Detection of cell-cyclic elements in mis-sampled gene expression data using a robust Capon estimator

We present a method for the estimation of possible cell cyclic elements in mis-sampled microarray data. Accurate assessment of the frequency content of microarray data gives insight into genes which could be cell-cycle regulated. Cell cycle regulation is one component of the complex network of genetic regulatory processes and is especially relevant to the study of cancer. As cDNA microarray experiments involve human sampling of cell populations, slight variations in the sampling times invariably occur. Here, we propose estimating the frequency content of microarray data using the recent robust Capon estimator, and formulate a suitable uncertainty region to minimize over. The estimator is shown to yield robust estimates with real microarray data and to identify cell-cyclic genes that elude both the traditional Periodogram and the Capon spectral estimator

Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study

Time series microarray measurements of gene expressions have been exploited to discover genes involved in cell cycles. Due to experimental constraints, most microarray observations are obtained through irregular sampling. In this paper three popular spectral analysis schemes, namely, Lomb-Scargle, Capon and missing-data amplitude and phase estimation (MAPES), are compared in terms of their ability and efficiency to recover periodically expressed genes. Based on in silico experiments for microarray measurements of Saccharomyces cerevisiae, Lomb-Scargle is found to be the most efficacious scheme. 149 genes are then identified to be periodically expressed in the Drosophila melanogaster data set

Signal processing techniques for the interpretation of microarray measurements

Microarray technology allows the measurement of gene transcription on a genome wide scale. Signal processing approaches to the analysis of data from microarray time course experiments are the focus of this thesis. Firstly, spectral estimation methods are explored as a method for the detection of cell-cyclic elements within microarray data. High resolution data-dependent filterbank methods are proposed as an improvement to the traditional periodogram approach. A spectral estimator is then designed specifically to deal with the errors in the sampling times inherent in microarray experiments, which is based on the robust Capon beamformer. A beamforming inspired approach is shown to yield a more robust, and higher resolution, estimate of the magnitude spectrum of the whole data set than the previous spectral estimation approaches. Blind source separation is examined as a method for recovering sources which represent fundamental cellular processes. The linear mixing model is compared to its transpose form, and a dual form, in terms of their finite sample performance with real microarray data. Second order methods are proposed to recover sources which are spatio-temporally uncorrelated and may be more suitable with microarray data. Both the spectral and blind source separation techniques are shown to yield useful feature extraction measures for microarray data clustering. The spectral feature extraction allows the clustering of cell-cyclic genes into a single functional group. Finally, sparse source separation is introduced as a possible blind separation technique with microarray data

Comparative Performance Analysis of the Algorithms for Detecting Periodically Expressed Genes

Thus far, a plethora of analysis on genome-wide gene expression microarray experiments on the cell cycle have been reported. Time series data from these experiments include gene expression profiles that might be periodically expressed. However, the numbers and actual genes that are periodically expressed have not been reported with consistency, analysis on similar experiments reports disparate numbers of genes that are periodically expressed with scant overlap. This work ultimately compares the performance of five spectral estimation schemes in their ability to recover periodically expressed genes profiles. Lomb-Scargle (LS), Capon, Missing-Data Amplitude and Phase Estimation (MAPES), Real Value Iterative Adaptive Approach (RIAA) and Lomb-Scargle Periodogram Regression (LSPR) are rigorously studied and pitted against each other in various simulated testing conditions. Results obtained using synthetic and microarray data reveals that RIAA is an efficient and robust method for the detection of periodically expressed genes in short time series data that might be characterized with noisy and irregularly sampled data points

Genomic applications of statistical signal processing

Biological phenomena in the cells can be explained in terms of the interactions among biological macro-molecules, e.g., DNAs, RNAs and proteins. These interactions can be modeled by genetic regulatory networks (GRNs). This dissertation proposes to reverse engineering the GRNs based on heterogeneous biological data sets, including time-series and time-independent gene expressions, Chromatin ImmunoPrecipatation (ChIP) data, gene sequence and motifs and other possible sources of knowledge. The objective of this research is to propose novel computational methods to catch pace with the fast evolving biological databases. Signal processing techniques are exploited to develop computationally efficient, accurate and robust algorithms, which deal individually or collectively with various data sets. Methods of power spectral density estimation are discussed to identify genes participating in various biological processes. Information theoretic methods are applied for non-parametric inference. Bayesian methods are adopted to incorporate several sources with prior knowledge. This work aims to construct an inference system which takes into account different sources of information such that the absence of some components will not interfere with the rest of the system. It has been verified that the proposed algorithms achieve better inference accuracy and higher computational efficiency compared with other state-of-the-art schemes, e.g. REVEAL, ARACNE, Bayesian Networks and Relevance Networks, at presence of artificial time series and steady state microarray measurements. The proposed algorithms are especially appealing when the the sample size is small. Besides, they are able to integrate multiple heterogeneous data sources, e.g. ChIP and sequence data, so that a unified GRN can be inferred. The analysis of biological literature and in silico experiments on real data sets for fruit fly, yeast and human have corroborated part of the inferred GRN. The research has also produced a set of potential control targets for designing gene therapy strategies

OFDM passive radar employing compressive processing in MIMO configurations

A key advantage of passive radar is that it provides a means of performing position detection and tracking without the need for transmission of energy pulses. In this respect, passive radar systems utilising (receiving) orthogonal frequency division multiplexing (OFDM) communications signals from transmitters using OFDM standards such as long term evolution (LTE), WiMax or WiFi, are considered. Receiving a stronger reference signal for the matched filtering, detecting a lower target signature is one of the challenges in the passive radar. Impinging at the receiver, the OFDM waveforms supply two-dimensional virtual uniform rectangul ararray with the first and second dimensions refer to time delays and Doppler frequencies respectively. A subspace method, multiple signals classification (MUSIC) algorithm, demonstrated the signal extraction using multiple time samples. Apply normal measurements, this problem requires high computational resources regarding the number of OFDM subcarriers. For sub-Nyquist sampling, compressive sensing (CS) becomes attractive. A single snap shot measurement can be applied with Basis Pursuit (BP), whereas l1-singular value decomposition (l1-SVD) is applied for the multiple snapshots. Employing multiple transmitters, the diversity in the detection process can be achieved. While a passive means of attaining three-dimensional large-set measurements is provided by co-located receivers, there is a significant computational burden in terms of the on-line analysis of such data sets. In this thesis, the passive radar problem is presented as a mathematically sparse problem and interesting solutions, BP and l1-SVD as well as Bayesian compressive sensing, fast-Besselk, are considered. To increase the possibility of target signal detection, beamforming in the compressive domain is also introduced with the application of conve xoptimization and subspace orthogonality. An interference study is also another problem when reconstructing the target signal. The networks of passive radars are employed using stochastic geometry in order to understand the characteristics of interference, and the effect of signal to interference plus noise ratio (SINR). The results demonstrate the outstanding performance of l1-SVD over MUSIC when employing multiple snapshots. The single snapshot problem along with fast-BesselK multiple-input multiple-output configuration can be solved using fast-BesselK and this allows the compressive beamforming for detection capability

Molecular Techniques Reveal Wide Phyletic Diversity of Heterotrophic Microbes Associated with Discodermia spp. (Porifera: Demospongiae)

Sponges are well known to harbor large numbers of heterotrophic microbes within their mesohyl. Studies to determine the diversity of these associated microbes have been attempted for only a few shallow water species. We cultured various microorganisms from several species of Discodermia collected from deep water using the \u27Johnson-Sea-Link\u27 manned submersibles, and characterised them by standard microbiological identification methods. Characterisation of a small proportion (ca. 10%) of the total and potential eubacterial isolate collection with molecular systematics techniques revealed a wide diversity of microbes. Phylogenetic analyses of 32 small subunit (SSU) 16S-like rRNA gene sequences from different micorbes indicated high levels of taxonomic diversity assoiated with this genus of sponge. For example, bacteria from at least five cubacterial subdivisions - gamma, alpha, beta, Cytophaga and Gram positive - were isolated from the mesohyl of Discodermia. Several strains were unidentifiable from current sequence databases. No overlap was found between sequences of 24 isolates and 8 sequences obtained by PCR and cloning directly from sponge samples. The abundance and diversity of microbes associated with sponges such as Discodermia suggest that they may play important roles in marine microbial ecology, dispersal and evolution

Lack of Chemical Defense in Two Species of Stalked Crinoids: Support for the Predation Hypothesis for Mesozoic Bathymetric Restriction

Methanol/dichloromethane extracts of (1) the arms and pinnules, and (2) the stalk and cirri of the deep water stalked crinoids Endoxocrinus parrae (Gervais) and Neocrinus decorus (Carpenter) were imbedded at ecologically relevant volumetric concentrations in alginate food pellets containing 2% krill as a feeding stimulant and presented in situ to an assemblage of shallow-water reef fish. Experimental pellets were highly palatable to reef fish; no significant differences in pellet consumption occurred between experimental pellets containing extracts from either species of stalked crinoid or control pellets. Small pieces of cirri, stalks, calyx, arms and pinnules of both species were also tested in in situ feeding assays. While immediate consumption by fish was not apparent, Blue Headed Wrasse (Thalassoma bifasciatum (Block)) and Dusky Damselfish (Stegastes fuscus (Cuvier)) bit at pieces of each body component. Similar fish biting behaviors were also observed when two living Endoxocrinus parrae were deployed on the shallow reef. Observations indicate that neither species of stalked crinoid is chemically defended from predation by a natural assemblage of reef fish. This supports the predation hypothesis that restriction of stalked crinoids in deep-water habitats may have resulted from the Mesozoic radiation of durophagous fishes in shallow seas, resulting in a reduction of stalked crinoids from shallow water

GNSS array-based acquisition: theory and implementation

This Dissertation addresses the signal acquisition problem using antenna arrays in the general framework of Global Navigation Satellite Systems (GNSS) receivers. The term GNSS classi es those navigation systems based on a constellation of satellites, which emit ranging signals useful for positioning. Although the American GPS is already available, which coexists with the renewed Russian Glonass, the forthcoming European contribution (Galileo) along with the Chinese Compass will be operative soon. Therefore, a variety of satellite constellations and signals will be available in the next years. GNSSs provide the necessary infrastructures for a myriad of applications and services that demand a robust and accurate positioning service. The positioning availability must be guaranteed all the time, specially in safety-critical and mission-critical services. Examining the threats against the service availability, it is important to take into account that all the present and the forthcoming GNSSs make use of Code Division Multiple Access (CDMA) techniques. The ranging signals are received with very low precorrelation signal-to-noise ratio (in the order of ���22 dB for a receiver operating at the Earth surface). Despite that the GNSS CDMA processing gain o ers limited protection against Radio Frequency interferences (RFI), an interference with a interference-to-signal power ratio that exceeds the processing gain can easily degrade receivers' performance or even deny completely the GNSS service, specially conventional receivers equipped with minimal or basic level of protection towards RFIs. As a consequence, RFIs (either intentional or unintentional) remain as the most important cause of performance degradation. A growing concern of this problem has appeared in recent times. Focusing our attention on the GNSS receiver, it is known that signal acquisition has the lowest sensitivity of the whole receiver operation, and, consequently, it becomes the performance bottleneck in the presence of interfering signals. A single-antenna receiver can make use of time and frequency diversity to mitigate interferences, even though the performance of these techniques is compromised in low SNR scenarios or in the presence of wideband interferences. On the other hand, antenna arrays receivers can bene t from spatial-domain processing, and thus mitigate the e ects of interfering signals. Spatial diversity has been traditionally applied to the signal tracking operation of GNSS receivers. However, initial tracking conditions depend on signal acquisition, and there are a number of scenarios in which the acquisition process can fail as stated before. Surprisingly, to the best of our knowledge, the application of antenna arrays to GNSS signal acquisition has not received much attention. This Thesis pursues a twofold objective: on the one hand, it proposes novel arraybased acquisition algorithms using a well-established statistical detection theory framework, and on the other hand demonstrates both their real-time implementation feasibility and their performance in realistic scenarios. The Dissertation starts with a brief introduction to GNSS receivers fundamentals, providing some details about the navigation signals structure and the receiver's architecture of both GPS and Galileo systems. It follows with an analysis of GNSS signal acquisition as a detection problem, using the Neyman-Pearson (NP) detection theory framework and the single-antenna acquisition signal model. The NP approach is used here to derive both the optimum detector (known as clairvoyant detector ) and the sov called Generalized Likelihood Ratio Test (GLRT) detector, which is the basis of almost all of the current state-of-the-art acquisition algorithms. Going further, a novel detector test statistic intended to jointly acquire a set of GNSS satellites is obtained, thus reducing both the acquisition time and the required computational resources. The eff ects of the front-end bandwidth in the acquisition are also taken into account. Then, the GLRT is extended to the array signal model to obtain an original detector which is able to mitigate temporally uncorrelated interferences even if the array is unstructured and moderately uncalibrated, thus becoming one of the main contributions of this Dissertation. The key statistical feature is the assumption of an arbitrary and unknown covariance noise matrix, which attempts to capture the statistical behavior of the interferences and other non-desirable signals, while exploiting the spatial dimension provided by antenna arrays. Closed form expressions for the detection and false alarm probabilities are provided. Performance and interference rejection capability are modeled and compared both to their theoretical bound. The proposed array-based acquisition algorithm is also compared to conventional acquisition techniques performed after blind null-steering beamformer approaches, such as the power minimization algorithm. Furthermore, the detector is analyzed under realistic conditions, accounting for the presence of errors in the covariance matrix estimation, residual Doppler and delay errors, and signal quantization e ects. Theoretical results are supported by Monte Carlo simulations. As another main contribution of this Dissertation, the second part of the work deals with the design and the implementation of a novel Field Programmable Gate Array (FPGA)-based GNSS real-time antenna-array receiver platform. The platform is intended to be used as a research tool tightly coupled with software de ned GNSS receivers. A complete signal reception chain including the antenna array and the multichannel phase-coherent RF front-end for the GPS L1/ Galileo E1 was designed, implemented and tested. The details of the digital processing section of the platform, such as the array signal statistics extraction modules, are also provided. The design trade-o s and the implementation complexities were carefully analyzed and taken into account. As a proof-of-concept, the problem of GNSS vulnerability to interferences was addressed using the presented platform. The array-based acquisition algorithms introduced in this Dissertation were implemented and tested under realistic conditions. The performance of the algorithms were compared to single antenna acquisition techniques, measured under strong in-band interference scenarios, including narrow/wide band interferers and communication signals. The platform was designed to demonstrate the implementation feasibility of novel array-based acquisition algorithms, leaving the rest of the receiver operations (mainly, tracking, navigation message decoding, code and phase observables, and basic Position, Velocity and Time (PVT) solution) to a Software De ned Radio (SDR) receiver running in a personal computer, processing in real-time the spatially- ltered signal sample stream coming from the platform using a Gigabit Ethernet bus data link. In the last part of this Dissertation, we close the loop by designing and implementing such software receiver. The proposed software receiver targets multi-constellation/multi-frequency architectures, pursuing the goals of e ciency, modularity, interoperability, and exibility demanded by user domains that require non-standard features, such as intermediate signals or data extraction and algorithms interchangeability. In this context, we introduce an open-source, real-time GNSS software de ned receiver (so-named GNSS-SDR) that contributes with several novel features such as the use of software design patterns and shared memory techniques to manage e ciently the data ow between receiver blocks, the use of hardware-accelerated instructions for time-consuming vector operations like carrier wipe-o and code correlation, and the availability to compile and run on multiple software platforms and hardware architectures. At this time of writing (April 2012), the receiver enjoys of a 2-dimensional Distance Root Mean Square (DRMS) error lower than 2 meters for a GPS L1 C/A scenario with 8 satellites in lock and a Horizontal Dilution Of Precision (HDOP) of 1.2.Esta tesis aborda el problema de la adquisición de la señal usando arrays de antenas en el marco general de los receptores de Sistemas Globales de Navegación por Satélite (GNSS). El término GNSS engloba aquellos sistemas de navegación basados en una constelación de satélites que emiten señales útiles para el posicionamiento. Aunque el GPS americano ya está disponible, coexistiendo con el renovado sistema ruso GLONASS, actualmente se está realizando un gran esfuerzo para que la contribución europea (Galileo), junto con el nuevo sistema chino Compass, estén operativos en breve. Por lo tanto, una gran variedad de constelaciones de satélites y señales estarán disponibles en los próximos años. Estos sistemas proporcionan las infraestructuras necesarias para una multitud de aplicaciones y servicios que demandan un servicio de posicionamiento confiable y preciso. La disponibilidad de posicionamiento se debe garantizar en todo momento, especialmente en los servicios críticos para la seguridad de las personas y los bienes. Cuando examinamos las amenazas de la disponibilidad del servicio que ofrecen los GNSSs, es importante tener en cuenta que todos los sistemas presentes y los sistemas futuros ya planificados hacen uso de técnicas de multiplexación por división de código (CDMA). Las señales transmitidas por los satélites son recibidas con una relación señal-ruido (SNR) muy baja, medida antes de la correlación (del orden de -22 dB para un receptor ubicado en la superficie de la tierra). A pesar de que la ganancia de procesado CDMA ofrece una protección inherente contra las interferencias de radiofrecuencia (RFI), esta protección es limitada. Una interferencia con una relación de potencia de interferencia a potencia de la señal que excede la ganancia de procesado puede degradar el rendimiento de los receptores o incluso negar por completo el servicio GNSS. Este riesgo es especialmente importante en receptores convencionales equipados con un nivel mínimo o básico de protección frente las RFIs. Como consecuencia, las RFIs (ya sean intencionadas o no intencionadas), se identifican como la causa más importante de la degradación del rendimiento en GNSS. El problema esta causando una preocupación creciente en los últimos tiempos, ya que cada vez hay más servicios que dependen de los GNSSs Si centramos la atención en el receptor GNSS, es conocido que la adquisición de la señal tiene la menor sensibilidad de todas las operaciones del receptor, y, en consecuencia, se convierte en el factor limitador en la presencia de señales interferentes. Un receptor de una sola antena puede hacer uso de la diversidad en tiempo y frecuencia para mitigar las interferencias, aunque el rendimiento de estas técnicas se ve comprometido en escenarios con baja SNR o en presencia de interferencias de banda ancha. Por otro lado, los receptores basados en múltiples antenas se pueden beneficiar del procesado espacial, y por lo tanto mitigar los efectos de las señales interferentes. La diversidad espacial se ha aplicado tradicionalmente a la operación de tracking de la señal en receptores GNSS. Sin embargo, las condiciones iniciales del tracking dependen del resultado de la adquisición de la señal, y como hemos visto antes, hay un número de situaciones en las que el proceso de adquisición puede fallar. En base a nuestro grado de conocimiento, la aplicación de los arrays de antenas a la adquisición de la señal GNSS no ha recibido mucha atención, sorprendentemente. El objetivo de esta tesis doctoral es doble: por un lado, proponer nuevos algoritmos para la adquisición basados en arrays de antenas, usando como marco la teoría de la detección de señal estadística, y por otro lado, demostrar la viabilidad de su implementación y ejecución en tiempo real, así como su medir su rendimiento en escenarios realistas. La tesis comienza con una breve introducción a los fundamentos de los receptores GNSS, proporcionando algunos detalles sobre la estructura de las señales de navegación y la arquitectura del receptor aplicada a los sistemas GPS y Galileo. Continua con el análisis de la adquisición GNSS como un problema de detección, aplicando la teoría del detector Neyman-Pearson (NP) y el modelo de señal de una única antena. El marco teórico del detector NP se utiliza aquí para derivar tanto el detector óptimo (conocido como detector clarividente) como la denominada Prueba Generalizada de la Razón de Verosimilitud (en inglés, Generalized Likelihood Ratio Test (GLRT)), que forma la base de prácticamente todos los algoritmos de adquisición del estado del arte actual. Yendo más lejos, proponemos un nuevo detector diseñado para adquirir simultáneamente un conjunto de satélites, por lo tanto, obtiene una reducción del tiempo de adquisición y de los recursos computacionales necesarios en el proceso, respecto a las técnicas convencionales. El efecto del ancho de banda del receptor también se ha tenido en cuenta en los análisis. A continuación, el detector GLRT se extiende al modelo de señal de array de antenas para obtener un detector nuevo que es capaz de mitigar interferencias no correladas temporalmente, incluso utilizando arrays no estructurados y moderadamente descalibrados, convirtiéndose así en una de las principales aportaciones de esta tesis. La clave del detector es asumir una matriz de covarianza de ruido arbitraria y desconocida en el modelo de señal, que trata de captar el comportamiento estadístico de las interferencias y otras señales no deseadas, mientras que utiliza la dimensión espacial proporcionada por los arrays de antenas. Se han derivado las expresiones que modelan las probabilidades teóricas de detección y falsa alarma. El rendimiento del detector y su capacidad de rechazo a interferencias se han modelado y comparado con su límite teórico. El algoritmo propuesto también ha sido comparado con técnicas de adquisición convencionales, ejecutadas utilizando la salida de conformadores de haz que utilizan algoritmos de filtrado de interferencias, como el algoritmo de minimización de la potencia. Además, el detector se ha analizado bajo condiciones realistas, representadas con la presencia de errores en la estimación de covarianzas, errores residuales en la estimación del Doppler y el retardo de señal, y los efectos de la cuantificación. Los resultados teóricos se apoyan en simulaciones de Monte Carlo. Como otra contribución principal de esta tesis, la segunda parte del trabajo trata sobre el diseño y la implementación de una nueva plataforma para receptores GNSS en tiempo real basados en array de antenas que utiliza la tecnología de matriz programable de puertas lógicas (en ingles Field Programmable Gate Array (FPGA)). La plataforma está destinada a ser utilizada como una herramienta de investigación estrechamente acoplada con receptores GNSS definidos por software. Se ha diseñado, implementado y verificado la cadena completa de recepción, incluyendo el array de antenas y el front-end multi-canal para las señales GPS L1 y Galileo E1. El documento explica en detalle el procesado de señal que se realiza, como por ejemplo, la implementación del módulo de extracción de estadísticas de la señal. Los compromisos de diseño y las complejidades derivadas han sido cuidadosamente analizadas y tenidas en cuenta. La plataforma ha sido utilizada como prueba de concepto para solucionar el problema presentado de la vulnerabilidad del GNSS a las interferencias. Los algoritmos de adquisición introducidos en esta tesis se han implementado y probado en condiciones realistas. El rendimiento de los algoritmos se comparó con las técnicas de adquisición basadas en una sola antena. Se han realizado pruebas en escenarios que contienen interferencias dentro de la banda GNSS, incluyendo interferencias de banda estrecha y banda ancha y señales de comunicación. La plataforma fue diseñada para demostrar la viabilidad de la implementación de nuevos algoritmos de adquisición basados en array de antenas, dejando el resto de las operaciones del receptor (principalmente, los módulos de tracking, decodificación del mensaje de navegación, los observables de código y fase, y la solución básica de Posición, Velocidad y Tiempo (PVT)) a un receptor basado en el concepto de Radio Definida por Software (SDR), el cual se ejecuta en un ordenador personal. El receptor procesa en tiempo real las muestras de la señal filltradas espacialmente, transmitidas usando el bus de datos Gigabit Ethernet. En la última parte de esta Tesis, cerramos ciclo diseñando e implementando completamente este receptor basado en software. El receptor propuesto está dirigido a las arquitecturas de multi-constalación GNSS y multi-frecuencia, persiguiendo los objetivos de eficiencia, modularidad, interoperabilidad y flexibilidad demandada por los usuarios que requieren características no estándar, tales como la extracción de señales intermedias o de datos y intercambio de algoritmos. En este contexto, se presenta un receptor de código abierto que puede trabajar en tiempo real, llamado GNSS-SDR, que contribuye con varias características nuevas. Entre ellas destacan el uso de patrones de diseño de software y técnicas de memoria compartida para administrar de manera eficiente el uso de datos entre los bloques del receptor, el uso de la aceleración por hardware para las operaciones vectoriales más costosas, como la eliminación de la frecuencia Doppler y la correlación de código, y la disponibilidad para compilar y ejecutar el receptor en múltiples plataformas de software y arquitecturas de hardware. A fecha de la escritura de esta Tesis (abril de 2012), el receptor obtiene un rendimiento basado en la medida de la raíz cuadrada del error cuadrático medio en la distancia bidimensional (en inglés, 2-dimensional Distance Root Mean Square (DRMS) error) menor de 2 metros para un escenario GPS L1 C/A con 8 satélites visibles y una dilución de la precisión horizontal (en inglés, Horizontal Dilution Of Precision (HDOP)) de 1.2

Expanding the Horizons of Manufacturing: Towards Wide Integration, Smart Systems and Tools

This research topic aims at enterprise-wide modeling and optimization (EWMO) through the development and application of integrated modeling, simulation and optimization methodologies, and computer-aided tools for reliable and sustainable improvement opportunities within the entire manufacturing network (raw materials, production plants, distribution, retailers, and customers) and its components. This integrated approach incorporates information from the local primary control and supervisory modules into the scheduling/planning formulation. That makes it possible to dynamically react to incidents that occur in the network components at the appropriate decision-making level, requiring fewer resources, emitting less waste, and allowing for better responsiveness in changing market requirements and operational variations, reducing cost, waste, energy consumption and environmental impact, and increasing the benefits. More recently, the exploitation of new technology integration, such as through semantic models in formal knowledge models, allows for the capture and utilization of domain knowledge, human knowledge, and expert knowledge toward comprehensive intelligent management. Otherwise, the development of advanced technologies and tools, such as cyber-physical systems, the Internet of Things, the Industrial Internet of Things, Artificial Intelligence, Big Data, Cloud Computing, Blockchain, etc., have captured the attention of manufacturing enterprises toward intelligent manufacturing systems