A key collaborative hub for many software development projects is the issue tracking system, or bug repository. The use of a bug repository can improve the software development process in a number of ways including allowing developers who are geographically distributed to communicate about project development. However, reports added to the repository need to be triaged by a human, called the triager, to determine if reports are meaningful. If a report is meaningful, the triager decides how to organize the report for integration into the project's development process. We call triager decisions with the goal of determining if a report is meaningful, repository-oriented decisions, and triager decisions that organize reports for the development process, development-oriented decisions. Triagers can become overwhelmed by the number of reports added to the repository. Time spent triaging also typically diverts valuable resources away from the improvement of the product to the managing of the development process. To assist triagers, this dissertation presents a machine learning approach to create recommenders that assist with a variety of development-oriented decisions. In this way, we strive to reduce human involvement in triage by moving the triager's role from having to gather information to make a decision to that of confirming a suggestion. This dissertation introduces a triage-assisting recommender creation process that can create a variety of different development-oriented decision recommenders for a range of projects. The recommenders created with this approach are accurate: recommenders for which developer to assign a report have a precision of 70% to 98% over five open source projects, recommenders for which product component the report is for have a recall of 72% to 92%, and recommenders for who to add to the cc: list of a report that have a recall of 46% to 72%. We have evaluated recommenders created with our triage-assisting recommender creation process using both an analytic evaluation and a field study. In addition, we present in this dissertation an approach to assist project members to specify the project-specific values for the triage-assisting recommender creation process, and show that such recommenders can be created with a subset of the repository data.

Self-paced Brain computer interface (SBCI) systems allow individuals with motor disabilities to use their brain signals to control devices, whenever they wish. These systems are required to identify the user’s “intentional control (IC)” commands and they must remain inactive during all periods in which users do not intend control (called “no control (NC)” periods). This dissertation addresses three issues related to the design of SBCI systems: 1) their presently high false positive (FP) rates, 2) the presence of artifacts and 3) the identification of a suitable evaluation metric. To improve the performance of SBCI systems, the following are proposed: 1) a method for the automatic user-customization of a 2-state SBCI system, 2) a two-stage feature reduction method for selecting wavelet coefficients extracted from movement-related potentials (MRP), 3) an SBCI system that classifies features extracted from three neurological phenomena: MRPs, changes in the power of the Mu and Beta rhythms; 4) a novel method that effectively combines methods developed in 2) and 3 ) and 5) generalizing the system developed in 3) for detecting a right index finger flexion to detecting the right hand extension. Results of these studies using actual movements show an average true positive (TP) rate of 56.2% at the FP rate of 0.14% for the finger flexion study and an average TP rate of 33.4% at the FP rate of 0.12% for the hand extension study. These FP results are significantly lower than those achieved in other SBCI systems, where FP rates vary between 1-10%. We also conduct a comprehensive survey of the BCI literature. We demonstrate that many BCI papers do not properly deal with artifacts. We show that the proposed BCI achieves a good performance of TP=51.8% and FP=0.4% in the presence of eye movement artifacts. Further tests of the performance of the proposed system in a pseudo-online environment, shows an average TP rate =48.8% at the FP rate of 0.8%. Finally, we propose a framework for choosing a suitable evaluation metric for SBCI systems. This framework shows that Kappa coefficient is more suitable than other metrics in evaluating the performance during the model selection procedure.

Generalized Radial Basis Functions were used to construct networks that learn input-output mappings from given data. They are developed out of a theoretical framework for approximation based on regularization techniques and represent a class of three-layer networks similar to backpropagation networks with one hidden layer. A network using Gaussian base functions was implemented and applied to several domains. It was found to perform very well on the two-spirals problem and on the nettalk task. This paper explains what Generalized Radial Basis Functions are, describes the algorithm, its implementation, and the tests that have been conducted. It draws the conclusion that network. implementations using Generalized Radial Basis Functions are a successful approach for learning from examples. / Graduation date: 1991

Grasping and manipulation of objects is an integral part of a robot’s physical interaction with the environment. In order to cope with real-world situations, sensor based grasping of objects and grasp stability estimation is an important skill. This thesis addresses the problem of predicting the stability of a grasp from the perceptions available to a robot once fingers close around the object before attempting to lift it. A regrasping step can be triggered if an unstable grasp is identified. The percepts considered consist of object features (visual), gripper configurations (proprioceptive) and tactile imprints (haptic) when fingers contact the object. This thesis studies tactile based stability estimation by applying machine learning methods such as Hidden Markov Models. An approach to integrate visual and tactile feedback is also introduced to further improve the predictions of grasp stability, using Kernel Logistic Regression models. Like humans, robots are expected to grasp and manipulate objects in a goal-oriented manner. In other words, objects should be grasped so to afford subsequent actions: if I am to hammer a nail, the hammer should be grasped so to afford hammering. Most of the work on grasping commonly addresses only the problem of finding a stable grasp without considering the task/action a robot is supposed to fulfill with an object. This thesis also studies grasp stability assessment in a task-oriented way based on a generative approach using probabilistic graphical models, Bayesian Networks. We integrate high-level task information introduced by a teacher in a supervised setting with low-level stability requirements acquired through a robot’s exploration. The graphical model is used to encode probabilistic relationships between tasks and sensory data (visual, tactile and proprioceptive). The generative modeling approach enables inference of appropriate grasping configurations, as well as prediction of grasp stability. Overall, results indicate that the idea of exploiting learning approaches for grasp stability assessment is applicable in realistic scenarios. / <p>QC 20121026</p>

Current robotics research is largely driven by the vision of creatingan intelligent being that can perform dangerous, difficult orunpopular tasks. These can for example be exploring the surface of planet mars or the bottomof the ocean, maintaining a furnace or assembling a car.   They can also be more mundane such as cleaning an apartment or fetching groceries. This vision has been pursued since the 1960s when the first robots were built. Some of the tasks mentioned above, especially those in industrial manufacturing, arealready frequently performed by robots. Others are still completelyout of reach. Especially, household robots are far away from beingdeployable as general purpose devices. Although advancements have beenmade in this research area, robots are not yet able to performhousehold chores robustly in unstructured and open-ended environments givenunexpected events and uncertainty in perception and execution.In this thesis, we are analyzing which perceptual andmotor capabilities are necessaryfor the robot to perform common tasks in a household scenario. In that context, an essential capability is tounderstand the scene that the robot has to interact with. This involvesseparating objects from the background but also from each other.Once this is achieved, many other tasks becomemuch easier. Configuration of objectscan be determined; they can be identified or categorized; their pose can be estimated; free and occupied space in the environment can be outlined.This kind of scene model can then inform grasp planning algorithms to finally pick up objects.However, scene understanding is not a trivial problem and evenstate-of-the-art methods may fail. Given an incomplete, noisy andpotentially erroneously segmented scene model, the questions remain howsuitable grasps can be planned and how they can be executed robustly.In this thesis, we propose to equip the robot with a set of predictionmechanisms that allow it to hypothesize about parts of the sceneit has not yet observed. Additionally, the robot can alsoquantify how uncertain it is about this prediction allowing it toplan actions for exploring the scene at specifically uncertainplaces. We consider multiple modalities includingmonocular and stereo vision, haptic sensing and information obtainedthrough a human-robot dialog system. We also study several scene representations of different complexity and their applicability to a grasping scenario. Given an improved scene model from this multi-modalexploration, grasps can be inferred for each objecthypothesis. Dependent on whether the objects are known, familiar orunknown, different methodologies for grasp inference apply. In thisthesis, we propose novel methods for each of these cases. Furthermore,we demonstrate the execution of these grasp both in a closed andopen-loop manner showing the effectiveness of the proposed methods inreal-world scenarios. / <p>QC 20111125</p> / GRASP

To understand biology at a system level, I presented novel machine learning algorithms to reveal the underlying mechanisms of how genes and their products function in different biological levels in this thesis. Specifically, at sequence level, based on Kernel Support Vector Machines (SVMs), I proposed learned random-walk kernel and learned empirical-map kernel to identify protein remote homology solely based on sequence data, and I proposed a discriminative motif discovery algorithm to identify sequence motifs that characterize protein sequences' remote homology membership. The proposed approaches significantly outperform previous methods, especially on some challenging protein families. At expression and protein level, using hierarchical Bayesian graphical models, I developed the first high-throughput computational predictive model to filter sequence-based predictions of microRNA targets by incorporating the proteomic data of putative microRNA target genes, and I proposed another probabilistic model to explore the underlying mechanisms of microRNA regulation by combining the expression profile data of messenger RNAs and microRNAs. At cellular level, I further investigated how yeast genes manifest their functions in cell morphology by performing gene function prediction from the morphology data of yeast temperature-sensitive alleles. The developed prediction models enable biologists to choose some interesting yeast essential genes and study their predicted novel functions.

Protein identification has been more helpful than before in the diagnosis and treatment of many diseases, such as cancer, heart disease and HIV. Tandem mass spectrometry is a powerful tool for protein identification. In a typical experiment, proteins are broken into small amino acid oligomers called peptides. By determining the amino acid sequence of several peptides of a protein, its whole amino acid sequence can be inferred. Therefore, peptide identification is the first step and a central issue for protein identification. Tandem mass spectrometers can produce a large number of tandem mass spectra which are used for peptide identification. Two issues should be addressed to improve the performance of current peptide identification algorithms. Firstly, nearly all spectra are noise-contaminated. As a result, the accuracy of peptide identification algorithms may suffer from the noise in spectra. Secondly, the majority of spectra are not identifiable because they are of too poor quality. Therefore, much time is wasted attempting to identify these unidentifiable spectra.<p> The goal of this research is to design spectrum pre-processing algorithms to both speedup and improve the reliability of peptide identification from tandem mass spectra. Firstly, as a tandem mass spectrum is a one dimensional signal consisting of dozens to hundreds of peaks, and majority of peaks are noisy peaks, a spectrum denoising algorithm is proposed to remove most noisy peaks of spectra. Experimental results show that our denoising algorithm can remove about 69% of peaks which are potential noisy peaks among a spectrum. At the same time, the number of spectra that can be identified by Mascot algorithm increases by 31% and 14% for two tandem mass spectrum datasets. Next, a two-stage recursive feature elimination based on support vector machines (SVM-RFE) and a sparse logistic regression method are proposed to select the most relevant features to describe the quality of tandem mass spectra. Our methods can effectively select the most relevant features in terms of performance of classifiers trained with the different number of features. Thirdly, both supervised and unsupervised machine learning methods are used for the quality assessment of tandem mass spectra. A supervised classifier, (a support vector machine) can be trained to remove more than 90% of poor quality spectra without removing more than 10% of high quality spectra. Clustering methods such as model-based clustering are also used for quality assessment to cancel the need for a labeled training dataset and show promising results.

Given the breadth of constraint satisfaction problems (CSPs) and the wide variety of CSP solvers, it is often very difficult to determine a priori which solving method is best suited to a problem. This work explores the use of machine learning to predict which solving method will be most effective for a given problem. We use four different problem sets to determine the CSP attributes that can be used to determine which solving method should be applied. After choosing an appropriate set of attributes, we determine how well j48 decision trees can predict which solving method to apply. Furthermore, we take a cost sensitive approach such that problem instances where there is a great difference in runtime between algorithms are emphasized. We also attempt to use information gained on one class of problems to inform decisions about a second class of problems. Finally, we show that the additional costs of deciding which method to apply are outweighed by the time savings compared to applying the same solving method to all problem instances.

Stroke rehabilitation is to train the motor function of a patients limb. In this process, functional assessment is of importance, and it is primarily based on a patients task performance. The context of the rehabilitation discussed in this thesis is such that functional assessment is conducted through a computer system and the Internet. In particular, a patient performs the task at home in a haptic virtual environment, and the task performance is transmitted to the therapist over the Internet. One problem with this approach to functional assessment is that a patients mind state is little known to the therapist. This immediately leads to one question, that is, whether an elevated mind state will have some significant effect on the patients task performance? If so, this approach can result in a considerable error. The overall objective of this thesis study was to generate an answer to the aforementioned question. The study focused on a patients elevated fatigue state. The specific objectives of the study include: (i) developing a haptic virtual environment prototype system for functional assessment, (ii) developing a physiological-based inference system for fatigue state, and (iii) performing an experiment to generate knowledge regarding the fatigue effect on task performance. With a limited resource in recruiting patients in the experiment, the study conducted few experiments on patients but mostly on healthy subjects. The study has concluded: (1) the proposed haptic virtual environment system is effective for the wrist coordination task and is likely promising to other tasks, (2) the accuracy of proposed fatigue inference system achieves 89.54%, for two levels of fatigue state, which is promising, (3) the elevated fatigue state significantly affects task performance in the context of wrist coordination task, and (4) the accuracy of the individual-based inference approach is significantly higher than that of the group-based inference approach. The main contributions of the thesis are (1) generation of the new knowledge regarding the fatigue effect on task performance in the context of home-based rehabilitation, (2) provision of the new fatigue inference system with the highest accuracy in comparison with the existing approaches in literature, and (3) generation of the new knowledge regarding the difference between the individual-based inference and group-based inference approaches.

Fall among the elderly is an important health issue. Fall detection and movement tracking techniques are therefore instrumental in dealing with this issue. This thesis responds to the challenge of classifying different movement types as a part of a system designed to fulfill the need for a wearable device to collect data for fall and near-fall analysis. Four different fall activities (forward, backward, left and right), three normal activities (standing, walking and lying down) and near-fall situations are identified and detected. Different machine learning algorithms are compared and the best one is used for the real time classification. The comparison is made using Waikato Environment for Knowledge Analysis or in short WEKA. The system also has the ability to adapt to different gaits of different people. A feature selection algorithm is also introduced to reduce the number of features required for the classification problem.