Simulation and graph mining tools for improving gene mapping efficiency

Gene mapping is a systematic search for genes that affect observable characteristics of an organism. In this thesis we offer computational tools to improve the efficiency of (disease) gene-mapping efforts. In the first part of the thesis we propose an efficient simulation procedure for generating realistic genetical data from isolated populations. Simulated data is useful for evaluating hypothesised gene-mapping study designs and computational analysis tools. As an example of such evaluation, we demonstrate how a population-based study design can be a powerful alternative to traditional family-based designs in association-based gene-mapping projects. In the second part of the thesis we consider a prioritisation of a (typically large) set of putative disease-associated genes acquired from an initial gene-mapping analysis. Prioritisation is necessary to be able to focus on the most promising candidates. We show how to harness the current biomedical knowledge for the prioritisation task by integrating various publicly available biological databases into a weighted biological graph. We then demonstrate how to find and evaluate connections between entities, such as genes and diseases, from this unified schema by graph mining techniques. Finally, in the last part of the thesis, we define the concept of reliable subgraph and the corresponding subgraph extraction problem. Reliable subgraphs concisely describe strong and independent connections between two given vertices in a random graph, and hence they are especially useful for visualising such connections. We propose novel algorithms for extracting reliable subgraphs from large random graphs. The efficiency and scalability of the proposed graph mining methods are backed by extensive experiments on real data. While our application focus is in genetics, the concepts and algorithms can be applied to other domains as well. We demonstrate this generality by considering coauthor graphs in addition to biological graphs in the experiments.

Mining Land Cover Information Using Multilayer Perceptron and Decision Tree from MODIS Data

Land cover (LC) changes play a major role in global as well as at regional scale patterns of the climate and biogeochemistry of the Earth system. LC information presents critical insights in understanding of Earth surface phenomena, particularly useful when obtained synoptically from remote sensing data. However, for developing countries and those with large geographical extent, regular LC mapping is prohibitive with data from commercial sensors (high cost factor) of limited spatial coverage (low temporal resolution and band swath). In this context, free MODIS data with good spectro-temporal resolution meet the purpose. LC mapping from these data has continuously evolved with advances in classification algorithms. This paper presents a comparative study of two robust data mining techniques, the multilayer perceptron (MLP) and decision tree (DT) on different products of MODIS data corresponding to Kolar district, Karnataka, India. The MODIS classified images when compared at three different spatial scales (at district level, taluk level and pixel level) shows that MLP based classification on minimum noise fraction components on MODIS 36 bands provide the most accurate LC mapping with 86% accuracy, while DT on MODIS 36 bands principal components leads to less accurate classification (69%).

The complexity of certain incremental code generation problems

This paper looks at the complexity of four different incremental problems. The following are the problems considered: (1) Interval partitioning of a flow graph (2) Breadth first search (BFS) of a directed graph (3) Lexicographic depth first search (DFS) of a directed graph (4) Constructing the postorder listing of the nodes of a binary tree. The last problem arises out of the need for incrementally computing the Sethi-Ullman (SU) ordering [1] of the subtrees of a tree after it has undergone changes of a given type. These problems are among those that claimed our attention in the process of our designing algorithmic techniques for incremental code generation. BFS and DFS have certainly numerous other applications, but as far as our work is concerned, incremental code generation is the common thread linking these problems. The study of the complexity of these problems is done from two different perspectives. In [2] is given the theory of incremental relative lower bounds (IRLB). We use this theory to derive the IRLBs of the first three problems. Then we use the notion of a bounded incremental algorithm [4] to prove the unboundedness of the fourth problem with respect to the locally persistent model of computation. Possibly, the lower bound result for lexicographic DFS is the most interesting. In [5] the author considers lexicographic DFS to be a problem for which the incremental version may require the recomputation of the entire solution from scratch. In that sense, our IRLB result provides further evidence for this possibility with the proviso that the incremental DFS algorithms considered be ones that do not require too much of preprocessing.

Incremental-angle and angular velocity estimation using a star sensor

A method is described for estimating the incremental angle and angular velocity of a spacecraft using integrated rate parameters with the help of a star sensor alone. The chief advantage of this method is that the measured stars need not be identified, whereas the identification of the stars is necessary in earlier methods. This proposed estimation can be carried out with all of the available measurements by a simple linear Kalman filter, albeit with a time-varying sensitivity matrix. The residuals of estimated angular velocity by the proposed spacecraft incremental-angle and angular velocity estimation method are as accurate as the earlier methods. This method also enables the spacecraft attitude to be reconstructed for mapping the stars into an imaginary unit sphere in the body reference frame, which will preserve the true angular separation of the stars. This will pave the way for identification of the stars using any angular separation or triangle matching techniques applied to even a narrow field of view sensor that is made to sweep the sky. A numerical simulation for inertial as well as Earth pointing spacecraft is carried out to establish the results.

Dynamic subspace clustering for very large high-dimensional databases

Emerging high-dimensional data mining applications needs to find interesting clusters embeded in arbitrarily aligned subspaces of lower dimensionality. It is difficult to cluster high-dimensional data objects, when they are sparse and skewed. Updations are quite common in dynamic databases and they are usually processed in batch mode. In very large dynamic databases, it is necessary to perform incremental cluster analysis only to the updations. We present a incremental clustering algorithm for subspace clustering in very high dimensions, which handles both insertion and deletions of datapoints to the backend databases.

Tree structure for efficient data mining using rough sets

In data mining, an important goal is to generate an abstraction of the data. Such an abstraction helps in reducing the space and search time requirements of the overall decision making process. Further, it is important that the abstraction is generated from the data with a small number of disk scans. We propose a novel data structure, pattern count tree (PC-tree), that can be built by scanning the database only once. PC-tree is a minimal size complete representation of the data and it can be used to represent dynamic databases with the help of knowledge that is either static or changing. We show that further compactness can be achieved by constructing the PC-tree on segmented patterns. We exploit the flexibility offered by rough sets to realize a rough PC-tree and use it for efficient and effective rough classification. To be consistent with the sizes of the branches of the PC-tree, we use upper and lower approximations of feature sets in a manner different from the conventional rough set theory. We conducted experiments using the proposed classification scheme on a large-scale hand-written digit data set. We use the experimental results to establish the efficacy of the proposed approach. (C) 2002 Elsevier Science B.V. All rights reserved.

Stream-Close: Fast mining of Closed Frequent Itemsets in high speed data streams

With the emergence of large-volume and high-speed streaming data, the recent techniques for stream mining of CFIpsilas (closed frequent itemsets) will become inefficient. When concept drift occurs at a slow rate in high speed data streams, the rate of change of information across different sliding windows will be negligible. So, the user wonpsilat be devoid of change in information if we slide window by multiple transactions at a time. Therefore, we propose a novel approach for mining CFIpsilas cumulatively by making sliding width(ges1) over high speed data streams. However, it is nontrivial to mine CFIpsilas cumulatively over stream, because such growth may lead to the generation of exponential number of candidates for closure checking. In this study, we develop an efficient algorithm, stream-close, for mining CFIpsilas over stream by exploring some interesting properties. Our performance study reveals that stream-close achieves good scalability and has promising results.

Faster Algorithms for Incremental Topological Ordering.Robert Tarjan

We present two online algorithms for maintaining a topological order of a directed acyclic graph as arcs are added, and detecting a cycle when one is created. Our first algorithm takes O(m 1/2) amortized time per arc and our second algorithm takes O(n 2.5/m) amortized time per arc, where n is the number of vertices and m is the total number of arcs. For sparse graphs, our O(m 1/2) bound improves the best previous bound by a factor of logn and is tight to within a constant factor for a natural class of algorithms that includes all the existing ones. Our main insight is that the two-way search method of previous algorithms does not require an ordered search, but can be more general, allowing us to avoid the use of heaps (priority queues). Instead, the deterministic version of our algorithm uses (approximate) median-finding; the randomized version of our algorithm uses uniform random sampling. For dense graphs, our O(n 2.5/m) bound improves the best previously published bound by a factor of n 1/4 and a recent bound obtained independently of our work by a factor of logn. Our main insight is that graph search is wasteful when the graph is dense and can be avoided by searching the topological order space instead. Our algorithms extend to the maintenance of strong components, in the same asymptotic time bounds.

Spatial Data Mining and Modeling for visualisation of Rapid Urbanisation

Rapid urbanisation in India has posed serious challenges to the decision makers in regional planning involving plethora of issues including provision of basic amenities (like electricity, water, sanitation, transport, etc.). Urban planning entails an understanding of landscape and urban dynamics with causal factors. Identifying, delineating and mapping landscapes on temporal scale provide an opportunity to monitor the changes, which is important for natural resource management and sustainable planning activities. Multi-source, multi-sensor, multi-temporal, multi-frequency or multi-polarization remote sensing data with efficient classification algorithms and pattern recognition techniques aid in capturing these dynamics. This paper analyses the landscape dynamics of Greater Bangalore by: (i) characterisation of direct impervious surface, (ii) computation of forest fragmentation indices and (iii) modeling to quantify and categorise urban changes. Linear unmixing is used for solving the mixed pixel problem of coarse resolution super spectral MODIS data for impervious surface characterisation. Fragmentation indices were used to classify forests – interior, perforated, edge, transitional, patch and undetermined. Based on this, urban growth model was developed to determine the type of urban growth – Infill, Expansion and Outlying growth. This helped in visualising urban growth poles and consequence of earlier policy decisions that can help in evolving strategies for effective land use policies.

Incremental natural-gradient actor-critic algorithms

We present four new reinforcement learning algorithms based on actor-critic and natural-gradient ideas, and provide their convergence proofs. Actor-critic rein- forcement learning methods are online approximations to policy iteration in which the value-function parameters are estimated using temporal difference learning and the policy parameters are updated by stochastic gradient descent. Methods based on policy gradients in this way are of special interest because of their com- patibility with function approximation methods, which are needed to handle large or infinite state spaces. The use of temporal difference learning in this way is of interest because in many applications it dramatically reduces the variance of the gradient estimates. The use of the natural gradient is of interest because it can produce better conditioned parameterizations and has been shown to further re- duce variance in some cases. Our results extend prior two-timescale convergence results for actor-critic methods by Konda and Tsitsiklis by using temporal differ- ence learning in the actor and by incorporating natural gradients, and they extend prior empirical studies of natural actor-critic methods by Peters, Vijayakumar and Schaal by providing the first convergence proofs and the first fully incremental algorithms.

Association rule mining activity : A general formalism

Mining association rules from a large collection of databases is based on two main tasks. One is generation of large itemsets; and the other is finding associations between the discovered large itemsets. Existing formalism for association rules are based on a single transaction database which is not sufficient to describe the association rules based on multiple database environment. In this paper, we give a general characterization of association rules and also give a framework for knowledge-based mining of multiple databases for association rules.

A survey of temporal data mining

Data mining is concerned with analysing large volumes of (often unstructured) data to automatically discover interesting regularities or relationships which in turn lead to better understanding of the underlying processes. The field of temporal data mining is concerned with such analysis in the case of ordered data streams with temporal interdependencies. Over the last decade many interesting techniques of temporal data mining were proposed and shown to be useful in many applications. Since temporal data mining brings together techniques from different fields such as statistics, machine learning and databases, the literature is scattered among many different sources. In this article, we present an overview of techniques of temporal data mining.We mainly concentrate on algorithms for pattern discovery in sequential data streams.We also describe some recent results regarding statistical analysis of pattern discovery methods.

Root cause diagnostics using temporal data mining

A method, system, and computer program product for fault data correlation in a diagnostic system are provided. The method includes receiving the fault data including a plurality of faults collected over a period of time, and identifying a plurality of episodes within the fault data, where each episode includes a sequence of the faults. The method further includes calculating a frequency of the episodes within the fault data, calculating a correlation confidence of the faults relative to the episodes as a function of the frequency of the episodes, and outputting a report of the faults with the correlation confidence.