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Increasing the efficiency of fuzzy logic-based gene expression data analysis.

DNA microarray technology can accommodate a multifaceted analysis of the expression of genes in an organism. The wealth of spatiotemporal data generated by this technology allows researchers to potentially reverse engineer a particular genetic network. "Fuzzy logic" has been proposed as a method to analyze the relationships between genes and help decipher a genetic network. This method can identify interacting genes that fit a known "fuzzy" model of gene interaction by testing all combinations of gene expression profiles. This paper introduces improvements made over previous fuzzy gene regulatory models in terms of computation time and robustness to noise. Improvement in computation time is achieved by using a cluster analysis as a preprocessing method to reduce the total number of gene combinations analyzed. This approach speeds up the algorithm by a factor of 50% with minimal effect on the results. The model's sensitivity to noise is reduced by implementing appropriate methods of "fuzzy rule aggregation" and "conjunction" that produce reliable results in the face of minor changes in model input.

Animals↗

Preliminary evaluation of a fuzzy logic-based automatic quantitative analysis in myocardial SPECT.

UNLABELLED: This study validates a new quantitative myocardial perfusion SPECT software. METHODS: The processing starts with the extraction of the morphologic skeleton of the left ventricular myocardium from reconstructed transverse sections. Fuzzy logic is used to decide whether a pixel belongs to the myocardium and any perfusion defect is filled according to a truncated bullet model. The resulting image is partitioned in 18 isovolumetric sectors. Sex-matched normal limits, criteria of abnormality for rest (201)Tl and (99m)Tc-labeled perfusion tracers, reproducibility studies, and detection of coronary artery disease were developed and validated in an overall population of 343 patients. The sex- and tracer-matched means and SDs of a normal response were calculated in 93 male and 93 female patients with a <5% likelihood of coronary artery disease. Reproducibility measurements and assignment of different sectors of the myocardium to a specific coronary were performed from data collected in 49 and 60 patients, respectively. The accuracy of the detection of a coronary artery occlusion was assessed in 48 patients who also underwent coronary angiography. RESULTS: The intra- and interoperator reproducibility of the sectorial activity was high with a linear regression coefficient of 0.97 and a SD of the difference measurement at 4.4% and 3.8%, respectively. Overall sensitivity and specificity for the detection of occluded coronary artery were 90% and 80%, respectively. For the detection of left anterior descending, left circumflex, and right artery coronary occlusion, sensitivity was 92%, 75%, and 92.5%, respectively, and specificity was 75%, 78%, and 90%, respectively. CONCLUSION: The new quantitative myocardial perfusion SPECT software appears to be a very helpful program for the objective analysis of perfusion tracer distribution in myocardial SPECT and a very accurate tool in the detection and localization of coronary artery occlusion.

Algorithms↗

A fuzzy logic-based model for the multistage high-pressure inactivation of Lactococcus lactis ssp. cremoris MG 1363.

The high-pressure inactivation (200 to 600 MPa) of Lactococcus lactis ssp. cremoris MG 1363 suspended in milk buffer was investigated with both experimental and theoretical methods. The inactivation kinetics were characterised by the determination of the viable cell counts, cell counts of undamaged cells, LmrP activity, membrane integrity, and metabolic activity. Pressures between 200 and 600 MPa were applied, and pressure holding times were varied between 0 and 120 min. Experiments were carried out in milk buffer at pH values ranging between 4.0 and 6.5, and the effect of the addition of molar concentrations of NaCl and sucrose was furthermore determined. The inactivation curves of L. lactis, as characterised by viable cell counts, exhibited typical sigmoid asymmetric shapes. Generally, inactivation of the membrane transport system LmrP was the most sensitive indicator of pressure-induced sublethal injury. Furthermore, the metabolic activity was inactivated concomitant with or prior to the loss of viability. Membrane integrity was lost concomitant with or later than cell death. For example, treatments at 200 MPa for 60 min in milk buffer did not inactivate L. lactis, but fully inactivated LmrP activity and reduced the metabolic activity by 50%. The membrane integrity was unaffected. Thus, the assay systems chosen are suitable to dissect the multistep high-pressure inactivation of L. lactis ssp. cremoris MG 1363. A fuzzy logic model accounting for the specific knowledge on the multistep pressure inactivation and allowing the prediction of the quantities of sublethally damaged cells was formulated. Furthermore, the fuzzy model could be used to accurately predict pressure inactivation of L. lactis using conditions not taken into account in model generation. It consists of 160 rules accounting for several dependent and independent variables. The rules were generated automatically with fuzzy clustering methods and rule-oriented statistical analysis. The set is open for the integration of further knowledge-based rules. A very good overall agreement between measured and predicted values was obtained. Single, deviating results have been identified and can be explained to be measurement errors or model intrinsic deficiencies.

Animals↗

Fuzzy branching temporal logic.

Intelligent systems require a systematic way to represent and handle temporal information containing uncertainty. In particular, a logical framework is needed that can represent uncertain temporal information and its relationships with logical formulae. Fuzzy linear temporal logic (FLTL), a generalization of propositional linear temporal logic (PLTL) with fuzzy temporal events and fuzzy temporal states defined on a linear time model, was previously proposed for this purpose. However, many systems are best represented by branching time models in which each state can have more than one possible future path. In this paper, fuzzy branching temporal logic (FBTL) is proposed to address this problem. FBTL adopts and generalizes concurrent tree logic (CTL*), which is a classical branching temporal logic. The temporal model of FBTL is capable of representing fuzzy temporal events and fuzzy temporal states, and the order relation among them is represented as a directed graph. The utility of FBTL is demonstrated using a fuzzy job shop scheduling problem as an example.

Journal Article↗

A fuzzy logic-controlled classifier for use in implantable cardioverter defibrillators.

PURPOSE: Implantable cardioverters defibrillators (ICDs) are increasingly used in the management of life-threatening arrhythmias. Correct recognition of a treatable arrhythmia is crucial to this application. However, the computational power of microprocessors currently used in ICDs limits the range of traditional algorithms available for this application. METHODS: Classification based on fuzzy inference systems (FIS) were trained to recognize different cardiac rhythms (AF, VF, SVT, VT) from the Ann Arbor Electrogram Library. The FIS used were designed using adaptive-network-based fuzzy inference methods to optimize the classification procedure. Only computational techniques suitable for ICD design were used. RESULTS: After pretraining with the ANFIS correct rhythm classification was observed for the rhythms studied. CONCLUSION: In this preliminary study, successful rhythm classification was demonstrated using fuzzy logic techniques. In view of the computational efficiency this may have application in ICD design.

Arrhythmias, Cardiac↗

Development of river ecosystem models for Flemish watercourses: case studies in the Zwalm river basin.

Only recently, modelling has been accepted as an interesting and powerful tool to support river quality assessment and management. The 'River Invertebrate Prediction and Classification System' (RIVPACS), based on statistical modelling, was one of the first and best known systems in this context. RIVPACS was developed to classify macroinvertebrate community types and to predict the fauna expected to occur in different types of watercourses, based on a small number of environmental variables. The prediction is essentially a static 'target' of the fauna to be expected at a site with stated environmental features, in the absence of environmental stress. Therefore this system is rather limited to apply in river assessment and management. Models that offer a prediction of faunal responses to changes in environmental features (e.g. changes in discharge regime, dissolved oxygen level, ...) would be of considerable value for river management. In this context, models based on classification trees, artificial neural networks and fuzzy logic were developed and applied to predict macro-invertebrate communities in the Zwalm river basin located in Flanders, Belgium. Structural characteristics (meandering, substrate type, flow velocity, ...) and physical-chemical variables (dissolved oxygen, pH, ...) were used as inputs to predict the presence or absence of macroinvertebrate taxa in the headwaters and brooks of the Zwalm river basin. In total, data from 60 measurement sites were available. Reliability and particular strengths and weaknesses of these techniques were compared and evaluated. Classification trees performed in general well to predict the absence or presence of the different macroinvertebrate taxa and allowed also to deduct general relations from the dataset. Models based on artificial neural networks (ANNS) were also good in predicting the macroinvertebrate communities at the different sites. Sensitivity analyses related to ANNs allowed to study the impact of the input variables on the presence or absence of macroinvertebrate taxa and to determine the major variables that affect the ecosystem quality and should be taken under direct consideration in the management of river basins. Performance of the fuzzy logic models was significantly related to the methods that were used to set up the membership functions and the reliability of the information that was available. Fuzzy logic did not perform as well as the other two techniques with regard to short term predictions. Fuzzy logic appeared to be better and more robust for long term predictions, because of the easy and pragmatic integration of general expert knowledge and data derived rules in the transparent inference engine. The overall conclusion of our study is that all three techniques, classification trees, artificial neural networks and fuzzy logic appeared to be reliable to predict macroinvertebrate communities in polluted streams.

Animals↗

The brain/mind complex. An epistemological approach.

It is stressed that the brain/mind complex constitutes a monolithic system that functions with emergent properties at several levels of hierarchical organization. These hierarchical levels are non-reducible to one another; they are at least three (neuronal, functional, and semantic), and they function within an interactional plan. From the epistemological view-point, the brain/mind complex uses logical and non-logical mechanisms to deal with day-to-day problems. Logic is necessary for the thinking process, but it is not sufficient. Emphasis is given to non-logical mechanisms; fuzzy logic and heuristics, which allow the mind to develop strategies to find solutions, are analysed.

Behavior↗

[Biological versus artificial intelligence: a critical approach].

After brief considerations about intelligence, a comparative study between biologic and artificial intelligence is made. The specialists in Artificial Intelligence found that intelligence is purely a matter of physical symbol manipulation. The enterprise of Artificial Intelligence aims to understand what we might call Brain Intelligence in terms of concepts and techniques of engineering. However the philosophers believed that computer-machine can have syntax, but can never have semantics. In other words, that they can follow rules, such as those of arithmetic or grammar, but not understand what to us are meanings of symbols, such as words. In the present paper it is stressed that brain/mind complex constitutes a monolithic systemic that functions with emergent properties at several levels of hierarchical organization. These hierarchical levels are non-reducible to one another. They are at least three (neuronal, functional, and semantic), and they function within an interactional plan. The brain/mind complex, which transform informations in meanings, deals with problems by means of both logical and non-logical mechanisms; while logic allows the mind to arrange the elements for reasoning, the non-logical mechanisms (fuzzy logic, heuristics, insights) allows the mind to develop strategies to find solutions. The model for construction of the "intelligent machine" is the operating way of the brain/mind complex, which does not always use logical processes. The role of information science in Artificial Intelligence is to search for knowledge itself (virtual knowledge), rather than to simply attempt a logico-mathematical formalization of knowledge.

Artificial Intelligence↗

Fuzzy-control for improved nitrogen removal and energy saving in WWT-plants with pre-denitrification.

In the last few years, numerous studies were carried out, dealing with the application of fuzzy-logic to improve the control of the activated sludge process. In this paper, fuzzy-logic based control strategies for wastewater treatment plants with pre-denitrification are presented that should lead to better effluent quality and, in parallel, to a reduction of energy consumption. Extensive experimental investigations on a large scale pilot plant as well as simulation studies (ASM1 with SIMBA) were carried out in order to design, evaluate and compare different fuzzy-controllers with each other and with comparable conventional control systems. The fuzzy-controllers were designed as high-level controllers that determine the DO-setpoints in the aerated zones and the ratio between aerated and non-aerated zones. Conventional PI-controllers were used to maintain the DO-concentration at the set-point levels. The ammonia and nitrate concentration in the effluent and the ammonia load in the influent were considered as input variables for the different fuzzy-controllers. Compared to the operation with fixed nitrification/denitrification zones and constant DO concentrations, the required air-flow could be reduced up to 24% by using fuzzy-logic based control strategies. In comparison with a more advanced conventional control strategy (relay controller with two thresholds and the NH4-N concentration in the effluent as single control variable) a reduction of air-flow-rate up to 14% could be achieved. At the same time, NH4-N peaks in the effluent that are normally caused by peak flow conditions could be reduced significantly. The large scale experiments show that the fuzzy-controllers can be easily implemented in modern control and supervision systems and that the control characteristics can be followed and modified during operation. It therefore can be expected that the developed fuzzy-control systems will be accepted by the operating personnel in wastewater treatment plants.

Automation↗

Advanced clinical monitoring: considerations for real-time hemodynamic diagnostics.

In an effort to ease staffing burdens and potentially improve patient outcome in an intensive care unit (ICU) environment, we are developing a real-time system to accurately and efficiently diagnose cardiopulmonary emergencies. The system is being designed to utilize all relevant routinely-monitored physiological data in order to automatically diagnose potentially fatal events. The initial stage of this project involved formulating the overall system design and appropriate methods for real-time data acquisition, data storage, data trending, waveform analysis, and implementing diagnostic rules. Initially, we defined a conceptual analysis of the minimum physiologic data set, and the monitoring time-frames (trends) which would be required to diagnose cardiopulmonary emergencies. Following that analysis, we used a fuzzy logic diagnostic engine to analyze physiological data during a simulated arrhythmic cardiac arrest (ACA) in order to assess the validity of our diagnostic methodology. We used rate, trend, and morphologic data extracted from the following signals: expired CO2 time-concentration curve (capnogram), electrocardiogram, and arterial blood pressure. The system performed well: The fuzzy logic engine effectively diagnosed the likelihood of ACA from the subtle hemodynamic trends which preceded the complete arrest. As the clinical picture worsened, the fuzzy logic-based system accurately indicated the change in patient condition. Termination of the simulated arrest was rapidly detected by the diagnostic engine. In view of the effectiveness of this fuzzy logic implementation, we plan to develop additional fuzzy logic modules to diagnose other cardiopulmonary emergencies.

Algorithms↗

[Automated detection of estrus and mastitis in dairy cows].

The development and test of detection models for oestrus and mastitis in dairy cows is described in a PhD thesis that was defended in Wageningen on June 5, 2000. These models were based on sensors for milk yield, milk temperature, electrical conductivity of milk, and cow activity and concentrate intake, and on combined processing of the sensor data. The models alert farmers to cows that need attention, because of possible oestrus or mastitis. A first detection model for cows, milked twice a day, was based on time series models for the sensor variables. A time series model describes the dependence between successive observations. The parameters of the time series models were fitted on-line for each cow after each milking by means of a Kalman filter, a mathematical method to estimate the state of a system on-line. The Kalman filter gives the best estimate of the current state of a system based on all preceding observations. This model was tested for 2 years on two experimental farms, and under field conditions on four farms over several years. A second detection model, for cow milked in an automatic milking system (AMS), was based on a generalization of the first model. Two data sets (one small, one large) were used for testing. The results for oestrus detection were good for both models. The results for mastitis detection were varying (in some cases good, in other cases moderate). Fuzzy logic was used to classify mastitis and oestrus alerts with both detection models, to reduce the number of false positive alerts. Fuzzy logic makes approximate reasoning possible, where statements can be partly true or false. Input for the fuzzy logic model were alerts from the detection models and additional information. The number of false positive alerts decreased considerably, while the number of detected cases remained at the same level. These models make automated detection possible in practice.

Animals↗

Database mining using soft computing techniques. An integrated neural network-fuzzy logic-genetic algorithm approach.

Two different soft computing (SC) techniques (a competitive learning neural network and an integrated neural network-fuzzy logic-genetic algorithm approach) are employed in the analysis of a database subset obtained from the Cambridge Structural Database. The chemical problem chosen for study is relevant to the relationship between various metric parameters in transition metal imido (LnMdNZ, Z = carbon-based substituent) complexes and the chemical consequences of such relationships. The SC techniques confirmed and quantified the suspected relationship between the metal-nitrogen bond length and the metal-nitrogen-substituent bond angle for transition metal imidos: increased metal-nitrogen-carbon angles correlate with shortened metal-nitrogen distances. The mining effort also yielded an unexpected correlation between the NC distance and the MNC angle-shorter NC correlate with larger MNC. A fuzzy inference system is used to construct an MNred-NC-MNC hypersurface. This hypersurface suggests a complicated interdependence among NC, MNred, and the angle subtended by these two bonds. Also, major portions of the hypersurface are very flat, in regions where MNC is approaching linearity. The relationships are also seen to be influenced by whether the imido substituent is an alkyl or aryl group. Computationally, the present results are of particular interest in two respects. First, SC classification was able to isolate an "outlier" cluster. Identification of outliers is important as they may correspond to unreported experimental errors in the database or novel chemical entities, both of which warrant further investigation. Second, the SC database mining not only confirmed and quantified a suspected relationship (MNred versus MNC) within the data but also yielded a trend that was not suspected (NC versus MNC).

Journal Article↗

Fuzzy rule-based models for decision support in ecosystem management.

To facilitate decision support in the ecosystem management, ecological expertise and site-specific data need to be integrated. Fuzzy logic can deal with highly variable, linguistic, vague and uncertain data or knowledge and, therefore, has the ability to allow for a logical, reliable and transparent information stream from data collection down to data usage in decision-making. Several environmental applications already implicate the use of fuzzy logic. Most of these applications have been set up by trial and error and are mainly limited to the domain of environmental assessment. In this article, applications of fuzzy logic for decision support in ecosystem management are reviewed and assessed, with an emphasis on rule-based models. In particular, the identification, optimisation, validation, the interpretability and uncertainty aspects of fuzzy rule-based models for decision support in ecosystem management are discussed.

Conservation of Natural Resources↗

Optical generation of fuzzy-based rules.

In the last third of the 20th century, fuzzy logic has risen from a mathematical concept to an applicable approach in soft computing. Today, fuzzy logic is used in control systems for various applications, such as washing machines, train-brake systems, automobile automatic gear, and so forth. The approach of optical implementation of fuzzy inferencing was given by the authors in previous papers, giving an extra emphasis to applications with two dominant inputs. In this paper the authors introduce a real-time optical rule generator for the dual-input fuzzy-inference engine. The paper briefly goes over the dual-input optical implementation of fuzzy-logic inferencing. Then, the concept of constructing a set of rules from given data is discussed. Next, the authors show ways to implement this procedure optically. The discussion is accompanied by an example that illustrates the transformation from raw data into fuzzy set rules.

Journal Article↗

Medical concepts related to individual risk are better explained with "plausibility" rather than "probability".

BACKGROUND: The concept of risk has pervaded medical literature in the last decades and has become a familiar topic, and the concept of probability, linked to binary logic approach, is commonly applied in epidemiology and clinical medicine. The application of probability theory to groups of individuals is quite straightforward but can pose communication challenges at individual level. Few articles by the way have tried to focus the concept of "risk" at the individual subject level rather than at population level. DISCUSSION: The author has reviewed the conceptual framework which has led to the use of probability theory in the medical field in a time when the principal causes of death were represented by acute disease often of infective origin. In the present scenario, in which chronic degenerative disease dominate and there are smooth transitions between health and disease the use of fuzzy logic rather than binary logic would be more appropriate. The use of fuzzy logic in which more than two possible truth-value assignments are allowed overcomes the trap of probability theory when dealing with uncertain outcomes, thereby making the meaning of a certain prognostic statement easier to understand by the patient. SUMMARY: At individual subject level the recourse to the term plausibility, related to fuzzy logic, would help the physician to communicate to the patient more efficiently in comparison with the term probability, related to binary logic. This would represent an evident advantage for the transfer of medical evidences to individual subjects.

Chronic Disease↗

Identification of critical genes in microarray experiments by a Neuro-Fuzzy approach.

Gene expression profiling by microarray technology is usually difficult to interpret into a simpler pattern. One approach to resolve the complexity of gene expression profiles is the application of artificial neural networks (ANNs). A potential difficulty in this strategy, however, is that the non-linear nature of ANN makes it essentially a 'black-box' computation process. Addition of a fuzzy logic approach is useful because it can complement ANN by explicitly specifying membership function during computation. We employed a hybrid approach of neural network and fuzzy logic to further analyze a published microarray study of gene responses to eight bacteria in human macrophages. The original analysis by hierarchical clustering found common gene responses to all bacteria but did not address individual responses. Our method allowed exploration of the gene response of the host to individual bacterium. We implemented a two-layer, feed-forward neural network containing the principle of 'competitive learning' (i.e. 'winner-take-all'). The weights of the trained neural network were fed into a fuzzy logic inference system. A new measurement, called the impact rating (IR) was also introduced to explore the degree of importance of each gene. To assess the reliability of the IR value, a bootstrap re-sampling method was applied to the dataset and a confidence level for each IR was obtained. Our approach has successfully uncovered the unique features of host response to individual bacterium. Further, application of gene ontology (GO) annotation to the genes of high IR values in each response has suggested new biological pathways for individual host-pathogen interactions.

Algorithms↗

Fuzzy-control of a hand orthosis for restoring tip pinch, lateral pinch, and cylindrical prehensions to patients with elbow flexion intact.

This study examines, through simulation, the use of fuzzy logic as a feasible control scheme for a hand orthosis that can restore fingertip pinch, lateral pinch, and cylindrical grasps to individuals suffering from C5-C7 spinal cord injuries. A simplified hand orthosis model, consisting of four fingers and a thumb, was derived for the purpose of planning appropriate grasp trajectories and for validating the fuzzy logic control architecture. For comparison a proportional-plus-integral-plus-derivative (PID) controller was also designed. Fuzzy logic is advantageous for this system since it eliminates solving coupled nonlinear equations of motion. For the various grips, the fuzzy controller produced better performance than the PID controller.

Artificial Intelligence↗

[Identification of rhubarb samples based on IR spectra by using Takagi-Sugeno fuzzy systems].

Takagi-Sugeno fuzzy system is composed of several back-propagation neural networks (BP-NNs), and has some fuzzy logic properties. In this paper, the Takagi-Sugeno fuzzy logic system is applied to identifying official and unofficial rhubarb samples based on their infrared spectra. The effects of the number of hidden neurons and the momentum parameters on the prediction were investigated. The results obtained by using Takagi-Sugeno fuzzy system were better than those by commonly used BP-networks. With a proper network training parameter, 100% correctness can be obtained by using Takagi-Sugeno fuzzy system. This method is more accurate than the common methods, and is more scientific than traditional methods. So it is applied to identifying rhubarb easily and rapidly.

Drugs, Chinese Herbal↗