Techniques for clustering gene expression data

Many clustering techniques have been proposed for the analysis of gene expression data obtained from microarray experiments. However, choice of suitable method(s) for a given experimental dataset is not straightforward. Common approaches do not translate well and fail to take account of the data profile. This review paper surveys state of the art applications which recognises these limitations and implements procedures to overcome them. It provides a framework for the evaluation of clustering in gene expression analyses. The nature of microarray data is discussed briefly. Selected examples are presented for the clustering methods considered

Engineering Resilient Collective Adaptive Systems by Self-Stabilisation

Collective adaptive systems are an emerging class of networked computational systems, particularly suited in application domains such as smart cities, complex sensor networks, and the Internet of Things. These systems tend to feature large scale, heterogeneity of communication model (including opportunistic peer-to-peer wireless interaction), and require inherent self-adaptiveness properties to address unforeseen changes in operating conditions. In this context, it is extremely difficult (if not seemingly intractable) to engineer reusable pieces of distributed behaviour so as to make them provably correct and smoothly composable. Building on the field calculus, a computational model (and associated toolchain) capturing the notion of aggregate network-level computation, we address this problem with an engineering methodology coupling formal theory and computer simulation. On the one hand, functional properties are addressed by identifying the largest-to-date field calculus fragment generating self-stabilising behaviour, guaranteed to eventually attain a correct and stable final state despite any transient perturbation in state or topology, and including highly reusable building blocks for information spreading, aggregation, and time evolution. On the other hand, dynamical properties are addressed by simulation, empirically evaluating the different performances that can be obtained by switching between implementations of building blocks with provably equivalent functional properties. Overall, our methodology sheds light on how to identify core building blocks of collective behaviour, and how to select implementations that improve system performance while leaving overall system function and resiliency properties unchanged.Comment: To appear on ACM Transactions on Modeling and Computer Simulatio

Proactive Assessment of Accident Risk to Improve Safety on a System of Freeways, Research Report 11-15

This report describes the development and evaluation of real-time crash risk-assessment models for four freeway corridors: U.S. Route 101 NB (northbound) and SB (southbound) and Interstate 880 NB and SB. Crash data for these freeway segments for the 16-month period from January 2010 through April 2011 are used to link historical crash occurrences with real-time traffic patterns observed through loop-detector data. \u27The crash risk-assessment models are based on a binary classification approach (crash and non-crash outcomes), with traffic parameters measured at surrounding vehicle detection station (VDS) locations as the independent variables. The analysis techniques used in this study are logistic regression and classification trees. Prior to developing the models, some data-related issues such as data cleaning and aggregation were addressed. The modeling efforts revealed that the turbulence resulting from speed variation is significantly associated with crash risk on the U.S. 101 NB corridor. The models estimated with data from U.S. 101 NB were evaluated on the basis of their classification performance, not only on U.S. 101 NB, but also on the other three freeway segments for transferability assessment. It was found that the predictive model derived from one freeway can be readily applied to other freeways, although the classification performance decreases. The models that transfer best to other roadways were determined to be those that use the least number of VDSs–that is, those that use one upstream or downstream station rather than two or three.\ The classification accuracy of the models is discussed in terms of how the models can be used for real-time crash risk assessment. The models can be applied to developing and testing variable speed limits (VSLs) and ramp-metering strategies that proactively attempt to reduce crash risk

Document Collection Visualization and Clustering Using An Atom Metaphor for Display and Interaction

Visual Data Mining have proven to be of high value in exploratory data analysis and data mining because it provides an intuitive feedback on data analysis and support decision-making activities. Several visualization techniques have been developed for cluster discovery such as Grand Tour, HD-Eye, Star Coordinates, etc. They are very useful tool which are visualized in 2D or 3D; however, they have not simple for users who are not trained. This thesis proposes a new approach to build a 3D clustering visualization system for document clustering by using k-mean algorithm. A cluster will be represented by a neutron (centroid) and electrons (documents) which will keep a distance with neutron by force. Our approach employs quantified domain knowledge and explorative observation as prediction to map high dimensional data onto 3D space for revealing the relationship among documents. User can perform an intuitive visual assessment of the consistency of the cluster structure

State-of-the-art on research and applications of machine learning in the building life cycle

Fueled by big data, powerful and affordable computing resources, and advanced algorithms, machine learning has been explored and applied to buildings research for the past decades and has demonstrated its potential to enhance building performance. This study systematically surveyed how machine learning has been applied at different stages of building life cycle. By conducting a literature search on the Web of Knowledge platform, we found 9579 papers in this field and selected 153 papers for an in-depth review. The number of published papers is increasing year by year, with a focus on building design, operation, and control. However, no study was found using machine learning in building commissioning. There are successful pilot studies on fault detection and diagnosis of HVAC equipment and systems, load prediction, energy baseline estimate, load shape clustering, occupancy prediction, and learning occupant behaviors and energy use patterns. None of the existing studies were adopted broadly by the building industry, due to common challenges including (1) lack of large scale labeled data to train and validate the model, (2) lack of model transferability, which limits a model trained with one data-rich building to be used in another building with limited data, (3) lack of strong justification of costs and benefits of deploying machine learning, and (4) the performance might not be reliable and robust for the stated goals, as the method might work for some buildings but could not be generalized to others. Findings from the study can inform future machine learning research to improve occupant comfort, energy efficiency, demand flexibility, and resilience of buildings, as well as to inspire young researchers in the field to explore multidisciplinary approaches that integrate building science, computing science, data science, and social science