Evolving Ensemble Fuzzy Classifier

The concept of ensemble learning offers a promising avenue in learning from data streams under complex environments because it addresses the bias and variance dilemma better than its single model counterpart and features a reconfigurable structure, which is well suited to the given context. While various extensions of ensemble learning for mining non-stationary data streams can be found in the literature, most of them are crafted under a static base classifier and revisits preceding samples in the sliding window for a retraining step. This feature causes computationally prohibitive complexity and is not flexible enough to cope with rapidly changing environments. Their complexities are often demanding because it involves a large collection of offline classifiers due to the absence of structural complexities reduction mechanisms and lack of an online feature selection mechanism. A novel evolving ensemble classifier, namely Parsimonious Ensemble pENsemble, is proposed in this paper. pENsemble differs from existing architectures in the fact that it is built upon an evolving classifier from data streams, termed Parsimonious Classifier pClass. pENsemble is equipped by an ensemble pruning mechanism, which estimates a localized generalization error of a base classifier. A dynamic online feature selection scenario is integrated into the pENsemble. This method allows for dynamic selection and deselection of input features on the fly. pENsemble adopts a dynamic ensemble structure to output a final classification decision where it features a novel drift detection scenario to grow the ensemble structure. The efficacy of the pENsemble has been numerically demonstrated through rigorous numerical studies with dynamic and evolving data streams where it delivers the most encouraging performance in attaining a tradeoff between accuracy and complexity.Comment: this paper has been published by IEEE Transactions on Fuzzy System

Linear fuzzy gene network models obtained from microarray data by exhaustive search

BACKGROUND: Recent technological advances in high-throughput data collection allow for experimental study of increasingly complex systems on the scale of the whole cellular genome and proteome. Gene network models are needed to interpret the resulting large and complex data sets. Rationally designed perturbations (e.g., gene knock-outs) can be used to iteratively refine hypothetical models, suggesting an approach for high-throughput biological system analysis. We introduce an approach to gene network modeling based on a scalable linear variant of fuzzy logic: a framework with greater resolution than Boolean logic models, but which, while still semi-quantitative, does not require the precise parameter measurement needed for chemical kinetics-based modeling. RESULTS: We demonstrated our approach with exhaustive search for fuzzy gene interaction models that best fit transcription measurements by microarray of twelve selected genes regulating the yeast cell cycle. Applying an efficient, universally applicable data normalization and fuzzification scheme, the search converged to a small number of models that individually predict experimental data within an error tolerance. Because only gene transcription levels are used to develop the models, they include both direct and indirect regulation of genes. CONCLUSION: Biological relationships in the best-fitting fuzzy gene network models successfully recover direct and indirect interactions predicted from previous knowledge to result in transcriptional correlation. Fuzzy models fit on one yeast cell cycle data set robustly predict another experimental data set for the same system. Linear fuzzy gene networks and exhaustive rule search are the first steps towards a framework for an integrated modeling and experiment approach to high-throughput "reverse engineering" of complex biological systems

Development of an Automated Anesthesia System for the Stabilization of Physiological Parameters in Rodents

The testing of any physiological diagnostic system in-vivo depends critically on the stability of the anesthetized animal used. That is, if the systemic physiological parameters are not tightly controlled, it is exceedingly difficult to assess the precision and accuracy of the system or interpret the consequence of disease. In order to ensure that all measurements taken using the experimental system are not affected by fluctuations in physiological state, the animal must be maintained in a tightly controlled physiologic range. The main goal of this project was to develop a robust monitoring and control system capable of maintaining the physiological parameters of the anesthetized animal in a predetermined range, using the instrumentation already present in the laboratory, and based on the LabVIEWR software interface. A single user interface was developed that allowed for monitoring and control of key physiological parameters including body temperature (BT), mean arterial blood pressure (MAP) and end tidal CO2 (ETCO2). Embedded within this interface was a fuzzy logic based control system designed to mimic the decision making of an anesthetist. The system was tested by manipulating the blood pressure of a group of anesthetized animal subjects using bolus injections of epinephrine and continuous infusions of phenylephrine (a vasoconstrictor) and sodium nitroprusside (a vasodilator). This testing showed that the system was able to significantly reduce the deviation from the set pressure (as measured by the root mean square value) while under control in the hypotension condition (p \u3c 0.10). Though both the short-term and hypertension testing showed no significant improvement, the control system did successfully manipulate the anesthetic percentage in response to changes in MAP. Though currently limited by the control variables being used, this system is an important first step towards a fully automated monitoring and control system and can be used as the basis for further research

A Feasibility Study for the Automated Monitoring and Control of Mine Water Discharges

The chemical treatment of mine-influenced waters is a longstanding environmental challenge for many coal operators, particularly in Central Appalachia. Mining conditions in this region present several unique obstacles to meeting NPDES effluent limits. Outlets that discharge effluent are often located in remote areas with challenging terrain where conditions do not facilitate the implementation of large-scale commercial treatment systems. Furthermore, maintenance of these systems is often laborious, expensive, and time consuming. Many large mining complexes discharge water from numerous outlets, while using environmental technicians to assess the water quality and treatment process multiple times per day. Unfortunately, this treatment method when combined with the lower limits associated with increased regulatory scrutiny can lead to the discharge of non-compliant water off of the mine permit. As an alternative solution, this thesis describes the ongoing research and development of automated protocols for the treatment and monitoring of mine water discharges. In particular, the current work highlights machine learning algorithms as a potential solution for pH control.;In this research, a bench-scale treatment system was constructed. This system simulates a series of ponds such as those found in use by Central Appalachian coal companies to treat acid mine drainage. The bench-scale system was first characterized to determine the volumetric flow rates and resident time distributions at varying flow rates and reactor configurations. Next, data collection was conducted using the bench scale system to generate training data by introducing multilevel random perturbations to the alkaline and acidic water flow rates. A fuzzy controller was then implemented in this system to administer alkaline material with the goal of automating the chemical treatment process. Finally, the performance of machine learning algorithms in predicting future water quality was evaluated to identify the critical input variables required to build these algorithms. Results indicate the machine learning controllers are viable alternatives to the manual control used by many Appalachian coal producers

Explainable AI for clinical risk prediction: a survey of concepts, methods, and modalities

Recent advancements in AI applications to healthcare have shown incredible promise in surpassing human performance in diagnosis and disease prognosis. With the increasing complexity of AI models, however, concerns regarding their opacity, potential biases, and the need for interpretability. To ensure trust and reliability in AI systems, especially in clinical risk prediction models, explainability becomes crucial. Explainability is usually referred to as an AI system's ability to provide a robust interpretation of its decision-making logic or the decisions themselves to human stakeholders. In clinical risk prediction, other aspects of explainability like fairness, bias, trust, and transparency also represent important concepts beyond just interpretability. In this review, we address the relationship between these concepts as they are often used together or interchangeably. This review also discusses recent progress in developing explainable models for clinical risk prediction, highlighting the importance of quantitative and clinical evaluation and validation across multiple common modalities in clinical practice. It emphasizes the need for external validation and the combination of diverse interpretability methods to enhance trust and fairness. Adopting rigorous testing, such as using synthetic datasets with known generative factors, can further improve the reliability of explainability methods. Open access and code-sharing resources are essential for transparency and reproducibility, enabling the growth and trustworthiness of explainable research. While challenges exist, an end-to-end approach to explainability in clinical risk prediction, incorporating stakeholders from clinicians to developers, is essential for success

Accelerated search for biomolecular network models to interpret high-throughput experimental data

<p>Abstract</p> <p>Background</p> <p>The functions of human cells are carried out by biomolecular networks, which include proteins, genes, and regulatory sites within DNA that encode and control protein expression. Models of biomolecular network structure and dynamics can be inferred from high-throughput measurements of gene and protein expression. We build on our previously developed fuzzy logic method for bridging quantitative and qualitative biological data to address the challenges of noisy, low resolution high-throughput measurements, i.e., from gene expression microarrays. We employ an evolutionary search algorithm to accelerate the search for hypothetical fuzzy biomolecular network models consistent with a biological data set. We also develop a method to estimate the probability of a potential network model fitting a set of data by chance. The resulting metric provides an estimate of both model quality and dataset quality, identifying data that are too noisy to identify meaningful correlations between the measured variables.</p> <p>Results</p> <p>Optimal parameters for the evolutionary search were identified based on artificial data, and the algorithm showed scalable and consistent performance for as many as 150 variables. The method was tested on previously published human cell cycle gene expression microarray data sets. The evolutionary search method was found to converge to the results of exhaustive search. The randomized evolutionary search was able to converge on a set of similar best-fitting network models on different training data sets after 30 generations running 30 models per generation. Consistent results were found regardless of which of the published data sets were used to train or verify the quantitative predictions of the best-fitting models for cell cycle gene dynamics.</p> <p>Conclusion</p> <p>Our results demonstrate the capability of scalable evolutionary search for fuzzy network models to address the problem of inferring models based on complex, noisy biomolecular data sets. This approach yields multiple alternative models that are consistent with the data, yielding a constrained set of hypotheses that can be used to optimally design subsequent experiments.</p

Stochastic techniques for the design of robust and efficient emission trading mechanisms

The assessment of greenhouse gases (GHGs) emitted to and removed from the atmosphere is highon both political and scientific agendas internationally. As increasing international concern and cooper- ation aim at policy-oriented solutions to the climate change problem, several issues have begun to arise regarding verification and compliance under both proposed and legislated schemes meant to reduce the human-induced global climate impact. The issues of concern are rooted in the level of confidence with which national emission assessments can be performed, as well as the management of uncertainty and its role in developing informed policy. The approaches to addressing uncertainty that was discussed at the 2nd International Workshop on Uncertainty in Greenhouse Gas Inventories 1 attempt to improve national inventories or to provide a basis for the standardization of inventory estimates to enable comparison of emissions and emission changes across countries. Some authors use detailed uncertainty analyses to enforce the current structure of the emissions trading system while others attempt to internalize high levels of uncertainty by tailoring the emissions trading market rules. In all approaches, uncertainty analysis is regarded as a key component of national GHG inventory analyses. This presentation will provide an overview of the topics that are discussed among scientists at the aforementioned workshop to support robust decision making. These range from achieving and report- ing GHG emission inventories at global, national and sub-national scales; to accounting for uncertainty of emissions and emission changes across these scales; to bottom-up versus top-down emission analy- ses; to detecting and analyzing emission changes vis-a-vis their underlying uncertainties; to reconciling short-term emission commitments and long-term concentration targets; to dealing with verification, com- pliance and emissions trading; to communicating, negotiating and effectively using uncertainty