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.
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Multimodality Representation Learning, as a technique of learning to embed information from different modalities and their correlations, has achieved remarkable success on a variety of applications, such as Visual Question Answering (VQA), Natural Language for Visual Reasoning (NLVR), and Vision Language Retrieval (VLR). Among these applications, cross-modal interaction and complementary information from different modalities are crucial for advanced models to perform any multimodal task, e.g., understand, recognize, retrieve, or generate optimally. Researchers have proposed diverse methods to address these tasks. The different variants of transformer-based architectures performed extraordinarily on multiple modalities. This survey presents the comprehensive literature on the evolution and enhancement of deep learning multimodal architectures to deal with textual, visual and audio features for diverse cross-modal and modern multimodal tasks. This study summarizes the (i) recent task-specific deep learning methodologies, (ii) the pretraining types and multimodal pretraining objectives, (iii) from state-of-the-art pretrained multimodal approaches to unifying architectures, and (iv) multimodal task categories and possible future improvements that can be devised for better multimodal learning. Moreover, we prepare a dataset section for new researchers that covers most of the benchmarks for pretraining and finetuning. Finally, major challenges, gaps, and potential research topics are explored. A constantly-updated paperlist related to our survey is maintained at //github.com/marslanm/multimodality-representation-learning.
Protein representation learning has primarily benefited from the remarkable development of language models (LMs). Accordingly, pre-trained protein models also suffer from a problem in LMs: a lack of factual knowledge. The recent solution models the relationships between protein and associated knowledge terms as the knowledge encoding objective. However, it fails to explore the relationships at a more granular level, i.e., the token level. To mitigate this, we propose Knowledge-exploited Auto-encoder for Protein (KeAP), which performs token-level knowledge graph exploration for protein representation learning. In practice, non-masked amino acids iteratively query the associated knowledge tokens to extract and integrate helpful information for restoring masked amino acids via attention. We show that KeAP can consistently outperform the previous counterpart on 9 representative downstream applications, sometimes surpassing it by large margins. These results suggest that KeAP provides an alternative yet effective way to perform knowledge enhanced protein representation learning.
The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to optimize laboratory operations and fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose a multi-domain, multi-task language model to solve a wide range of tasks in both the chemical and natural language domains. By leveraging multi-task learning, our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.
Image reconstruction based on indirect, noisy, or incomplete data remains an important yet challenging task. While methods such as compressive sensing have demonstrated high-resolution image recovery in various settings, there remain issues of robustness due to parameter tuning. Moreover, since the recovery is limited to a point estimate, it is impossible to quantify the uncertainty, which is often desirable. Due to these inherent limitations, a sparse Bayesian learning approach is sometimes adopted to recover a posterior distribution of the unknown. Sparse Bayesian learning assumes that some linear transformation of the unknown is sparse. However, most of the methods developed are tailored to specific problems, with particular forward models and priors. Here, we present a generalized approach to sparse Bayesian learning. It has the advantage that it can be used for various types of data acquisitions and prior information. Some preliminary results on image reconstruction/recovery indicate its potential use for denoising, deblurring, and magnetic resonance imaging.
Connecting Vision and Language plays an essential role in Generative Intelligence. For this reason, in the last few years, a large research effort has been devoted to image captioning, i.e. the task of describing images with syntactically and semantically meaningful sentences. Starting from 2015 the task has generally been addressed with pipelines composed of a visual encoding step and a language model for text generation. During these years, both components have evolved considerably through the exploitation of object regions, attributes, and relationships and the introduction of multi-modal connections, fully-attentive approaches, and BERT-like early-fusion strategies. However, regardless of the impressive results obtained, research in image captioning has not reached a conclusive answer yet. This work aims at providing a comprehensive overview and categorization of image captioning approaches, from visual encoding and text generation to training strategies, used datasets, and evaluation metrics. In this respect, we quantitatively compare many relevant state-of-the-art approaches to identify the most impactful technical innovations in image captioning architectures and training strategies. Moreover, many variants of the problem and its open challenges are analyzed and discussed. The final goal of this work is to serve as a tool for understanding the existing state-of-the-art and highlighting the future directions for an area of research where Computer Vision and Natural Language Processing can find an optimal synergy.
Images can convey rich semantics and induce various emotions in viewers. Recently, with the rapid advancement of emotional intelligence and the explosive growth of visual data, extensive research efforts have been dedicated to affective image content analysis (AICA). In this survey, we will comprehensively review the development of AICA in the recent two decades, especially focusing on the state-of-the-art methods with respect to three main challenges -- the affective gap, perception subjectivity, and label noise and absence. We begin with an introduction to the key emotion representation models that have been widely employed in AICA and description of available datasets for performing evaluation with quantitative comparison of label noise and dataset bias. We then summarize and compare the representative approaches on (1) emotion feature extraction, including both handcrafted and deep features, (2) learning methods on dominant emotion recognition, personalized emotion prediction, emotion distribution learning, and learning from noisy data or few labels, and (3) AICA based applications. Finally, we discuss some challenges and promising research directions in the future, such as image content and context understanding, group emotion clustering, and viewer-image interaction.
Deep Learning has revolutionized the fields of computer vision, natural language understanding, speech recognition, information retrieval and more. However, with the progressive improvements in deep learning models, their number of parameters, latency, resources required to train, etc. have all have increased significantly. Consequently, it has become important to pay attention to these footprint metrics of a model as well, not just its quality. We present and motivate the problem of efficiency in deep learning, followed by a thorough survey of the five core areas of model efficiency (spanning modeling techniques, infrastructure, and hardware) and the seminal work there. We also present an experiment-based guide along with code, for practitioners to optimize their model training and deployment. We believe this is the first comprehensive survey in the efficient deep learning space that covers the landscape of model efficiency from modeling techniques to hardware support. Our hope is that this survey would provide the reader with the mental model and the necessary understanding of the field to apply generic efficiency techniques to immediately get significant improvements, and also equip them with ideas for further research and experimentation to achieve additional gains.
Large-scale pre-trained models (PTMs) such as BERT and GPT have recently achieved great success and become a milestone in the field of artificial intelligence (AI). Owing to sophisticated pre-training objectives and huge model parameters, large-scale PTMs can effectively capture knowledge from massive labeled and unlabeled data. By storing knowledge into huge parameters and fine-tuning on specific tasks, the rich knowledge implicitly encoded in huge parameters can benefit a variety of downstream tasks, which has been extensively demonstrated via experimental verification and empirical analysis. It is now the consensus of the AI community to adopt PTMs as backbone for downstream tasks rather than learning models from scratch. In this paper, we take a deep look into the history of pre-training, especially its special relation with transfer learning and self-supervised learning, to reveal the crucial position of PTMs in the AI development spectrum. Further, we comprehensively review the latest breakthroughs of PTMs. These breakthroughs are driven by the surge of computational power and the increasing availability of data, towards four important directions: designing effective architectures, utilizing rich contexts, improving computational efficiency, and conducting interpretation and theoretical analysis. Finally, we discuss a series of open problems and research directions of PTMs, and hope our view can inspire and advance the future study of PTMs.
In this paper, we propose a novel Feature Decomposition and Reconstruction Learning (FDRL) method for effective facial expression recognition. We view the expression information as the combination of the shared information (expression similarities) across different expressions and the unique information (expression-specific variations) for each expression. More specifically, FDRL mainly consists of two crucial networks: a Feature Decomposition Network (FDN) and a Feature Reconstruction Network (FRN). In particular, FDN first decomposes the basic features extracted from a backbone network into a set of facial action-aware latent features to model expression similarities. Then, FRN captures the intra-feature and inter-feature relationships for latent features to characterize expression-specific variations, and reconstructs the expression feature. To this end, two modules including an intra-feature relation modeling module and an inter-feature relation modeling module are developed in FRN. Experimental results on both the in-the-lab databases (including CK+, MMI, and Oulu-CASIA) and the in-the-wild databases (including RAF-DB and SFEW) show that the proposed FDRL method consistently achieves higher recognition accuracy than several state-of-the-art methods. This clearly highlights the benefit of feature decomposition and reconstruction for classifying expressions.
Multi-Task Learning (MTL) is a learning paradigm in machine learning and its aim is to leverage useful information contained in multiple related tasks to help improve the generalization performance of all the tasks. In this paper, we give a survey for MTL from the perspective of algorithmic modeling, applications and theoretical analyses. For algorithmic modeling, we give a definition of MTL and then classify different MTL algorithms into five categories, including feature learning approach, low-rank approach, task clustering approach, task relation learning approach and decomposition approach as well as discussing the characteristics of each approach. In order to improve the performance of learning tasks further, MTL can be combined with other learning paradigms including semi-supervised learning, active learning, unsupervised learning, reinforcement learning, multi-view learning and graphical models. When the number of tasks is large or the data dimensionality is high, we review online, parallel and distributed MTL models as well as dimensionality reduction and feature hashing to reveal their computational and storage advantages. Many real-world applications use MTL to boost their performance and we review representative works in this paper. Finally, we present theoretical analyses and discuss several future directions for MTL.
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