NNVA: Neural Network Assisted Visual Analysis of Yeast Cell Polarization Simulation

Complex computational models are often designed to simulate real-world physical phenomena in many scientific disciplines. However, these simulation models tend to be computationally very expensive and involve a large number of simulation input parameters which need to be analyzed and properly calibrated before the models can be applied for real scientific studies. We propose a visual analysis system to facilitate interactive exploratory analysis of high-dimensional input parameter space for a complex yeast cell polarization simulation. The proposed system can assist the computational biologists, who designed the simulation model, to visually calibrate the input parameters by modifying the parameter values and immediately visualizing the predicted simulation outcome without having the need to run the original expensive simulation for every instance. Our proposed visual analysis system is driven by a trained neural network-based surrogate model as the backend analysis framework. Surrogate models are widely used in the field of simulation sciences to efficiently analyze computationally expensive simulation models. In this work, we demonstrate the advantage of using neural networks as surrogate models for visual analysis by incorporating some of the recent advances in the field of uncertainty quantification, interpretability and explainability of neural network-based models. We utilize the trained network to perform interactive parameter sensitivity analysis of the original simulation at multiple levels-of-detail as well as recommend optimal parameter configurations using the activation maximization framework of neural networks. We also facilitate detail analysis of the trained network to extract useful insights about the simulation model, learned by the network, during the training process.Comment: Published at IEEE Transactions on Visualization and Computer Graphic

A survey on utilization of data mining approaches for dermatological (skin) diseases prediction

Due to recent technology advances, large volumes of medical data is obtained. These data contain valuable information. Therefore data mining techniques can be used to extract useful patterns. This paper is intended to introduce data mining and its various techniques and a survey of the available literature on medical data mining. We emphasize mainly on the application of data mining on skin diseases. A categorization has been provided based on the different data mining techniques. The utility of the various data mining methodologies is highlighted. Generally association mining is suitable for extracting rules. It has been used especially in cancer diagnosis. Classification is a robust method in medical mining. In this paper, we have summarized the different uses of classification in dermatology. It is one of the most important methods for diagnosis of erythemato-squamous diseases. There are different methods like Neural Networks, Genetic Algorithms and fuzzy classifiaction in this topic. Clustering is a useful method in medical images mining. The purpose of clustering techniques is to find a structure for the given data by finding similarities between data according to data characteristics. Clustering has some applications in dermatology. Besides introducing different mining methods, we have investigated some challenges which exist in mining skin data

A Spatio-Temporal Bayesian Network Classifier for Understanding Visual Field Deterioration

Progressive loss of the field of vision is characteristic of a number of eye diseases such as glaucoma which is a leading cause of irreversible blindness in the world. Recently, there has been an explosion in the amount of data being stored on patients who suffer from visual deterioration including field test data, retinal image data and patient demographic data. However, there has been relatively little work in modelling the spatial and temporal relationships common to such data. In this paper we introduce a novel method for classifying Visual Field (VF) data that explicitly models these spatial and temporal relationships. We carry out an analysis of this method and compare it to a number of classifiers from the machine learning and statistical communities. Results are very encouraging showing that our classifiers are comparable to existing statistical models whilst also facilitating the understanding of underlying spatial and temporal relationships within VF data. The results reveal the potential of using such models for knowledge discovery within ophthalmic databases, such as networks reflecting the ‘nasal step’, an early indicator of the onset of glaucoma. The results outlined in this paper pave the way for a substantial program of study involving many other spatial and temporal datasets, including retinal image and clinical data

A network inference method for large-scale unsupervised identification of novel drug-drug interactions

Characterizing interactions between drugs is important to avoid potentially harmful combinations, to reduce off-target effects of treatments and to fight antibiotic resistant pathogens, among others. Here we present a network inference algorithm to predict uncharacterized drug-drug interactions. Our algorithm takes, as its only input, sets of previously reported interactions, and does not require any pharmacological or biochemical information about the drugs, their targets or their mechanisms of action. Because the models we use are abstract, our approach can deal with adverse interactions, synergistic/antagonistic/suppressing interactions, or any other type of drug interaction. We show that our method is able to accurately predict interactions, both in exhaustive pairwise interaction data between small sets of drugs, and in large-scale databases. We also demonstrate that our algorithm can be used efficiently to discover interactions of new drugs as part of the drug discovery process

Inferring Anomalies from Data using Bayesian Networks

Existing studies on data mining has largely focused on the design of measures and algorithms to identify outliers in large and high dimensional categorical and numeric databases. However, not much stress has been given on the interestingness of the reported outlier. One way to ascertain interestingness and usefulness of the reported outlier is by making use of domain knowledge. In this thesis, we present measures to discover outliers based on background knowledge, represented by a Bayesian network. Using causal relationships between attributes encoded in the Bayesian framework, we demonstrate that meaningful outliers, i.e., outliers which encode important or new information are those which violate causal relationships encoded in the model. Depending upon nature of data, several approaches are proposed to identify and explain anomalies using Bayesian knowledge. Outliers are often identified as data points which are ``rare'', ''isolated'', or ''far away from their nearest neighbors''. We show that these characteristics may not be an accurate way of describing interesting outliers. Through a critical analysis on several existing outlier detection techniques, we show why there is a mismatch between outliers as entities described by these characteristics and ``real'' outliers as identified using Bayesian approach. We show that the Bayesian approaches presented in this thesis has better accuracy in mining genuine outliers while, keeping a low false positive rate as compared to traditional outlier detection techniques

Trust Strategies for the Semantic Web

Everyone agrees on the importance of enabling trust on the SemanticWebto ensure more efficient agent interaction. Current research on trust seems to focus on developing computational models, semantic representations, inference techniques, etc. However, little attention has been given to the plausible trust strategies or tactics that an agent can follow when interacting with other agents on the Semantic Web. In this paper we identify five most common strategies of trust and discuss their envisaged costs and benefits. The aim is to provide some guidelines to help system developers appreciate the risks and gains involved with each trust strategy

Detection of Extrasolar Planets by Gravitational Microlensing

Gravitational microlensing provides a unique window on the properties and prevalence of extrasolar planetary systems because of its ability to find low-mass planets at separations of a few AU. The early evidence from microlensing indicates that the most common type of exoplanet yet detected are the so-called "super-Earth" planets of ~10 Earth-masses at a separation of a few AU from their host stars. The detection of two such planets indicates that roughly one third of stars have such planets in the separation range 1.5-4 AU, which is about an order of magnitude larger than the prevalence of gas-giant planets at these separations. We review the basic physics of the microlensing method, and show why this method allows the detection of Earth-mass planets at separations of 2-3 AU with ground-based observations. We explore the conditions that allow the detection of the planetary host stars and allow measurement of planetary orbital parameters. Finally, we show that a low-cost, space-based microlensing survey can provide a comprehensive statistical census of extrasolar planetary systems with sensitivity down to 0.1 Earth-masses at separations ranging from 0.5 AU to infinity.Comment: 43 pages. Very similar to chapter 3 of Exoplanets: Detection, Formation, Properties, Habitability, John Mason, ed. Springer (April 3, 2008