Deep learning has become a crucial tool in studying proteins. While the significance of modeling protein structure has been discussed extensively in the literature, amino acid types are typically included in the input as a default operation for many inference tasks. This study demonstrates with structure alignment task that embedding amino acid types in some cases may not help a deep learning model learn better representation. To this end, we propose ProtLOCA, a local geometry alignment method based solely on amino acid structure representation. The effectiveness of ProtLOCA is examined by a global structure-matching task on protein pairs with an independent test dataset based on CATH labels. Our method outperforms existing sequence- and structure-based representation learning methods by more quickly and accurately matching structurally consistent protein domains. Furthermore, in local structure pairing tasks, ProtLOCA for the first time provides a valid solution to highlight common local structures among proteins with different overall structures but the same function. This suggests a new possibility for using deep learning methods to analyze protein structure to infer function.
The recent success of large language models (LLMs) trained on static, pre-collected, general datasets has sparked numerous research directions and applications. One such direction addresses the non-trivial challenge of integrating pre-trained LLMs into dynamic data distributions, task structures, and user preferences. Pre-trained LLMs, when tailored for specific needs, often experience significant performance degradation in previous knowledge domains -- a phenomenon known as "catastrophic forgetting". While extensively studied in the continual learning (CL) community, it presents new manifestations in the realm of LLMs. In this survey, we provide a comprehensive overview of the current research progress on LLMs within the context of CL. This survey is structured into four main sections: we first describe an overview of continually learning LLMs, consisting of two directions of continuity: vertical continuity (or vertical continual learning), i.e., continual adaptation from general to specific capabilities, and horizontal continuity (or horizontal continual learning), i.e., continual adaptation across time and domains (Section 3). We then summarize three stages of learning LLMs in the context of modern CL: Continual Pre-Training (CPT), Domain-Adaptive Pre-training (DAP), and Continual Fine-Tuning (CFT) (Section 4). Then we provide an overview of evaluation protocols for continual learning with LLMs, along with the current available data sources (Section 5). Finally, we discuss intriguing questions pertaining to continual learning for LLMs (Section 6). The full list of papers examined in this survey is available at //github.com/Wang-ML-Lab/llm-continual-learning-survey.
In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.
Designing and generating new data under targeted properties has been attracting various critical applications such as molecule design, image editing and speech synthesis. Traditional hand-crafted approaches heavily rely on expertise experience and intensive human efforts, yet still suffer from the insufficiency of scientific knowledge and low throughput to support effective and efficient data generation. Recently, the advancement of deep learning induces expressive methods that can learn the underlying representation and properties of data. Such capability provides new opportunities in figuring out the mutual relationship between the structural patterns and functional properties of the data and leveraging such relationship to generate structural data given the desired properties. This article provides a systematic review of this promising research area, commonly known as controllable deep data generation. Firstly, the potential challenges are raised and preliminaries are provided. Then the controllable deep data generation is formally defined, a taxonomy on various techniques is proposed and the evaluation metrics in this specific domain are summarized. After that, exciting applications of controllable deep data generation are introduced and existing works are experimentally analyzed and compared. Finally, the promising future directions of controllable deep data generation are highlighted and five potential challenges are identified.
The remarkable success of deep learning has prompted interest in its application to medical diagnosis. Even tough state-of-the-art deep learning models have achieved human-level accuracy on the classification of different types of medical data, these models are hardly adopted in clinical workflows, mainly due to their lack of interpretability. The black-box-ness of deep learning models has raised the need for devising strategies to explain the decision process of these models, leading to the creation of the topic of eXplainable Artificial Intelligence (XAI). In this context, we provide a thorough survey of XAI applied to medical diagnosis, including visual, textual, and example-based explanation methods. Moreover, this work reviews the existing medical imaging datasets and the existing metrics for evaluating the quality of the explanations . Complementary to most existing surveys, we include a performance comparison among a set of report generation-based methods. Finally, the major challenges in applying XAI to medical imaging are also discussed.
The existence of representative datasets is a prerequisite of many successful artificial intelligence and machine learning models. However, the subsequent application of these models often involves scenarios that are inadequately represented in the data used for training. The reasons for this are manifold and range from time and cost constraints to ethical considerations. As a consequence, the reliable use of these models, especially in safety-critical applications, is a huge challenge. Leveraging additional, already existing sources of knowledge is key to overcome the limitations of purely data-driven approaches, and eventually to increase the generalization capability of these models. Furthermore, predictions that conform with knowledge are crucial for making trustworthy and safe decisions even in underrepresented scenarios. This work provides an overview of existing techniques and methods in the literature that combine data-based models with existing knowledge. The identified approaches are structured according to the categories integration, extraction and conformity. Special attention is given to applications in the field of autonomous driving.
Deep learning has shown great potential for modeling the physical dynamics of complex particle systems such as fluids (in Lagrangian descriptions). Existing approaches, however, require the supervision of consecutive particle properties, including positions and velocities. In this paper, we consider a partially observable scenario known as fluid dynamics grounding, that is, inferring the state transitions and interactions within the fluid particle systems from sequential visual observations of the fluid surface. We propose a differentiable two-stage network named NeuroFluid. Our approach consists of (i) a particle-driven neural renderer, which involves fluid physical properties into the volume rendering function, and (ii) a particle transition model optimized to reduce the differences between the rendered and the observed images. NeuroFluid provides the first solution to unsupervised learning of particle-based fluid dynamics by training these two models jointly. It is shown to reasonably estimate the underlying physics of fluids with different initial shapes, viscosity, and densities. It is a potential alternative approach to understanding complex fluid mechanics, such as turbulence, that are difficult to model using traditional methods of mathematical physics.
Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.
Few sample learning (FSL) is significant and challenging in the field of machine learning. The capability of learning and generalizing from very few samples successfully is a noticeable demarcation separating artificial intelligence and human intelligence since humans can readily establish their cognition to novelty from just a single or a handful of examples whereas machine learning algorithms typically entail hundreds or thousands of supervised samples to guarantee generalization ability. Despite the long history dated back to the early 2000s and the widespread attention in recent years with booming deep learning technologies, little surveys or reviews for FSL are available until now. In this context, we extensively review 200+ papers of FSL spanning from the 2000s to 2019 and provide a timely and comprehensive survey for FSL. In this survey, we review the evolution history as well as the current progress on FSL, categorize FSL approaches into the generative model based and discriminative model based kinds in principle, and emphasize particularly on the meta learning based FSL approaches. We also summarize several recently emerging extensional topics of FSL and review the latest advances on these topics. Furthermore, we highlight the important FSL applications covering many research hotspots in computer vision, natural language processing, audio and speech, reinforcement learning and robotic, data analysis, etc. Finally, we conclude the survey with a discussion on promising trends in the hope of providing guidance and insights to follow-up researches.
The LSTM network was proposed to overcome the difficulty in learning long-term dependence, and has made significant advancements in applications. With its success and drawbacks in mind, this paper raises the question - do RNN and LSTM have long memory? We answer it partially by proving that RNN and LSTM do not have long memory from a statistical perspective. A new definition for long memory networks is further introduced, and it requires the model weights to decay at a polynomial rate. To verify our theory, we convert RNN and LSTM into long memory networks by making a minimal modification, and their superiority is illustrated in modeling long-term dependence of various datasets.
Compared with cheap addition operation, multiplication operation is of much higher computation complexity. The widely-used convolutions in deep neural networks are exactly cross-correlation to measure the similarity between input feature and convolution filters, which involves massive multiplications between float values. In this paper, we present adder networks (AdderNets) to trade these massive multiplications in deep neural networks, especially convolutional neural networks (CNNs), for much cheaper additions to reduce computation costs. In AdderNets, we take the $\ell_1$-norm distance between filters and input feature as the output response. The influence of this new similarity measure on the optimization of neural network have been thoroughly analyzed. To achieve a better performance, we develop a special back-propagation approach for AdderNets by investigating the full-precision gradient. We then propose an adaptive learning rate strategy to enhance the training procedure of AdderNets according to the magnitude of each neuron's gradient. As a result, the proposed AdderNets can achieve 74.9% Top-1 accuracy 91.7% Top-5 accuracy using ResNet-50 on the ImageNet dataset without any multiplication in convolution layer.