Zero-Shot Fault Diagnosis for Smart Process Manufacturing via Tensor Prototype Alignment.

Identifying unseen faults is a crux of the digital transformation of process manufacturing. The ever-changing manufacturing process requires preset models to cope with unseen problems. However, most current works focus on recognizing objects seen during the training phase. Conventional zero-shot recognition methods perform poorly when they are applied directly to these tasks due to the different scenarios and limited generalizability. This article yields a tensor-based zero-shot fault diagnosis framework, termed MetaEvolver, which is dedicated to improving fault diagnosis accuracy and unseen domain generalizability for practical process manufacturing scenarios. MetaEvolver learns to evolve the dual prototype distributions for each uncertain meta-domain from seen faults and then adapt to unseen faults. We first propose the concept of the uncertain meta-domain and then construct corresponding sample prototypes with the guidance of class-level attributes, which produce the sample-attribute alignment at the prototype level. MetaEvolver further collaboratively evolves the uncertain meta-domain dual prototypes by injecting the prototype distribution information of another modality, boosting the sample-attribute alignment at the distribution level. Building on the uncertain meta-domain strategy, MetaEvolver is prone to achieving knowledge transferring and unseen domain generalization with the optimization of several devised loss functions. Comprehensive experimental results on five process manufacturing data groups and five zero-shot benchmarks demonstrate that our MetaEvolver has great superiority and potential to tackle zero-shot fault diagnosis for smart process manufacturing.

Industrial Metaverse for Smart Manufacturing: Model, Architecture, and Applications.

Smart manufacturing has been transforming toward industrial digitalization integrated with various advanced technologies. Metaverse has been evolving as a next-generation paradigm of a digital space extended and augmented by reality. In the metaverse, users are interconnected for various virtual activities. In consideration of advanced possibilities that may be brought by the metaverse, it is envisioned that industrial metaverse should be integrated into smart manufacturing to upgrade industry for more visible, intelligent and efficient production in the future. Therefore, a conceptual model, named IMverse Model, and novel characteristics of the industrial metaverse for smart manufacturing are proposed in this article. Besides, an industrial metaverse architecture, named IMverse Architecture, is proposed involving several key enabling technologies. Typical innovative applications of the industrial metaverse throughout the whole product life cycle for smart manufacturing are presented with insights. Nonetheless, in prospect of future, the industrial metaverse still faces limitations and is far from implementation. Thus, challenges and open issues of the industrial metaverse for smart manufacturing are discussed, then outlook is provided for further research and application.

StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses.

Generalist microbes have adapted to a multitude of environmental stresses through their integrated stress response system. Individual stress responses have been quantified by E. coli metabolism and expression (ME) models under thermal, oxidative and acid stress, respectively. However, the systematic quantification of cross-stress & cross-talk among these stress responses remains lacking. Here, we present StressME: the unified stress response model of E. coli combining thermal (FoldME), oxidative (OxidizeME) and acid (AcidifyME) stress responses. StressME is the most up to date ME model for E. coli and it reproduces all published single-stress ME models. Additionally, it includes refined rate constants to improve prediction accuracy for wild-type and stress-evolved strains. StressME revealed certain optimal proteome allocation strategies associated with cross-stress and cross-talk responses. These stress-optimal proteomes were shaped by trade-offs between protective vs. metabolic enzymes; cytoplasmic vs. periplasmic chaperones; and expression of stress-specific proteins. As StressME is tuned to compute metabolic and gene expression responses under mild acid, oxidative, and thermal stresses, it is useful for engineering and health applications. The modular design of our open-source package also facilitates model expansion (e.g., to new stress mechanisms) by the computational biology community.

A Lightweight Group Transformer-Based Time Series Reduction Network for Edge Intelligence and Its Application in Industrial RUL Prediction.

Recently, deep learning-based models such as transformer have achieved significant performance for industrial remaining useful life (RUL) prediction due to their strong representation ability. In many industrial practices, RUL prediction algorithms are deployed on edge devices for real-time response. However, the high computational cost of deep learning models makes it difficult to meet the requirements of edge intelligence. In this article, a lightweight group transformer with multihierarchy time-series reduction (GT-MRNet) is proposed to alleviate this problem. Different from most existing RUL methods computing all time series, GT-MRNet can adaptively select necessary time steps to compute the RUL. First, a lightweight group transformer is constructed to extract features by employing group linear transformation with significantly fewer parameters. Then, a time-series reduction strategy is proposed to adaptively filter out unimportant time steps at each layer. Finally, a multihierarchy learning mechanism is developed to further stabilize the performance of time-series reduction. Extensive experimental results on the real-world condition datasets demonstrate that the proposed method can significantly reduce up to 74.7% parameters and 91.8% computation cost without sacrificing accuracy.

Lightweight Authentication Scheme for IoT based E-Healthcare Service Communication.

Remote Patient Monitoring (RPM) using Electronic Healthcare (E-health) is a growing phenomenon enabling doctors predict patient health such as possible cardiac arrests from identified abnormal arrythmia. Remote Patient Monitoring enables healthcare staff to notify patients with preventive measures to avoid a medical emergency reducing patient stress. However weak authentication security protocols in IoT wearables such as pacemakers, enable cyberattacks to transmit corrupt data, preventing patients from receiving medical care. In this paper we focus on the security of wearable devices for reliable healthcare services and propose a Lightweight Key Agreement (LKA) based authentication scheme for securing Device-to-Device (D2D) communication. A Network Key Manager on the edge builds keys for each device for device validation. Device authentication requests are verified using certificates, reducing network communication costs. E-health empowered mobile devices are store authentication certificates for future seamless device validation. The LKA scheme is evaluated and compared with existing studies and exhibits reduced operation time for key generation operation costs and lower communication costs incurred during the execution of the device authentication protocol compared with other studies. The LKA scheme further exhibits reduced latency when compared with the three existing schemes due to reduced communication costs.

Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance.

Relationships between the genome, transcriptome, and metabolome underlie all evolved phenotypes. However, it has proved difficult to elucidate these relationships because of the high number of variables measured. A recently developed data analytic method for characterizing the transcriptome can simplify interpretation by grouping genes into independently modulated sets (iModulons). Here, we demonstrate how iModulons reveal deep understanding of the effects of causal mutations and metabolic rewiring. We use adaptive laboratory evolution to generate E. coli strains that tolerate high levels of the redox cycling compound paraquat, which produces reactive oxygen species (ROS). We combine resequencing, iModulons, and metabolic models to elucidate six interacting stress-tolerance mechanisms: (1) modification of transport, (2) activation of ROS stress responses, (3) use of ROS-sensitive iron regulation, (4) motility, (5) broad transcriptional reallocation toward growth, and (6) metabolic rewiring to decrease NADH production. This work thus demonstrates the power of iModulon knowledge mapping for evolution analysis.

Domain-Adaptive Graph Attention-Supervised Network for Cross-Network Edge Classification.

Graph neural networks (GNNs) have shown great ability in modeling graphs; however, their performance would significantly degrade when there are noisy edges connecting nodes from different classes. To alleviate negative effect of noisy edges on neighborhood aggregation, some recent GNNs propose to predict the label agreement between node pairs within a single network. However, predicting the label agreement of edges across different networks has not been investigated yet. Our work makes the pioneering attempt to study a novel problem of cross-network homophilous and heterophilous edge classification (CNHHEC) and proposes a novel domain-adaptive graph attention-supervised network (DGASN) to effectively tackle the CNHHEC problem. First, DGASN adopts multihead graph attention network (GAT) as the GNN encoder, which jointly trains node embeddings and edge embeddings via the node classification and edge classification losses. As a result, label-discriminative embeddings can be obtained to distinguish homophilous edges from heterophilous edges. In addition, DGASN applies direct supervision on graph attention learning based on the observed edge labels from the source network, thus lowering the negative effects of heterophilous edges while enlarging the positive effects of homophilous edges during neighborhood aggregation. To facilitate knowledge transfer across networks, DGASN employs adversarial domain adaptation to mitigate domain divergence. Extensive experiments on real-world benchmark datasets demonstrate that the proposed DGASN achieves the state-of-the-art performance in CNHHEC.

Tensor-Empowered Adaptive Learning for Few-Shot Streaming Tasks.

Various stream learning methods are emerging in an endless stream to provide a wealth of solutions for artificial intelligence in streaming data scenarios. However, when each data stream is oriented to a different target space, it forces stream learning approaches oriented to the same task to be no longer applicable. Due to inconsistent target spaces for different tasks, the previous approaches fail on the new streaming tasks or it is impracticable to be trained from scratch with few labeled samples at the beginning. To this end, we have proposed an adaptive learning scheme for few-shot streaming tasks with the contributions of tensor and meta-learning. This adaptive scheme is conducive to mitigating the domain shift when a new task has few labeled samples. We elaborate a novel tensor-empowered attention mechanism derived from nonlocal neural networks, which enables to capture long-range dependency and preserve the high-dimensional structure to refine the global features of streaming tasks. Furthermore, we develop a fine-grained similarity computing approach, which is prone to better characterize the difference across few-shot streaming tasks. To show the superiority of our method, we have carried out extensive experiments on three popular few-shot datasets to simulate streaming tasks and evaluate the performance of adaptation. The results show that our proposed method has achieved competitive performance for few-shot streaming tasks compared with the state-of-the-art (SOTA).

An Edge-cloud-aided Private High-order Fuzzy C-means Clustering Algorithm in Smart Healthcare.

Smart healthcare has emerged to provide healthcare services using data analysis techniques. Especially, clustering is playing an indispensable role in analyzing healthcare records. However, large multi-modal healthcare data imposes great challenges on clustering. Specifically, it is hard for traditional approaches to obtain desirable results for healthcare data clustering since they are not able to work for multi-modal data. This paper presents a new high-order multi-modal learning approach using multimodal deep learning and the Tucker decomposition (F- HoFCM). Furthermore, we propose an edge-cloud-aided private scheme to facilitate the clustering efficiency for its embedding in edge resources. Specifically, the computationally intensive tasks, such as parameter updating with high-order back propagation algorithm and clustering through high-order fuzzy c-means, are processed in a centralized location with cloud computing. The other tasks such as multi-modal data fusion and Tucker decomposition are performed at the edge resources. Since the feature fusion and Tucker decomposition are nonlinear operations, the cloud cannot obtain the raw data, thus protecting the privacy. Experimental results state that the presented approach produces significantly more accurate results than the existing high-order fuzzy c-means (HOFCM) on multi-modal healthcare datasets and furthermore the clustering efficiency are significantly improved by the developed edge-cloud-aided private healthcare system.

Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation.

Pseudomonas aeruginosa is one of the leading causes of hospital-acquired infections. To decipher the metabolic mechanisms associated with virulence and antibiotic resistance, we have developed an updated genome-scale model (GEM) of P. aeruginosa. The model (iSD1509) is an extensively curated, three-compartment, and mass-and-charge balanced BiGG model containing 1509 genes, the largest gene content for any P. aeruginosa GEM to date. It is the most accurate with prediction accuracies as high as 92.4% (gene essentiality) and 93.5% (substrate utilization). In iSD1509, we newly added a recently discovered pathway for ubiquinone-9 biosynthesis which is required for anaerobic growth. We used a modified iSD1509 to demonstrate the role of virulence factor (phenazines) in the pathogen survival within biofilm/oxygen-limited condition. Further, the model can mechanistically explain the overproduction of a drug susceptibility biomarker in the P. aeruginosa mutants. Finally, we use iSD1509 to demonstrate the drug potentiation by metabolite supplementation, and elucidate the mechanisms behind the phenotype, which agree with experimental results.

Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli.

The establishment of experimental conditions for transcriptional regulator network (TRN) reconstruction in bacteria continues to be impeded by the limited knowledge of activating conditions for transcription factors (TFs). Here, we present a novel genome-scale model-driven workflow for designing experimental conditions, which optimally activate specific TFs. Our model-driven workflow was applied to elucidate transcriptional regulation under nitrogen limitation by Nac and NtrC, in Escherichia coli. We comprehensively predict alternative nitrogen sources, including cytosine and cytidine, which trigger differential activation of Nac using a model-driven workflow. In accordance with the prediction, genome-wide measurements with ChIP-exo and RNA-seq were performed. Integrative data analysis reveals that the Nac and NtrC regulons consist of 97 and 43 genes under alternative nitrogen conditions, respectively. Functional analysis of Nac at the transcriptional level showed that Nac directly down-regulates amino acid biosynthesis and restores expression of tricarboxylic acid (TCA) cycle genes to alleviate nitrogen-limiting stress. We also demonstrate that both TFs coherently modulate α-ketoglutarate accumulation stress due to nitrogen limitation by co-activating amino acid and diamine degradation pathways. A systems-biology approach provided a detailed and quantitative understanding of both TF's roles and how nitrogen and carbon metabolic networks respond complementarily to nitrogen-limiting stress.

Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii.

Gene expression data of cell cultures is commonly measured in biological and medical studies to understand cellular decision-making in various conditions. Metabolism, affected but not solely determined by the expression, is much more difficult to measure experimentally. Finding a reliable method to predict cell metabolism for expression data will greatly benefit metabolic engineering. We have developed a novel pipeline, OVERLAY, that can explore cellular fluxomics from expression data using only a high-quality genome-scale metabolic model. This is done through two main steps: first, construct a protein-constrained metabolic model (PC-model) by integrating protein and enzyme information into the metabolic model (M-model). Secondly, overlay the expression data onto the PC-model using a novel two-step nonconvex and convex optimization formulation, resulting in a context-specific PC-model with optionally calibrated rate constants. The resulting model computes proteomes and intracellular flux states that are consistent with the measured transcriptomes. Therefore, it provides detailed cellular insights that are difficult to glean individually from the omic data or M-model alone. We apply the OVERLAY to interpret triacylglycerol (TAG) overproduction by Chlamydomonas reinhardtii, using time-course RNA-Seq data. We show that OVERLAY can compute C. reinhardtii metabolism under nitrogen deprivation and metabolic shifts after an acetate boost. OVERLAY can also suggest possible 'bottleneck' proteins that need to be overexpressed to increase the TAG accumulation rate, as well as discuss other TAG-overproduction strategies.

QTT-DLSTM: A Cloud-Edge-Aided Distributed LSTM for Cyber-Physical-Social Big Data.

Cyber-physical-social systems (CPSS), an emerging cross-disciplinary research area, combines cyber-physical systems (CPS) with social networking for the purpose of providing personalized services for humans. CPSS big data, recording various aspects of human lives, should be processed to mine valuable information for CPSS services. To efficiently deal with CPSS big data, artificial intelligence (AI), an increasingly important technology, is used for CPSS data processing and analysis. Meanwhile, the rapid development of edge devices with fast processors and large memories allows local edge computing to be a powerful real-time complement to global cloud computing. Therefore, to facilitate the processing and analysis of CPSS big data from the perspective of multi-attributes, a cloud-edge-aided quantized tensor-train distributed long short-term memory (QTT-DLSTM) method is presented in this article. First, a tensor is used to represent the multi-attributes CPSS big data, which will be decomposed into the QTT form to facilitate distributed training and computing. Second, a distributed cloud-edge computing model is used to systematically process the CPSS data, including global large-scale data processing in the cloud, and local small-scale data processed at the edge. Third, a distributed computing strategy is used to improve the efficiency of training via partitioning the weight matrix and large amounts of input data in the QTT form. Finally, the performance of the proposed QTT-DLSTM method is evaluated using experiments on a public discrete manufacturing process dataset, the Li-ion battery dataset, and a public social dataset.

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth.

Sustaining a robust metabolic network requires a balanced and fully functioning proteome. In addition to amino acids, many enzymes require cofactors (coenzymes and engrafted prosthetic groups) to function properly. Extensively validated resource allocation models, such as genome-scale models of metabolism and gene expression (ME-models), have the ability to compute an optimal proteome composition underlying a metabolic phenotype, including the provision of all required cofactors. Here we apply the ME-model for Escherichia coli K-12 MG1655 to computationally examine how environmental conditions change the proteome and its accompanying cofactor usage. We found that: (1) The cofactor requirements computed by the ME-model mostly agree with the standard biomass objective function used in models of metabolism alone (M-models); (2) ME-model computations reveal non-intuitive variability in cofactor use under different growth conditions; (3) An analysis of ME-model predicted protein use in aerobic and anaerobic conditions suggests an enrichment in the use of peroxyl scavenging acids in the proteins used to sustain aerobic growth; (4) The ME-model could describe how limitation in key protein components affect the metabolic state of E. coli. Genome-scale models have thus reached a level of sophistication where they reveal intricate properties of functional proteomes and how they support different E. coli lifestyles.

Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications.

Pyruvate dehydrogenase complex (PDC) functions as the main determinant of the respiro-fermentative balance because it converts pyruvate to acetyl-coenzyme A (CoA), which then enters the TCA (tricarboxylic acid cycle). PDC is repressed by the pyruvate dehydrogenase complex regulator (PdhR) in Escherichia coli. The deletion of the pdhR gene compromises fitness in aerobic environments. We evolve the E. coli pdhR deletion strain to examine its achievable growth rate and the underlying adaptive strategies. We find that (1) optimal proteome allocation to PDC is critical in achieving optimal growth rate; (2) expression of PDC in evolved strains is reduced through mutations in the Shine-Dalgarno sequence; (3) rewiring of the TCA flux and increased reactive oxygen species (ROS) defense occur in the evolved strains; and (4) the evolved strains adapt to an efficient biomass yield. Together, these results show how adaptation can find alternative regulatory mechanisms for a key cellular process if the primary regulatory mode fails.

A Unified Smart Chinese Medicine Framework for Healthcare and Medical Services.

Smart Chinese medicine has emerged to contribute to the evolution of healthcare and medical services by applying machine learning together with advanced computing techniques like cloud computing to computer-aided diagnosis and treatment in the health engineering and informatics. Specifically, smart Chinese medicine is considered to have the potential to treat difficult and complicated diseases such as diabetes and cancers. Unfortunately, smart Chinese medicine has made very limited progress in the past few years. In this paper, we present a unified smart Chinese medicine framework based on the edge-cloud computing system. The objective of the framework is to achieve computer-aided syndrome differentiation and prescription recommendation, and thus to provide pervasive, personalized, and patient-centralized services in healthcare and medicine. To accomplish this objective, we integrate deep learning and deep reinforcement learning into the traditional Chinese medicine. Furthermore, we propose a multi-modal deep computation model for syndrome recognition that is a crucial part of syndrome differentiation. Finally, we conduct experiments to validate the proposed model by comparing with the staked auto-encoder and multi-modal deep learning model for syndrome recognition of hypertension and cold.

Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models.

Omic technologies have enabled the complete readout of the molecular state of a cell at different biological scales. In principle, the combination of multiple omic data types can provide an integrated view of the entire biological system. This integration requires appropriate models in a systems biology approach. Here, genome-scale models (GEMs) are focused upon as one computational systems biology approach for interpreting and integrating multi-omic data. GEMs convert the reactions (related to metabolism, transcription, and translation) that occur in an organism to a mathematical formulation that can be modeled using optimization principles. A variety of genome-scale modeling methods used to interpret multiple omic data types, including genomics, transcriptomics, proteomics, metabolomics, and meta-omics are reviewed. The ability to interpret omics in the context of biological systems has yielded important findings for human health, environmental biotechnology, bioenergy, and metabolic engineering. The authors find that concurrent with advancements in omic technologies, genome-scale modeling methods are also expanding to enable better interpretation of omic data. Therefore, continued synthesis of valuable knowledge, through the integration of omic data with GEMs, are expected.

A Wide-Deep-Sequence Model-Based Quality Prediction Method in Industrial Process Analysis.

Product quality prediction, as an important issue of industrial intelligence, is a typical task of industrial process analysis, in which product quality will be evaluated and improved as feedback for industrial process adjustment. Data-driven methods, with predictive model to analyze various industrial data, have been received considerable attention in recent years. However, to get an accurate prediction, it is an essential issue to extract quality features from industrial data, including several variables generated from supply chain and time-variant machining process. In this article, a data-driven method based on wide-deep-sequence (WDS) model is proposed to provide a reliable quality prediction for industrial process with different types of industrial data. To process industrial data of high redundancy, in this article, data reduction is first conducted on different variables by different techniques. Also, an improved wide-deep (WD) model is proposed to extract quality features from key time-invariant variables. Meanwhile, an long short-term memory (LSTM)-based sequence model is presented for exploring quality information from time-domain features. Under the joint training strategy, these models will be combined and optimized by a designed penalty mechanism for unreliable predictions, especially on reduction of defective products. Finally, experiments on a real-world manufacturing process data set are carried out to present the effectiveness of the proposed method in product quality prediction.