The integration of multi-omics data is crucial for cancer patient classification and biomarker identification. While this integration presents significant potential, it necessitates the development of sophisticated methodological frameworks. There remains considerable opportunity for enhancement in existing approaches to simultaneously fulfill the demands of omics-specific feature extraction and cross-omics association modeling. Consequently, in this study, a deep learning framework based on improved autoencoders and attention mechanism, named MOAEAM, is proposed to address this issue. Specifically, a novel composite loss facilitates the extraction of omics-specific features, and a multi-omics integration module incorporates capture cross-omics information, collectively enhancing classification performance. Systematic evaluations across multiple cancer datasets show MOAEAM achieves consistently higher classification performance than current mainstream multi-omics integration methods. Ablation studies reveal that the auxiliary classifier introduced in the improved autoencoder plays a key role in performance improvements. The feature importance scores computed by the model identify potential clinically significant biomarkers, which are further validated through literature analysis and enrichment analysis.

Metabolism refers to a series of orderly chemical reactions used to maintain life activities in organisms. In healthy individuals, metabolism remains within a normal range. However, specific diseases can lead to abnormalities in the levels of certain metabolites, causing them to either increase or decrease. Detecting these deviations in metabolite levels can aid in diagnosing a disease. Traditional biological experiments often rely on a lot of manpower to do repeated experiments, which is time consuming and labor intensive. To address this issue, we develop a deep learning model based on the auto-encoder and non-negative matrix factorization named as MDA-AENMF to predict the potential associations between metabolites and diseases. We integrate a variety of similarity networks and then acquire the characteristics of both metabolites and diseases through three specific modules. First, we get the disease characteristics from the five-layer auto-encoder module. Later, in the non-negative matrix factorization module, we extract both the metabolite and disease characteristics. Furthermore, the graph attention auto-encoder module helps us obtain metabolite characteristics. After obtaining the features from three modules, these characteristics are merged into a single, comprehensive feature vector for each metabolite-disease pair. Finally, we send the corresponding feature vector and label to the multi-layer perceptron for training. The experiment demonstrates our area under the receiver operating characteristic curve of 0.975 and area under the precision-recall curve of 0.973 in 5-fold cross-validation, which are superior to those of existing state-of-the-art predictive methods. Through case studies, most of the new associations obtained by MDA-AENMF have been verified, further highlighting the reliability of MDA-AENMF in predicting the potential relationships between metabolites and diseases.

Long noncoding RNA (lncRNA) is a kind of noncoding RNA with a length of more than 200 nucleotide units. Numerous research studies have proven that although lncRNAs cannot be directly translated into proteins, lncRNAs still play an important role in human growth processes by interacting with proteins. Since traditional biological experiments often require a lot of time and material costs to explore potential lncRNA-protein interactions (LPI), several computational models have been proposed for this task. In this study, we introduce a novel deep learning method known as combined graph auto-encoders (LPICGAE) to predict potential human LPIs. First, we apply a variational graph auto-encoder to learn the low dimensional representations from the high-dimensional features of lncRNAs and proteins. Then the graph auto-encoder is used to reconstruct the adjacency matrix for inferring potential interactions between lncRNAs and proteins. Finally, we minimize the loss of the two processes alternately to gain the final predicted interaction matrix. The result in 5-fold cross-validation experiments illustrates that our method achieves an average area under receiver operating characteristic curve of 0.974 and an average accuracy of 0.985, which is better than those of existing six state-of-the-art computational methods. We believe that LPICGAE can help researchers to gain more potential relationships between lncRNAs and proteins effectively.

Metabolism is the process by which an organism continuously replaces old substances with new substances. It plays an important role in maintaining human life, body growth and reproduction. More and more researchers have shown that the concentrations of some metabolites in patients are different from those in healthy people. Traditional biological experiments can test some hypotheses and verify their relationships but usually take a considerable amount of time and money. Therefore, it is urgent to develop a new computational method to identify the relationships between metabolites and diseases. In this work, we present a new deep learning algorithm named as graph convolutional network with graph attention network (GCNAT) to predict the potential associations of disease-related metabolites. First, we construct a heterogeneous network based on known metabolite-disease associations, metabolite-metabolite similarities and disease-disease similarities. Metabolite and disease features are encoded and learned through the graph convolutional neural network. Then, a graph attention layer is used to combine the embeddings of multiple convolutional layers, and the corresponding attention coefficients are calculated to assign different weights to the embeddings of each layer. Further, the prediction result is obtained by decoding and scoring the final synthetic embeddings. Finally, GCNAT achieves a reliable area under the receiver operating characteristic curve of 0.95 and the precision-recall curve of 0.405, which are better than the results of existing five state-of-the-art predictive methods in 5-fold cross-validation, and the case studies show that the metabolite-disease correlations predicted by our method can be successfully demonstrated by relevant experiments. We hope that GCNAT could be a useful biomedical research tool for predicting potential metabolite-disease associations in the future.

Long non-coding RNA (lncRNA) and microRNA (miRNA) are two typical types of non-coding RNAs (ncRNAs), their interaction plays an important regulatory role in many biological processes. Exploring the interactions between unknown lncRNA and miRNA can help us better understand the functional expression between lncRNA and miRNA. At present, the interactions between lncRNA and miRNA are mainly obtained through biological experiments, but such experiments are often time-consuming and labor-intensive, it is necessary to design a computational method that can predict the interactions between lncRNA and miRNA. In this paper, we propose a method based on graph convolutional neural (GCN) network and conditional random field (CRF) for predicting human lncRNA-miRNA interactions, named GCNCRF. First, we construct a heterogeneous network using the known interactions of lncRNA and miRNA in the LncRNASNP2 database, the lncRNA/miRNA integration similarity network, and the lncRNA/miRNA feature matrix. Second, the initial embedding of nodes is obtained using a GCN network. A CRF set in the GCN hidden layer can update the obtained preliminary embeddings so that similar nodes have similar embeddings. At the same time, an attention mechanism is added to the CRF layer to reassign weights to nodes to better grasp the feature information of important nodes and ignore some nodes with less influence. Finally, the final embedding is decoded and scored through the decoding layer. Through a 5-fold cross-validation experiment, GCNCRF has an area under the receiver operating characteristic curve value of 0.947 on the main dataset, which has higher prediction accuracy than the other six state-of-the-art methods.

With computer vision-based technologies, current Augmented reality (AR) systems can effectively recognize multiple objects with different visual characteristics. However, only limited degrees of distinctions can be offered among different objects with similar natural features, and inherent information about these objects cannot be effectively extracted. In this paper, we propose TaggedAR, i.e., an RFID-based approach to assist the recognition of multiple tagged objects in AR systems, by deploying additional RFID antennas to the COTS depth camera. By sufficiently exploring the correlations between the depth of field and the received RF-signal, we propose a rotate scanning-based scheme to distinguish multiple tagged objects in the stationary situation, and propose a continuous scanning-based scheme to distinguish multiple tagged human subjects in the mobile situation. By pairing the tags with the objects according to the correlations between the depth of field and RF-signals, we can accurately identify and distinguish multiple tagged objects to realize the vision of “tell me what I see” from the AR system. We have implemented a prototype system to evaluate the actual performance with case studies in a real-world environment. The experiment results show that our solution achieves an average match ratio of 91 percent in distinguishing up to dozens of tagged objects with a high deployment density.

The human-computer interactions have moved from the conventional approaches of entering inputs into the keyboards/touchpads to the brand-new approaches of performing interactions in the air. In this paper, we propose RF-glove, a system that recognizes concurrent multiple finger micromovement using RF signals, so as to realize the vision of “multi-touch in the air.” It uses a commercial-off-the-shelf (COTS) RFID reader with three antennas and five COTS tags attached to the five fingers of a glove, one tag per finger. During the process of a user performing finger micromovements, we let the RFID reader continuously interrogate these tags and obtain the backscattered RF signals from each tag. For each antenna-tag pair, the reader obtains a sequence of RF phase values called a phase profile from the tag's responses over time. To tradeoff between accuracy and robustness in terms of matching resolution, we propose a two phase approach, including coarse-grained filtering and fine-grained matching. To tackle the variation of template phase profiles at different positions, we propose a phase-model-based solution to reconstruct the template phase profiles based on the exact locations. Experiment results show that we achieve an average accuracy of 92.1% under various moving speeds, orientation deviations, and so on.

Nowadays, people usually depend on augmented reality (AR) systems to obtain an augmented view in a real-world environment. With the help of advanced AR technology (e.g. object recognition), users can effectively distinguish multiple objects of different types. However, these techniques can only offer limited degrees of distinctions among different objects and cannot provide more inherent information about these objects. In this paper, we leverage RFID technology to further label different objects with RFID tags. We deploy additional RFID antennas to the COTS depth camera and propose a continuous scanning-based scheme to scan the objects, i.e., the system continuously rotates and samples the depth of field and RF-signals from these tagged objects. In this way, by pairing the tags with the objects according to the correlations between the depth of field and RF-signals, we can accurately identify and distinguish multiple tagged objects to realize the vision of "tell me what I see" from the augmented reality system. For example, in front of multiple unknown people wearing RFID tagged badges in public events, our system can identify these people and further show their inherent information from the RFID tags, such as their names, jobs, titles, etc. We have implemented a prototype system to evaluate the actual performance. The experiment results show that our solution achieves an average match ratio of 91% in distinguishing up to dozens of tagged objects with a high deployment density.

In this paper, we leverage RFID technology to label different objects with RFID tags, so as to realize the vision of "show me what I see from the augmented reality system". We deploy additional RFID antennas to the COTS depth camera and propose a continuous scanning-based scheme to scan the objects, i.e., the system continuously rotates and samples the depth of field and RF-signals from these tagged objects. In this way, we can accurately identify and distinguish multiple tagged objects, by pairing the tags with the objects according to the correlations between the depth of field and RF-signals. Our solution achieves an average match ratio of 91% in distinguishing up to dozens of tagged objects with a high deployment density.

BACKGROUND: RNA-seq is a powerful tool for measuring transcriptomes, especially for identifying differentially expressed genes or transcripts (DEGs) between sample groups. A number of methods have been developed for this task, and several evaluation studies have also been reported. However, those evaluations so far have been restricted to two-group comparisons. Accumulations of comparative studies for multi-group data are also desired. METHODS: We compare 12 pipelines available in nine R packages for detecting differential expressions (DE) from multi-group RNA-seq count data, focusing on three-group data with or without replicates. We evaluate those pipelines on the basis of both simulation data and real count data. RESULTS: As a result, the pipelines in the TCC package performed comparably to or better than other pipelines under various simulation scenarios. TCC implements a multi-step normalization strategy (called DEGES) that internally uses functions provided by other representative packages (edgeR, DESeq2, and so on). We found considerably different numbers of identified DEGs (18.5 ~ 45.7% of all genes) among the pipelines for the same real dataset but similar distributions of the classified expression patterns. We also found that DE results can roughly be estimated by the hierarchical dendrogram of sample clustering for the raw count data. CONCLUSION: We confirmed the DEGES-based pipelines implemented in TCC performed well in a three-group comparison as well as a two-group comparison. We recommend using the DEGES-based pipeline that internally uses edgeR (here called the EEE-E pipeline) for count data with replicates (especially for small sample sizes). For data without replicates, the DEGES-based pipeline with DESeq2 (called SSS-S) can be recommended.

BACKGROUND: Differential expression analysis based on "next-generation" sequencing technologies is a fundamental means of studying RNA expression. We recently developed a multi-step normalization method (called TbT) for two-group RNA-seq data with replicates and demonstrated that the statistical methods available in four R packages (edgeR, DESeq, baySeq, and NBPSeq) together with TbT can produce a well-ranked gene list in which true differentially expressed genes (DEGs) are top-ranked and non-DEGs are bottom ranked. However, the advantages of the current TbT method come at the cost of a huge computation time. Moreover, the R packages did not have normalization methods based on such a multi-step strategy. RESULTS: TCC (an acronym for Tag Count Comparison) is an R package that provides a series of functions for differential expression analysis of tag count data. The package incorporates multi-step normalization methods, whose strategy is to remove potential DEGs before performing the data normalization. The normalization function based on this DEG elimination strategy (DEGES) includes (i) the original TbT method based on DEGES for two-group data with or without replicates, (ii) much faster methods for two-group data with or without replicates, and (iii) methods for multi-group comparison. TCC provides a simple unified interface to perform such analyses with combinations of functions provided by edgeR, DESeq, and baySeq. Additionally, a function for generating simulation data under various conditions and alternative DEGES procedures consisting of functions in the existing packages are provided. Bioinformatics scientists can use TCC to evaluate their methods, and biologists familiar with other R packages can easily learn what is done in TCC. CONCLUSION: DEGES in TCC is essential for accurate normalization of tag count data, especially when up- and down-regulated DEGs in one of the samples are extremely biased in their number. TCC is useful for analyzing tag count data in various scenarios ranging from unbiased to extremely biased differential expression. TCC is available at http://www.iu.a.u-tokyo.ac.jp/~kadota/TCC/ and will appear in Bioconductor (http://bioconductor.org/) from ver. 2.13.