相比，蛋白质序列数据和语言序列数据之间的差异需要在蛋白质LMS中集成更多的域特异性知识。在这里，我们为培训数据，令牌化，令牌嵌入，序列嵌入和模型解释提供了基于语言学的路线图。将语言学与蛋白质LMS结合起来，可以发展下一代可解释的机器学习模型，并有可能发现序列功能关系基础的生物学机制。

在三维分子结构上运行的计算方法有可能解决生物学和化学的重要问题。特别地，深度神经网络的重视，但它们在生物分子结构域中的广泛采用受到缺乏系统性能基准或统一工具包的限制，用于与分子数据相互作用。为了解决这个问题，我们呈现Atom3D，这是一个新颖的和现有的基准数据集的集合，跨越几个密钥的生物分子。我们为这些任务中的每一个实施多种三维分子学习方法，并表明它们始终如一地提高了基于单维和二维表示的方法的性能。结构的具体选择对于性能至关重要，具有涉及复杂几何形状的任务的三维卷积网络，在需要详细位置信息的系统中表现出良好的图形网络，以及最近开发的设备越多的网络显示出显着承诺。我们的结果表明，许多分子问题符合三维分子学习的增益，并且有可能改善许多仍然过分曝光的任务。为了降低进入并促进现场进一步发展的障碍，我们还提供了一套全面的DataSet处理，模型培训和在我们的开源ATOM3D Python包中的评估工具套件。所有数据集都可以从https://www.atom3d.ai下载。

The rapid advancement of AI technology has made text generation tools like GPT-3 and ChatGPT increasingly accessible, scalable, and effective. This can pose serious threat to the credibility of various forms of media if these technologies are used for plagiarism, including scientific literature and news sources. Despite the development of automated methods for paraphrase identification, detecting this type of plagiarism remains a challenge due to the disparate nature of the datasets on which these methods are trained. In this study, we review traditional and current approaches to paraphrase identification and propose a refined typology of paraphrases. We also investigate how this typology is represented in popular datasets and how under-representation of certain types of paraphrases impacts detection capabilities. Finally, we outline new directions for future research and datasets in the pursuit of more effective paraphrase detection using AI.

Astounding results from Transformer models on natural language tasks have intrigued the vision community to study their application to computer vision problems. Among their salient benefits, Transformers enable modeling long dependencies between input sequence elements and support parallel processing of sequence as compared to recurrent networks e.g., Long short-term memory (LSTM). Different from convolutional networks, Transformers require minimal inductive biases for their design and are naturally suited as set-functions. Furthermore, the straightforward design of Transformers allows processing multiple modalities (e.g., images, videos, text and speech) using similar processing blocks and demonstrates excellent scalability to very large capacity networks and huge datasets. These strengths have led to exciting progress on a number of vision tasks using Transformer networks. This survey aims to provide a comprehensive overview of the Transformer models in the computer vision discipline. We start with an introduction to fundamental concepts behind the success of Transformers i.e., self-attention, large-scale pre-training, and bidirectional feature encoding. We then cover extensive applications of transformers in vision including popular recognition tasks (e.g., image classification, object detection, action recognition, and segmentation), generative modeling, multi-modal tasks (e.g., visual-question answering, visual reasoning, and visual grounding), video processing (e.g., activity recognition, video forecasting), low-level vision (e.g., image super-resolution, image enhancement, and colorization) and 3D analysis (e.g., point cloud classification and segmentation). We compare the respective advantages and limitations of popular techniques both in terms of architectural design and their experimental value. Finally, we provide an analysis on open research directions and possible future works. We hope this effort will ignite further interest in the community to solve current challenges towards the application of transformer models in computer vision.

在本文中，我们试图通过引入深度学习模型的句法归纳偏见来建立两所学校之间的联系。我们提出了两个归纳偏见的家族，一个家庭用于选区结构，另一个用于依赖性结构。选区归纳偏见鼓励深度学习模型使用不同的单位（或神经元）分别处理长期和短期信息。这种分离为深度学习模型提供了一种方法，可以从顺序输入中构建潜在的层次表示形式，即更高级别的表示由高级表示形式组成，并且可以分解为一系列低级表示。例如，在不了解地面实际结构的情况下，我们提出的模型学会通过根据其句法结构组成变量和运算符的表示来处理逻辑表达。另一方面，依赖归纳偏置鼓励模型在输入序列中找到实体之间的潜在关系。对于自然语言，潜在关系通常被建模为一个定向依赖图，其中一个单词恰好具有一个父节点和零或几个孩子的节点。将此约束应用于类似变压器的模型之后，我们发现该模型能够诱导接近人类专家注释的有向图，并且在不同任务上也优于标准变压器模型。我们认为，这些实验结果为深度学习模型的未来发展展示了一个有趣的选择。

多文件摘要（MDS）是信息聚合的有效工具，它从与主题相关文档集群生成信息和简洁的摘要。我们的调查是，首先，系统地概述了最近的基于深度学习的MDS模型。我们提出了一种新的分类学，总结神经网络的设计策略，并进行全面的最先进的概要。我们突出了在现有文献中很少讨论的各种客观函数之间的差异。最后，我们提出了与这个新的和令人兴奋的领域有关的几个方向。

我们从第一批原则提供了一个理论分析，该原则在预训练和微调性能的关系归纳偏差之间建立了新的联系，同时提供了一般预训练模型的延长视图。我们进一步探讨了现有的预训练方法如何强加相关的归纳偏差，发现绝大多数现有方法几乎专注于以帧内方式建模的关系，而不是每种样本方式。我们建立了这些调查结果，这些发现与跨越3个数据模式和10个下游任务的标准基准测试。这些调查验证了我们的理论分析，并提供了一种方法，以产生新的预训练方法，该方法与现有的方法符合用户指定的关系图。

本文对过去二十年来对自然语言生成（NLG）的研究提供了全面的审查，特别是与数据到文本生成和文本到文本生成深度学习方法有关，以及NLG的新应用技术。该调查旨在（a）给出关于NLG核心任务的最新综合，以及该领域采用的建筑;（b）详细介绍各种NLG任务和数据集，并提请注意NLG评估中的挑战，专注于不同的评估方法及其关系;（c）强调一些未来的强调和相对近期的研究问题，因为NLG和其他人工智能领域的协同作用而增加，例如计算机视觉，文本和计算创造力。

蛋白质RNA相互作用对各种细胞活性至关重要。已经开发出实验和计算技术来研究相互作用。由于先前数据库的限制，尤其是缺乏蛋白质结构数据，大多数现有的计算方法严重依赖于序列数据，只有一小部分使用结构信息。最近，alphafold彻底改变了整个蛋白质和生物领域。可预应学，在即将到来的年份，也将显着促进蛋白质-RNA相互作用预测。在这项工作中，我们对该字段进行了彻底的审查，调查绑定站点和绑定偏好预测问题，并覆盖常用的数据集，功能和模型。我们还指出了这一领域的潜在挑战和机遇。本调查总结了过去的RBP-RNA互动领域的发展，并预见到了alphafold时代未来的发展。

Natural Language Processing (NLP) has been revolutionized by the use of Pre-trained Language Models (PLMs) such as BERT. Despite setting new records in nearly every NLP task, PLMs still face a number of challenges including poor interpretability, weak reasoning capability, and the need for a lot of expensive annotated data when applied to downstream tasks. By integrating external knowledge into PLMs, \textit{\underline{K}nowledge-\underline{E}nhanced \underline{P}re-trained \underline{L}anguage \underline{M}odels} (KEPLMs) have the potential to overcome the above-mentioned limitations. In this paper, we examine KEPLMs systematically through a series of studies. Specifically, we outline the common types and different formats of knowledge to be integrated into KEPLMs, detail the existing methods for building and evaluating KEPLMS, present the applications of KEPLMs in downstream tasks, and discuss the future research directions. Researchers will benefit from this survey by gaining a quick and comprehensive overview of the latest developments in this field.

As an important fine-grained sentiment analysis problem, aspect-based sentiment analysis (ABSA), aiming to analyze and understand people's opinions at the aspect level, has been attracting considerable interest in the last decade. To handle ABSA in different scenarios, various tasks are introduced for analyzing different sentiment elements and their relations, including the aspect term, aspect category, opinion term, and sentiment polarity. Unlike early ABSA works focusing on a single sentiment element, many compound ABSA tasks involving multiple elements have been studied in recent years for capturing more complete aspect-level sentiment information. However, a systematic review of various ABSA tasks and their corresponding solutions is still lacking, which we aim to fill in this survey. More specifically, we provide a new taxonomy for ABSA which organizes existing studies from the axes of concerned sentiment elements, with an emphasis on recent advances of compound ABSA tasks. From the perspective of solutions, we summarize the utilization of pre-trained language models for ABSA, which improved the performance of ABSA to a new stage. Besides, techniques for building more practical ABSA systems in cross-domain/lingual scenarios are discussed. Finally, we review some emerging topics and discuss some open challenges to outlook potential future directions of ABSA.

变形金刚占据了自然语言处理领域，最近影响了计算机视觉区域。在医学图像分析领域中，变压器也已成功应用于全栈临床应用，包括图像合成/重建，注册，分割，检测和诊断。我们的论文旨在促进变压器在医学图像分析领域的认识和应用。具体而言，我们首先概述了内置在变压器和其他基本组件中的注意机制的核心概念。其次，我们回顾了针对医疗图像应用程序量身定制的各种变压器体系结构，并讨论其局限性。在这篇综述中，我们调查了围绕在不同学习范式中使用变压器，提高模型效率及其与其他技术的耦合的关键挑战。我们希望这篇评论可以为读者提供医学图像分析领域的读者的全面图片。