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Recently, microRNAs (miRNAs) are confirmed to be important molecules within many crucial biological processes and therefore related to various complex human diseases. However, previous methods of predicting miRNA–disease associations have their own deficiencies. Under this circumstance, we developed a prediction method called deep representations‐based miRNA–disease association (DRMDA) prediction. The original miRNA–disease association data were extracted from HDMM database. Meanwhile, stacked auto‐encoder, greedy layer‐wise unsupervised pre‐training algorithm and support vector machine were implemented to predict potential associations. We compared DRMDA with five previous classical prediction models (HGIMDA, RLSMDA, HDMP, WBSMDA and RWRMDA) in global leave‐one‐out cross‐validation (LOOCV), local LOOCV and fivefold cross‐validation, respectively. The AUCs achieved by DRMDA were 0.9177, 08339 and 0.9156 ± 0.0006 in the three tests above, respectively. In further case studies, we predicted the top 50 potential miRNAs for colon neoplasms, lymphoma and prostate neoplasms, and 88%, 90% and 86% of the predicted miRNA can be verified by experimental evidence, respectively. In conclusion, DRMDA is a promising prediction method which could identify potential and novel miRNA–disease associations.

Vision transformers have become popular as a possible substitute to convolutional neural networks (CNNs) for a variety of computer vision applications. These transformers, with their ability to focus on global relationships in images, offer large learning capacity. However, they may suffer from limited generalization as they do not tend to model local correlation in images. Recently, in vision transformers hybridization of both the convolution operation and self-attention mechanism has emerged, to exploit both the local and global image representations. These hybrid vision transformers, also referred to as CNN-Transformer architectures, have demonstrated remarkable results in vision applications. Given the rapidly growing number of hybrid vision transformers, it has become necessary to provide a taxonomy and explanation of these hybrid architectures. This survey presents a taxonomy of the recent vision transformer architectures and more specifically that of the hybrid vision transformers. Additionally, the key features of these architectures such as the attention mechanisms, positional embeddings, multi-scale processing, and convolution are also discussed. In contrast to the previous survey papers that are primarily focused on individual vision transformer architectures or CNNs, this survey uniquely emphasizes the emerging trend of hybrid vision transformers. By showcasing the potential of hybrid vision transformers to deliver exceptional performance across a range of computer vision tasks, this survey sheds light on the future directions of this rapidly evolving architecture.

Deep learning, which is a subfield of machine learning, has opened a new era for the development of neural networks. The auto-encoder is a key component of deep structure, which can be used to realize transfer learning and plays an important role in both unsupervised learning and non-linear feature extraction. By highlighting the contributions and challenges of recent research papers, this work aims to review state-of-the-art auto-encoder algorithms. Firstly, we introduce the basic auto-encoder as well as its basic concept and structure. Secondly, we present a comprehensive summarization of different variants of the auto-encoder. Thirdly, we analyze and study auto-encoders from three different perspectives. We also discuss the relationships between auto-encoders, shallow models and other deep learning models. The auto-encoder and its variants have successfully been applied in a wide range of fields, such as pattern recognition, computer vision, data generation, recommender systems, etc. Then, we focus on the available toolkits for auto-encoders. Finally, this paper summarizes the future trends and challenges in designing and training auto-encoders. We hope that this survey will provide a good reference when using and designing AE models.

Optimal integration of transcriptomics data and associated spatial information is essential towards fully exploiting spatial transcriptomics to dissect tissue heterogeneity and map out inter-cellular communications. We present SEDR, which uses a deep autoencoder coupled with a masked self-supervised learning mechanism to construct a low-dimensional latent representation of gene expression, which is then simultaneously embedded with the corresponding spatial information through a variational graph autoencoder. SEDR achieved higher clustering performance on manually annotated 10 × Visium datasets and better scalability on high-resolution spatial transcriptomics datasets than existing methods. Additionally, we show SEDR’s ability to impute and denoise gene expression (URL: https://github.com/JinmiaoChenLab/SEDR/ ).

Recently, researchers have been studying methods to introduce deep learning into automated optical inspection (AOI) systems to reduce labor costs. However, the integration of deep learning in the industry may encounter major challenges such as sample imbalance (defective products that only account for a small proportion). Therefore, in this study, an anomaly detection neural network, dual auto-encoder generative adversarial network (DAGAN), was developed to solve the problem of sample imbalance. With skip-connection and dual auto-encoder architecture, the proposed method exhibited excellent image reconstruction ability and training stability. Three datasets, namely public industrial detection training set, MVTec AD, with mobile phone screen glass and wood defect detection datasets, were used to verify the inspection ability of DAGAN. In addition, training with a limited amount of data was proposed to verify its detection ability. The results demonstrated that the areas under the curve (AUCs) of DAGAN were better than previous generative adversarial network-based anomaly detection models in 13 out of 17 categories in these datasets, especially in categories with high variability or noise. The maximum AUC improvement was 0.250 (toothbrush). Moreover, the proposed method exhibited better detection ability than the U-Net auto-encoder, which indicates the function of discriminator in this application. Furthermore, the proposed method had a high level of AUCs when using only a small amount of training data. DAGAN can significantly reduce the time and cost of collecting and labeling data when it is applied to industrial detection.

CRISPR‐Cas9 screens facilitate the discovery of gene functional relationships and phenotype‐specific dependencies. The Cancer Dependency Map (DepMap) is the largest compendium of whole‐genome CRISPR screens aimed at identifying cancer‐specific genetic dependencies across human cell lines. A mitochondria‐associated bias has been previously reported to mask signals for genes involved in other functions, and thus, methods for normalizing this dominant signal to improve co‐essentiality networks are of interest. In this study, we explore three unsupervised dimensionality reduction methods—autoencoders, robust, and classical principal component analyses (PCA)—for normalizing the DepMap to improve functional networks extracted from these data. We propose a novel “onion” normalization technique to combine several normalized data layers into a single network. Benchmarking analyses reveal that robust PCA combined with onion normalization outperforms existing methods for normalizing the DepMap. Our work demonstrates the value of removing low‐dimensional signals from the DepMap before constructing functional gene networks and provides generalizable dimensionality reduction‐based normalization tools. Synopsis Dimensionality reduction‐based methods are proposed for normalizing Cancer Dependency Map (DepMap) genome‐wide CRISPR screen data to enhance the functional information in co‐essentiality networks extracted from DepMap. Low‐dimensional patterns introduce dominant covariation in gene networks derived from DepMap data, obscuring more subtle functional relationships. Applying dimensionality reduction approaches to remove low‐dimensional signal, including robust and classical principal component analysis or autoencoders, can increase functional information captured by similarity networks derived from DepMap data. Onion normalization, which integrates several normalized data layers into a single network, outperforms existing methods for constructing co‐essentiality networks from the DepMap. Graphical Abstract Dimensionality reduction‐based methods are proposed for normalizing Cancer Dependency Map (DepMap) genome‐wide CRISPR screen data to enhance the functional information in co‐essentiality networks extracted from DepMap.

Medical image segmentation has the priori guiding significance for clinical diagnosis and treatment. In the past ten years, a large number of experimental facts have proved the great success of deep convolutional neural networks in various medical image segmentation tasks. However, the convolutional networks seem to focus too much on the local image details, while ignoring the long-range dependence. The Transformer structure can encode long-range dependencies in image and learn high-dimensional image information through the self-attention mechanism. But this structure currently depends on the database scale to give full play to its excellent performance, which limits its application in medical images with limited database size. In this paper, the characteristics of CNNs and Transformer are integrated to propose a dual encoding–decoding structure of the X-shaped network (X-Net). It can serve as a good alternative to the traditional pure convolutional medical image segmentation network. In the encoding phase, the local and global features are simultaneously extracted by two types of encoders, convolutional downsampling, and Transformer and then merged through jump connection. In the decoding phase, a variational auto-encoder branch is added to reconstruct the input image itself in order to weaken the impact of insufficient data. Comparative experiments on three medical image datasets show that X-Net can realize the organic combination of Transformer and CNNs.

Detecting an anomaly or an abnormal situation from given noise is highly useful in an environment where constantly verifying and monitoring a machine is required. As deep learning algorithms are further developed, current studies have focused on this problem. However, there are too many variables to define anomalies, and the human annotation for a large collection of abnormal data labeled at the class-level is very labor-intensive. In this paper, we propose to detect abnormal operation sounds or outliers in a very complex machine along with reducing the data-driven annotation cost. The architecture of the proposed model is based on an auto-encoder, and it uses the residual error, which stands for its reconstruction quality, to identify the anomaly. We assess our model using Surface-Mounted Device (SMD) machine sound, which is very complex, as experimental data, and state-of-the-art performance is successfully achieved for anomaly detection.

Quantum devices with a large number of gate electrodes allow for precise control of device parameters. This capability is hard to fully exploit due to the complex dependence of these parameters on applied gate voltages. We experimentally demonstrate an algorithm capable of fine-tuning several device parameters at once. The algorithm acquires a measurement and assigns it a score using a variational auto-encoder. Gate voltage settings are set to optimize this score in real-time in an unsupervised fashion. We report fine-tuning times of a double quantum dot device within approximately 40 min.

In recent years, deep learning has garnered tremendous success in a variety of application domains. This new field of machine learning has been growing rapidly and has been applied to most traditional application domains, as well as some new areas that present more opportunities. Different methods have been proposed based on different categories of learning, including supervised, semi-supervised, and un-supervised learning. Experimental results show state-of-the-art performance using deep learning when compared to traditional machine learning approaches in the fields of image processing, computer vision, speech recognition, machine translation, art, medical imaging, medical information processing, robotics and control, bioinformatics, natural language processing, cybersecurity, and many others. This survey presents a brief survey on the advances that have occurred in the area of Deep Learning (DL), starting with the Deep Neural Network (DNN). The survey goes on to cover Convolutional Neural Network (CNN), Recurrent Neural Network (RNN), including Long Short-Term Memory (LSTM) and Gated Recurrent Units (GRU), Auto-Encoder (AE), Deep Belief Network (DBN), Generative Adversarial Network (GAN), and Deep Reinforcement Learning (DRL). Additionally, we have discussed recent developments, such as advanced variant DL techniques based on these DL approaches. This work considers most of the papers published after 2012 from when the history of deep learning began. Furthermore, DL approaches that have been explored and evaluated in different application domains are also included in this survey. We also included recently developed frameworks, SDKs, and benchmark datasets that are used for implementing and evaluating deep learning approaches. There are some surveys that have been published on DL using neural networks and a survey on Reinforcement Learning (RL). However, those papers have not discussed individual advanced techniques for training large-scale deep learning models and the recently developed method of generative models.