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<p>Inferring phylogeny is a difficult computational problem. Heuristics are necessary to minimize the time spent evaluating non optimal trees. In paper I, we developed an approach for heuristic searching, using a genetic algorithm. Genetic algorithms mimic the natural selections ability to solve complex problems. The algorithm can reduce the time required for weighted maximum parsimony phylogenetic inference using protein sequences, especially for data sets involving large number of taxa. </p><p>Evaluating and comparing the ability of phylogenetic methods to infer the correct topology is complex. In paper II, we developed software that determines the minimum subtree prune and regraft (SPR) distance between binary trees to ease the process. The minimum SPR distance can be used to measure the incongruence between trees inferred using different methods. Given a known topology the methods could be evaluated on their ability to infer the correct phylogeny given specific data. </p><p>The minimum SPR software the intermediate trees that separate two binary trees. In paper III we developed software that given a set of incongruent trees determines the median SPR consensus tree i.e. the tree that explains the trees with a minimum of SPR operations. We investigated the median SPR consensus tree and its possible interpretation as a species tree given a set of gene trees. We used a set of α-proteobacteria gene trees to test the ability of the algorithm to infer a species tree and compared it to previous studies. The results show that the algorithm can successfully reconstruct a species tree.</p><p>Expressed sequence tag (EST) data is important in determining intron-exon boundaries, single nucleotide polymorphism and the coding sequence of genes. In paper IV we aligned ESTs to the genome to evaluate the quality of EST data. The results show that many ESTs are contaminated by vector sequences and low quality regions. The reliability of EST data is largely determined by the clustering of the ESTs and the association of the clusters to the correct portion of genome. We investigate the performance of EST clustering using the genome as template compared to previously existing methods using pair-wise alignments. The results show that using the genome as guidance improves the resulting EST clusters in respect to the extent ESTs originating from the same transcriptional unit are separated into disjunct clusters. </p>

This paper describes an intuitive way of defining geometry design variables for solving structural topology optimization problems using a genetic algorithm (GA). The geometry representation scheme works by defining a skeleton that represents the underlying topology/connectivity of the continuum structure. As the effectiveness of any GA is highly dependent on the chromosome encoding of the design variables, the encoding used here is a directed graph which reflects this underlying topology so that the genetic crossover and mutation operators of the GA can recombine and preserve any desirable geometric characteristics through succeeding generations of the evolutionary process. The overall optimization procedure is tested by solving a simulated topology optimization problem in which a 'target' geometry is pre-defined with the aim of having the design solutions converge towards this target shape. The procedure is also applied to design a straight-line compliant mechanism : a large displacement flexural structure that generates a vertical straight line path at some point when given a horizontal straight line input displacement at another point. / Singapore-MIT Alliance (SMA)

This paper describes the initial results of a project to create a self-supervised algorithm for learning object segmentation from video data. Developmental psychology and computational experience have demonstrated that the motion segmentation of objects is a simpler, more primitive process than the detection of object boundaries by static image cues. Therefore, motion information provides a plausible supervision signal for learning the static boundary detection task and for evaluating performance on a test set. A video camera and previously developed background subtraction algorithms can automatically produce a large database of motion-segmented images for minimal cost. The purpose of this work is to use the information in such a database to learn how to detect the object boundaries in novel images using static information, such as color, texture, and shape. / Singapore-MIT Alliance (SMA)

The Weapon Target Assignment (WTA) problem is a fundamental problem arising in defense-related applications of operations research. This problem consists of optimally assigning n weapons to m targets so that the total expected survival value of the targets after all the engagements is minimum. The WTA problem can be formulated as a nonlinear integer programming problem and is known to be NP-complete. There do not exist any exact methods for the WTA problem which can solve even small size problems (for example, with 20 weapons and 20 targets). Though several heuristic methods have been proposed to solve the WTA problem, due to the absence of exact methods, no estimates are available on the quality of solutions produced by such heuristics. In this paper, we suggest linear programming, integer programming, and network flow based lower bounding methods using which we obtain several branch and bound algorithms for the WTA problem. We also propose a network flow based construction heuristic and a very large-scale neighborhood (VLSN) search algorithm. We present computational results of our algorithms which indicate that we can solve moderately large size instances (up to 80 weapons and 80 targets) of the WTA problem optimally and obtain almost optimal solutions of fairly large instances (up to 200 weapons and 200 targets) within a few seconds

This paper develops a potential reduction algorithm for solving a linear-programming problem directly from a "warm start" initial point that is neither feasible nor optimal. The algorithm is of an "interior point" variety that seeks to reduce a single potential function which simultaneously coerces feasibility improvement (Phase I) and objective value improvement (Phase II). The key feature of the algorithm is the ability to specify beforehand the desired balance between infeasibility and nonoptimality in the following sense. Given a prespecified balancing parameter /3 > 0, the algorithm maintains the following Phase I - Phase II "/3-balancing constraint" throughout: (cTx- Z*) < /3TX, where cTx is the objective function, z* is the (unknown) optimal objective value of the linear program, and Tx measures the infeasibility of the current iterate x. This balancing constraint can be used to either emphasize rapid attainment of feasibility (set large) at the possible expense of good objective function values or to emphasize rapid attainment of good objective values (set /3 small) at the possible expense of a lower infeasibility gap. The algorithm exhibits the following advantageous features: (i) the iterate solutions monotonically decrease the infeasibility measure, (ii) the iterate solutions satisy the /3-balancing constraint, (iii) the iterate solutions achieve constant improvement in both Phase I and Phase II in O(n) iterations, (iv) there is always a possibility of finite termination of the Phase I problem, and (v) the algorithm is amenable to acceleration via linesearch of the potential function.

I present an algorithm which allows two agents to generate a simple language based only on observations of a shared environment. Vocabulary and roles for the language are learned in linear time. Communication is robust and degrades gradually as complexity increases. Dissimilar modes of experience will lead to a shared kernel vocabulary.

"Expectation-Maximization'' (EM) algorithm and gradient-based approaches for maximum likelihood learning of finite Gaussian mixtures. We show that the EM step in parameter space is obtained from the gradient via a projection matrix $P$, and we provide an explicit expression for the matrix. We then analyze the convergence of EM in terms of special properties of $P$ and provide new results analyzing the effect that $P$ has on the likelihood surface. Based on these mathematical results, we present a comparative discussion of the advantages and disadvantages of EM and other algorithms for the learning of Gaussian mixture models.

This work is aimed towards the development of an artificially intelligent search algorithm used in conjunction with an Auto Associative Neural Network (AANN) to help locate and reconstruct faulty sensor inputs in control systems. The AANN can be trained to detect when sensors go faulty but the problem of locating the faulty sensor still remains. The search algorithm aids the AANN to help locate the faulty sensors and reconstruct their actual values. The algorithm uses domain specific heuristics based on the inherent behavior of the AANN to achieve its task. Common sensor errors such as drift, shift and random errors and the algorithms response to them have been studied. The issue of noise has also been investigated. These areas cover the first part of this work. The second part focuses on the development of a web interface that implements and displays the working of the algorithm. The interface allows any client on the World Wide Web to connect to the engineering software called MATLAB. The client can then simulate a drift, shift or random error using the graphical user interface and observe the response of the algorithm.

In-process Optical Coordinate Measuring Machine (OCMM) offers the potential of diagnosing in a timely manner variation sources that are responsible for product quality defects. Such a sensor system can help manufacturers improve product quality and reduce process downtime. Effective use of sensory data in diagnosing variation sources depends on the optimal design of a sensor system, which is often known as the problem of sensor placements. This thesis addresses coordinate sensor placement in diagnosing dimensional variation sources in assembly processes. Sensitivity indices of detecting process mean and variance components are defined as the design criteria and are derived in terms of process layout and sensor deployment information. Exchange algorithms, originally developed in the research of optimal experiment deign, are employed and revised to maximize the detection sensitivity. A sort-and-cut procedure is used, which remarkably improve the algorithm efficiency of the current exchange routine. The resulting optimal sensor layouts and its implications are illustrated in the specific context of a panel assembly process.